[gmx-users] LINCS warnings generated in NPT ensemble and not in NVT

[Lee Soin]

The difference between "restraints" and "constraints" is indeed something
I'm aware of :-)
Even though distance restraint between COM of two domains worked just OK for
me, I would prefer to use distance constraint since that will introduce
fewer artifacts and can fix the distance between two domains exactly at the
desired distance. So now everything I'm going to ask is under the assumption
that I'm using distance constraint in COM pulling. The protein I'm using
consists of two domains, and the problem is as follows:

After energy minimization and a 100-ps equilibration in NPT, I applied a
distance constraint between COM of two domains and performed COM pulling in
the NPT ensemble. But after the first few steps I received such warnings:

Step 7  Warning: pressure scaling more than 1%, mu: 1.03819 1.03819 1.03819
Step 8  Warning: pressure scaling more than 1%, mu: 0.98123 0.98123 0.98123
Step 9  Warning: pressure scaling more than 1%, mu: 0.746615 0.746615
0.746615
Step 10  Warning: pressure scaling more than 1%, mu: 1.34141 1.34141 1.34141
Step 10, time 0.02 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.017756, max 0.670789 (between atoms 3187 and 3188)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  4334   4336   41.3    0.0813   0.1101      0.1090
  4334   4335   39.2    0.0813   0.1090      0.1090
  4332   4334   32.1    0.1139   0.1548      0.1529
  4325   4326   34.5    0.0813   0.1091      0.1090
  4299   4301   31.1    0.1077   0.1468      0.1449
  4293   4296   34.5    0.0814   0.1086      0.1090
  4284   4285   30.6    0.0812   0.1093      0.1090
  4225   4226   64.8    0.0812   0.1144      0.1090
  4208   4210   31.0    0.1140   0.1522      0.1529
                    ......

 and then the program exited for too many LINCS warnings.
If I change the ensemble to NVT, everything is OK.
So I think I have made everything clear, haven't I? And thank you if you can
help me again :-)

-- 
SUN Li
Department of Physics
Nanjing University, China
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