The protein is of 543 amino acids, its MD simulation is done using Gromacs, the problem is occurring when the duration is set for 1000 PS and contemporary steps. The problem occurs in 457 step showing "molecules too much far in the trajectory". Could any one suggest how to overcome this issue?
I am not familiar with gromacs but may be the problem is of periodic boundary condition......
You should tell that this problem occur in the production phase or..in .equilibration...phase....
Your .mdp file would be absolutely interesting to see. In addition, as already Prashant said, it is extremely important to know if you're trying to run an equilibration or a production run...even more important, have you experienced any problems with the energy minimization step?
Definitely check you energy minimization log. did your system converge prior to starting your run?
You simply expand the dimension of the box by using appropriate command option to do this you can go through GROMACS user manual or by going through any basic GROMACS tutorial.
First of all, what are you doing, NVT, NPT? Post here the .mdp file, please.
It must be the problem with energy minimization...just perform proper energy minimization........
I will post the related file once i repeat this step thanks all for suggestion
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