Re: Re velocity error

From: bo baker (bo.bybaker_at_gmail.com)
Date: Wed Jan 04 2006 - 17:20:51 CST

Hi, the periodic box is about:
22000 76.154 0 0 0 74.2013 0 0 0 79.083 25.5 37 23.3 -3.78574e-06-3.78574e-06 -3.78574e-06 0 0 0
at 22000 step, which is the starting for the next MD run. And I setthe cell basis vectors as:
cellBasisVector1 78.00 00.00 00.00cellBasisVector2 00.00 76.00 00.00cellBasisVector3 00.00 00.00 81.00cellOrigin 25.5 37.0 23.3
margin 5
Pme onPmeGridsizeX 78PmeGridsizeY 76PmeGridsizeZ 81
Thank you for any suggestions.
Bo

On 1/4/06, Boyang Wang <pkuwangboyang_at_yahoo.com.cn> wrote:> Hi. Can you check if your periodic box has enlarged?> If your box becomes bigger, the previous cell basis vectors are too small,> and this may be one of the reasons your have too fast moving atoms.>> best,> Boyang>> bo baker <bo.bybaker_at_gmail.com> 写道:> Hello, NAMD:>> I try to run the MD without any restrains on. But I got the following> error messages:>>> ERROR: Atom 1804 velocity is 12661.2 -18890.9 10218.8 (limit is 5000)> ERROR: Atom 1812 velocity is -12579.2 19072.4 -10061.2 (limit is 5000)> ERROR: Atoms moving too fast; simulation has become unstable.> ERROR: Exiting prematurely.>>> The coordinates were from the prievious runs ( 20 ps of> equilibration). I have included the .conf and .log files as> attachments.>> Thank you for advices.>> Bo>>>>> __________________________________________________> 赶快注册雅虎超大容量免费邮箱?> http://cn.mail.yahoo.com

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