Dear all,
I have been trying to perform an MD simulation using Gomacs. My system has two ligands in DMSO solvent. While performing the NPT equilibration , I'm getting the following :
Fatal error :
Too many LINCS warnings (1616)
Can anyone suggest how to solve the problem ?
Most of the times, this error is due to two reasons:
1) bad initial coordinate
2) wrong topology/parameters
Check these.
Sun Tiedong , I tried changing few things from the mdp file and it worked for NPT. Now I'm again facing the same issue for production run. I tried changing the parameters as I did for NPT. But its not working
Hi Bijaya,
It is not straightforward to diagnose a system error with so little info. You may need help from a mentor or supervisor who knows your system better.
A LINCS warning means that GROMACS cannot successfully keep part of your system rigid that you have asked to keep rigid. This includes bonds and angles that you have asked to keep fixed. This can happen if the dynamics of the system do not allow for those bonds and angles to stay rigid, i.e. they are either in a bad initial condition, or are subsequently moving so far and so fast, that a good rigid configuration can't be found.
So you need to check your initial coordinates, topologies, and your subsequent dynamics. Look carefully at the warning and see if you can find out which particles it corresponds to. It may help to see if there is a compound in your system which matches up in number with the number of warnings. E.g. if there are 808 DMSO molecules and you have 1616 warnings, there could be a type of bond that isn't specified, of which each DMSO molecule has two bonds.
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