<div>Hello!</div>
<div>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:</div>
<div><br clear="all">Step 7 Warning: pressure scaling more than 1%, mu: 1.03819 1.03819 1.03819</div>
<div>Step 8 Warning: pressure scaling more than 1%, mu: 0.98123 0.98123 0.98123</div>
<div>Step 9 Warning: pressure scaling more than 1%, mu: 0.746615 0.746615 0.746615</div>
<div>Step 10 Warning: pressure scaling more than 1%, mu: 1.34141 1.34141 1.34141</div>
<div>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>and then the program exited for too many LINCS warnings.</div>
<div>The following two changes lead to no problem:</div>
<div>(1) distance constraint between COM of two domains is applied, but the simulation is done in the NVT ensemble;</div>
<div>(2) distance restraint using an umbrella potential instead of distance constraint is applied, and the simulation is done in NPT.</div>
<div>So can anyone tell me what the problem is?</div>
<div>Thanks in advance.</div>
<div><br>-- <br>SUN Li<br>Department of Physics<br>Nanjing University, China<br></div>