Hi Vikas. The error should indicate that atoms in your system are moving away from each other too quickly, which may be a result of how you set up your system. If atoms start to close, that initial force "kick" that starts the atoms moving in the production run will cause atoms to repel too quickly, which pushes all the other atoms apart and you get a virtual explosion. Are you pulling the 25mer into the membrane, or did you start the simulation with the peptide inside the membrane? If you're doing a pulling simulation, your box may not be large enough to accommodate the shift in lipid positions. Pulling simulations require a larger than usual box because of the applied force and drastic atom location changes. If you're starting with your peptide in the membrane, did you remove lipids to compensate for the addition of the peptide? You may also need to run energy minimization more than once to relax all the atoms into a starting position where fewer clashes could occur before running NVT and NPT. The atoms are restrained in the NVT and NPT steps, which means that any clashes unresolved in the EM step will still be there when you start the production run. Therefore: Rapid expansion/explosion.

Alternatively, if you expect larger jumps in distance in your set up, your distance cutoff is too small. It's rare that this is the case, and typically the "explosion" error arises when atoms are set too close initially before the production run. I'm not sure if everything here fully addresses the details of your problem, but hopefully something here will help you arrive as the proper solution.

I think there may also be some helpful comments in the Gromacs forums: www.gromacs.org/Support/Mailing_Lists You should be able to do a search from the main gromacs page for the error and see what other users have done to fix the problem. Justin has also responded to a lot of forum questions, so you may even find some helpful hints from him in there.

Best of luck!

Hi Vikas. The error should indicate that atoms in your system are moving away from each other too quickly, which may be a result of how you set up your system. If atoms start to close, that initial force "kick" that starts the atoms moving in the production run will cause atoms to repel too quickly, which pushes all the other atoms apart and you get a virtual explosion. Are you pulling the 25mer into the membrane, or did you start the simulation with the peptide inside the membrane? If you're doing a pulling simulation, your box may not be large enough to accommodate the shift in lipid positions. Pulling simulations require a larger than usual box because of the applied force and drastic atom location changes. If you're starting with your peptide in the membrane, did you remove lipids to compensate for the addition of the peptide? You may also need to run energy minimization more than once to relax all the atoms into a starting position where fewer clashes could occur before running NVT and NPT. The atoms are restrained in the NVT and NPT steps, which means that any clashes unresolved in the EM step will still be there when you start the production run. Therefore: Rapid expansion/explosion.

Alternatively, if you expect larger jumps in distance in your set up, your distance cutoff is too small. It's rare that this is the case, and typically the "explosion" error arises when atoms are set too close initially before the production run. I'm not sure if everything here fully addresses the details of your problem, but hopefully something here will help you arrive as the proper solution.

I think there may also be some helpful comments in the Gromacs forums: www.gromacs.org/Support/Mailing_Lists You should be able to do a search from the main gromacs page for the error and see what other users have done to fix the problem. Justin has also responded to a lot of forum questions, so you may even find some helpful hints from him in there.

Best of luck!

Hi Stephanie,

Thanks for your answer. I had started simulation peptide inside the membrane. But, I am planning the perform the pulling simulations afterwards so, I will keep your advises in mind. My this problem is now solved now. I was constantly ignoring couple-intramol  in my mdp files, which was written as "no" before . After Putting it as "yes", gromacs stopped showing  warning. As far as I understand gromacs was ignoring 1-4 interactions between peptide atoms before but after setting up the option as "yes" , it started to take them into consideration.

Thank you again for suggestions.

Sometimes decreasing a time step also helps. 

yes, Sometimes it does. But I had checked all the recommended solutions by gromacs , Which are the following.

1)you didn't minimize well enough,

2)you have a bad starting structure, perhaps with steric clashes,

3)you are using too large a timestep (particularly given your choice of constraints),

4)you are doing particle insertion in free energy calculations without using soft core,

5)you are using inappropriate pressure coupling (e.g. when you are not in equilibrium, Berendsen can be best while relaxing the volume, but you will need to switch to a more accurate pressure-coupling algorithm later),

you are using inappropriate temperature coupling, perhaps on inappropriate groups, or your position restraints are to coordinates too different from those present in the system.

6)you have a single water molecule somewhere within the system that is isolated from the other water molecules.

I checked them all but didn't help.

http://www.gromacs.org/Documentation/Terminology/Blowing_Up

Hi Vikas could you send me necessary files?! I will try to solve that problem! 

Hi Jamoliddin,

My problem is solved now. I was constantly ignoring couple-intramol in my mdp files, which was written as "no" before . After Putting it as "yes", gromacs stopped showing warning. Thanks for the help.