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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