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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