[gmx-users] LINC warning after long time simulations
kavyani.sajjad at gmail.com
Tue Dec 1 00:58:07 CET 2015
When you see the LINCs warning it does not mean that your simulation is going wrong if there is no error or segmentation fault. In most case, the warning is due to bad energy minimization step or if ther is blowing up it can be due to bad topology which by modifying them it can be solved.
If there is no blowing up in the simulation you can skip the warning until the system reach the equilibrium state.
Actually you can do your simulation with no constrain since with constrains the results may be artificial somehow but if you insist on doing it with constraint and the simulation blows up, first consider running a nvt with posre and then a initial MD with "no constraint" on the system until it reaches an eq, then add the constraint on this system for the final MD.
I hope it can help you.
-------- Original message --------
From: 凌未风 <grx1985 at qq.com>
Date: 01/12/2015 01:31 (GMT+03:30)
To: "gromacs.org_gmx-users" <gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: [gmx-users] LINC warning after long time simulations
I pasted this once several days ago but no one replied. I know there are a lot of questions in the forum regarding LINC warning, but my problem seems quite strange. So I write here again.
My simulation system contains lipids and proteins, I am using gromos53a6 for the proteins and reaction field to deal with the long range electrostatic interactions for some reason.
My systems keep on complaining about LINC warning, such as some angle rotated more than 30 degrees, after very long simulations (one after 140 ns simulations, the other after 450 ns simulations).
I searched the website of gromacs regarding blowing up as well as the forum for discussions, however, my problem seemed not because of bad initial conformation or unreasonable pressure or temperature coupling.
I suspect if the problem is due to the topologies of the lipids I was using, because the topologies of lipids were built by myself. So I also run simulations of single lipids in solution and the topology works fine.
So I am really confused.
I really appreciate if anyone could give me some suggestions regarding this strange problem. Is it ok to set the GMX_CONSTRWARN to -1 or I should do something else to solve this problem.
With my best regards,
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