<div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Dear all,<br>
<br>
I figured out the problem. Error was in my mdp file options. I did not specify the acc-groups correctly. I can get 1/viscosity using g_energy.<br>
<br>
However, once the acc-groups are specified, now the NEW issue is not being able to run my job correctly.<br>
<br>
I get the following errors:<br>
<br>
Step 376, time 7.52 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>
rms 0.006964, max 0.163855 (between atoms 861 and 859)<br>
bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br></blockquote><div><br></div><div><br></div><div>1. To get viscosity from non-eq. MD, you should specify ONLY "cos_acceleration" in the MDP and then use g_energy utility.</div>
<div><br></div><div>2, To get viscosity from eq. MD, use "g_energy -vis", while saving the energy terms every 10-30 fs.</div><div><br></div><div>Your problems with lincs are probably connected with a high value for acceleration. The first step is to decrease it.</div>
<div><br></div><div><br></div><div>-- </div></div>Dr. Vitaly V. Chaban, Department of Chemistry<div>University of Rochester, Rochester, New York 14627-0216<br>
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