[gmx-users] Dear Gromaces users, I have a problem

JINGJING HUANG jjhuang0520 at gmail.com
Fri Nov 6 01:54:18 CET 2015

Dear Gromaces users,

I am trying to carry out a mdrun simulation with distance restraint (gmx mdrun -deffnm system). But I got these errors:

relative constraint deviation after LINCS:
rms 0.294533, max 23.000101 (between atoms 9932 and 9933)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   9929   9930   90.0    0.1095   2.4655      0.1090
   9929   9931   49.6    0.1096   0.1069      0.1090
   9932   9933   90.0    0.1210   2.6160      0.1090
   9932   9934   32.8    0.0898   0.1018      0.1090

I’ve read the debugging instructions on line, and also many previous discussions towards this issue (http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings <http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings>) But I believe for my system,  the problem is due to the distance restraint and also the parallel simulation. Because:

1. When I removed distance restraint, I didn’t get these errors.However, I need to keep this distance restraint to make peptides rigid for my purpose.
2. When I run this mdrun simulation ( gmx mdrun -deffnm system -nt 1) in my laptop (just with one cpu), I didn’t got these errors as well.

Because this is a inhomogeneous system, except for distance restraint, I guess I also need to do domain decomposition in order to simulate that system in many threads. But I don’t know how to do that.  I know in my lab, someone previously did particle decomposition (for a very similar system like this one ) in old version of gromacs, it worked and didn’t got these errors. But now PD was removed in gromacs 5.0.4 (This is version I use now), So I cannot try PD for my system.

Besides, I am not sure whether my analysis toward these errors is right or not. 

Thank you a lot in advance. I got stuck in this problem for a long time.


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