I would like to put more info about my last question. After those
errors happen (vlimit error shown below), I can see that temperature
also drastically increased. so, system size and temperature
drastically increased around 580ps, showing huge holes in the middle of
box.
Could you tell me how to handle this problem??
Thanks,
Hwankyu.
On Jun 6, 2005, at 6:47 PM, Hwankyu Lee wrote:
> When I looked at the beginning and end trajectories in VMD, I could
> see that water box around solutes looks bigger with increasing time.
> It looks like system size slowly and continuously blows up and then
> finally crashed around 580ps, although my system has reasonable
> temperature.
> Could you tell me how to solve this problem?
>
> Hwankyu.
>
> On Jun 6, 2005, at 1:19 PM, Ross Walker wrote:
>
>> Dear Hwankyu,
>>
>>> vlimit exceeded for step 93807 ; vmax =
>>> 23.91630977621595
>>> vlimit exceeded for step 93808 ; vmax =
>>> 40.75498760131579
>>>
>>> Coordinate resetting cannot be accomplished,
>>> deviation is too large
>>> iter_cnt, my_bond_idx, i and j are : 3 1 5140 5139
>>
>> It is strange that you see this error after 580ps. Although your
>> system may
>> have been unstable for a while before this and eventually blows up.
>> Your
>> temperature in the output you give looks good as well. I take it all
>> the
>> amber8 test cases pass on your machine.
>>
>> Can you zoom in around the time when things go wrong? I.e. Run from
>> say 450
>> -> 580ps with ntwx=1 so that you can carefully watch things in vmd.
>> Then you
>> can see where it starts to blow up from. This might make the problem
>> easier
>> to identify.
>>
>> I am sorry I can't help much more than that.
>>
>> All the best
>> Ross
>>
>> /\
>> \/
>> |\oss Walker
>>
>> | Department of Molecular Biology TPC15 |
>> | The Scripps Research Institute |
>> | Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
>> | http://www.rosswalker.co.uk/ | PGP Key available on request |
>>
>> Note: Electronic Mail is not secure, has no guarantee of delivery,
>> may not
>> be read every day, and should not be used for urgent or sensitive
>> issues.
>>
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>
>
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-------------------------------------------------------------------
Hwankyu Lee.
Ph.D. candidate.
Dept. of Biomedical Engineering.
University of Michigan - Ann Arbor.
Email: leehk.umich.edu, hklee910.hotmail.com
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Received on Tue Jun 07 2005 - 00:53:01 PDT
