[gmx-users] Re: Minimization

Gia Maisuradze gia at chem.unr.edu
Wed Jan 5 00:09:10 CET 2005


I am a new user of GROMACS. I am trying to run MD simulation of one of the proteins. I followed the "getting started" tutorial. My question is about minimization of my system in solvent. According to the tutorial the minimization should be finished when either the minimization has converged or a fixed number of steps has been performed. In my case the minimization has converged before it reached the fixed number of steps. But the potential energy after minimization IS NOT lower than potential energy calculated by formula: -42(kJ/mole)xN (N is a number of SPC water molecules). What is the problem? How can I fix it? The same problem I had for Ribonuclease S-peptide given in tutorial.

My second question is about short and full MD run. According to the tutorial to generate the input for the position restrained mdrun we have the following command:

grompp -f pr -o pr -c after_em -r after_em -p speptide

for full md to do the same thing we have the following command:

grompp -v -f full -o full -c after_pr -p speptide

We can see that full MD is quite similar to the restrained MD, but there is a difference which makes impossible to run full MD without restrained MD. In full MD we have "-c after_pr" which is an input file and "after_pr" can be obtained from short MD run. Is it correct that we can't run full MD run without short MD or is there any other way to run directly full MD (for example, use the same files for full MD as used for short MD)?

I look forward to hearing your reply,

With best wishes,

Gia Maisuradze  
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