[AMBER] problem with amber11 dcd file when runing a 20ns MD at a time

From: xueqin pang <pangxueqintea.yahoo.com.cn>
Date: Mon, 10 Jan 2011 21:04:12 +0800 (CST)

Hello everyone,

      I am using Amber11 for MD simulation. It works nice but when run a segment for 20ns ( that is 5000 snapshots) at a time, I got problem with the last several snapshots in the output dcd file. Taking the rmsd of the protein backbone for example it is about 230A while the normal ones is around 3A and the trajout pdbs for these snapshots also look like a mass. However, it looks prety ok with the final .rst file and its pdb ( done with ambpdb ) and can go one smoothly with a following segments. And all the 3 segments of 20ns for two different protein systems have this same problem.

       So have anyone ever had such problem and is their any suggestion how to deal with this problem? I guess it did not work well when matching the .prmtop and the position of those snapshots.

Thanks very much for your kind help.

Best wishes


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Received on Mon Jan 10 2011 - 05:30:04 PST
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