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

[Lee Soin]

Hello!
I'm using COM pulling with distance constraint between two domains of a
protein. The energy minimization and a 100-ps equilibrating process in the
NPT ensemble with position restraints on protein atoms all passed OK. Then I
applied a distance constraint between COM of two domains and performed the
simulaiton 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.
The following two changes lead to no problem:
(1) distance constraint between COM of two domains is applied, but the
simulation is done in the NVT ensemble;
(2) distance restraint using an umbrella potential instead of distance
constraint is applied, and the simulation is done in NPT.
So can anyone tell me what the problem is?
Thanks in advance.

-- 
SUN Li
Department of Physics
Nanjing University, China
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