It is impossible to answer the question without more information:

What is C6S? What is the force field you are using? What is the source of the .mdp file? What modifications did you make? Did energy minimization succeed?

It is impossible to answer the question without more information:

What is C6S? What is the force field you are using? What is the source of the .mdp file? What modifications did you make? Did energy minimization succeed?

C6S stands for chondroitin 6 sulfate. I am using forcefield as gromos53a6.ff

I had used a model of the mdp file available on your tutorial for lysozyme. i changed the the time step and also the nstlist to 1.4 as was suggested from a response given in gromacs user's forum. I am attaching the potential.xvg file obtained after energy minimization. the maximum force was 723.34 kJ/mol which is less than 1000 kJ/mol specified in the mdp file. Please advise as to what can be the possible reason for the failure of NVT equilibration.

Thank you for help.

Libin.

Neither time step nor nstlist should be 1.4. The lysozyme tutorial is designed for OPLS-AA, so there are several changes that would be necessary with Gromos96 53A6. The values of rlist and rcoulomb should be 0.9, rvdw should be 1.4. Another possibility is that the C6S parameters are inadequate. How did you derive them?

Thank you for the correction. Can you please suggest where I can find the suitable parameters to be given for Gromos96 53A6?

I couldn't find C6S pdb file, so based on its geometry I had drawn a structure using a software and then created a pdb file from it. I was able to find some journals that discussed the structure and all the simulations have been done are on a minimum of 5 to 6 units C6S chain as its persistence length is considered in all the journals. I was wondering what would happen if a simulation was done with a single unit, so just tried the same. Do you think that these LINCS errors refer to the structural instability of a single unit C6S?

Thanks for the help extended.

LINCS warnings just indicate the constraints are failing. That doesn't mean you need to troubleshoot the structures, it just means that when forces get too large, the first thing in the MD algorithm that fails is the constraints. Gromos96 parametrization is somewhat tricky because it's very empirical, but is also somewhat easy because the functional groups are transferable. That means you can build a molecule up based on existing building blocks. Sugar parameters exist, but they are complex and must be applied very carefully. There are sulfate parameters out there, as well - people have done similar simulations before and I know of parameters for SDS under an older Gromos96 parameter set.

Try ATB as an initial source for the topology; it should at least provide you with a decent starting point for further refinement.

Do double precision emery minimization before starting your MD simulation. Make sure that all constraints are on when you are doing so.

I created the .itp file for C6S single unit using ATB and then used #include option in writing the .top file.

Also I avoided pdb2gmx and used editconf to generate .gro file, as there was an issue of residue name missing when I tried pdb2gmx since the residue name was not defined in the force field.

@Abolfazi: Can you give me some directions regarding how to do double precision emery minimization?

@Justin: Can you please tell me how to find the values that we must give as input for rlist, rcoulomb and rvdw etc in nvt.mdp file for gromos53a6.ff?

Thank you for your help.

Read the Gromos96 53a6 paper. Use those values. Note that PME has subsequently been shown to be superior to RF for long-range electrostatics.

I have make an Ionic liquid itp file (for cation Bmim and anion NTf2 ion) but when I try to equilibrate by NPT then the following error comes out can anybody help me ?

Program grompp_mpi, VERSION 4.6.2

Source code file: /home/krishna/program/gpu_gmx/gromacs-4.6.2/src/kernel/grompp.c, line: 1910

Fatal error:

Too many warnings (2), grompp_mpi terminated.

If you are sure all warnings are harmless, use the -maxwarn option.

For more information and tips for troubleshooting, please check the GROMACS

website at http://www.gromacs.org/Documentation/Errors