<div>The difference between "restraints" and "constraints" is indeed something I'm aware of :-)</div>
<div>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:</div>
<div> </div>
<div>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:</div>
<div> </div>
<div>Step 7 Warning: pressure scaling more than 1%, mu: 1.03819 1.03819 1.03819<br>Step 8 Warning: pressure scaling more than 1%, mu: 0.98123 0.98123 0.98123<br>Step 9 Warning: pressure scaling more than 1%, mu: 0.746615 0.746615 0.746615<br>
Step 10 Warning: pressure scaling more than 1%, mu: 1.34141 1.34141 1.34141<br>Step 10, time 0.02 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>rms 0.017756, max 0.670789 (between atoms 3187 and 3188)<br>
bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br> 4334 4336 41.3 0.0813 0.1101 0.1090<br> 4334 4335 39.2 0.0813 0.1090 0.1090<br> 4332 4334 32.1 0.1139 0.1548 0.1529<br>
4325 4326 34.5 0.0813 0.1091 0.1090<br> 4299 4301 31.1 0.1077 0.1468 0.1449<br> 4293 4296 34.5 0.0814 0.1086 0.1090<br> 4284 4285 30.6 0.0812 0.1093 0.1090<br> 4225 4226 64.8 0.0812 0.1144 0.1090<br>
4208 4210 31.0 0.1140 0.1522 0.1529</div>
<div> ......</div>
<div><br> and then the program exited for too many LINCS warnings.</div>
<div>If I change the ensemble to NVT, everything is OK.</div>
<div>So I think I have made everything clear, haven't I? And thank you if you can help me again :-)</div>
<div><br>-- <br>SUN Li<br>Department of Physics<br>Nanjing University, China<br></div>