<br><br><div class="gmail_quote">---------- Forwarded message ----------<br>From: <b class="gmail_sendername">PRADEEP VENKATARAMAN</b> <span dir="ltr"><<a href="mailto:pvtulane@gmail.com">pvtulane@gmail.com</a>></span><br>
Date: Tue, Jun 2, 2009 at 5:37 PM<br>Subject: Simulating Gases with GROMACS 4.0<br>To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><br><br><span style="border-collapse:collapse"><div>Hi</div><div><br>
</div><div>I am trying to simulate all atom methane gas (no solvent) at 1 bar and 300 K.</div><div><br></div><div>I minimized 300 methane molecules in 25X25X25 ang^3 box.</div>
<div><br></div><div>When I try running at NPT simulation using the following pressure coupling parameters,</div><div><br></div><div><div>Pcoupl = parrinello-rahman</div><div>Pcoupltype = isotropic</div>
<div>tau_p = 2.0</div><div>compressibility = 9.9e-1</div><div>ref_p = 1.0</div><div><br></div></div><div>I encounter the following error. Please help</div><div><br></div><div>======================================================</div>
<div>Step 16271, time 32.542 (ps) LINCS WARNING</div><div>relative constraint deviation after LINCS:</div><div>rms 0.001545, max 0.019029 (between atoms 556 and 557)</div><div>bonds that rotated more than 30 degrees:</div>
<div> atom 1 atom 2 angle previous, current, constraint length</div><div> 556 560 55.3 0.1113 0.1072 0.1092</div><div> 556 557 50.9 0.1114 0.1071 0.1092</div><div><br></div><div>-------------------------------------------------------</div>
<div>Program mdrun_mpi, VERSION 4.0.5</div><div>Source code file: constr.c, line: 136</div><div><br></div><div>Fatal error:</div><div>Too many LINCS warnings (1001)</div><div>If you know what you are doing you can adjust the lincs warning threshold in your mdp file</div>
<div>or set the environment variable GMX_MAXCONSTRWARN to -1,</div><div>but normally it is better to fix the problem</div><div>============================================================</div><div><br></div><div>Thanks,</div>
<div><br></div><font color="#888888"><font color="#888888"><div>Pradeep</div></font></font></span>
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