Thanks a lot for your help!
On Sat Aug 30 14:41:02 EDT 2008, Ross Walker
<ross.rosswalker.co.uk> wrote:
> Hi Wang,
>
>> I'm running a 30,000 atoms system in vacuo and get the error
>> messages as below:
>>
>> vlimit exceeded for step 21771; vmax = 20.9636
>>
>> my .in file is as below:
>>
>> cell_NPT: 100ps MD
>> &cntrl
>> imin = 0, irest = 1, ntx = 7,
>> ntb = 0,
>> cut = 12, ntr=1,
>> ntc = 2, ntf = 2,
>> tempi = 300.0, temp0 = 300.0,
>> ntt = 3, gamma_ln = 2.0,
>> nstlim = 50000, dt = 0.001,
>> ntpr = 1000, ntwx = 1000, ntwr = 1000
>> /
>> keep restraints
>> 100.0
>> RES 217 954
>> END
>> keep out
>> 10.0
>> RES 955 1692
>> END
>> END
>>
>> could you tell me how to fix it? It will be appreciated greatly!
>
> 100.0 is probably too large of a restraint to be using for MD and
> could be
> partly responsible for the problems you are seeing. Although more
> likely I
> suspect it is because you are running without periodic boundaries
> (ntb=0)
> and you are not using Generalized Born here (igb=0) hence this is
> a gas
> phase simulation and your protein probably just isn't stable in a
> vacuum.
> See the first tutorial on the AMBER website for an example +
> explanation of
> this.
>
>> And my second question is:
>> If I get the message as below
>> | RE_POSITION Moving by 0.063118 -3.392424 -0.241462
>>
>> how can I align the .rst and .mdcrd files to let the center come
>> back to the oringinal position? Thanks a lot!!
>
> I'm not sure exactly what you mean here. Do you mean you want to
> keep the
> origin fixed during the simulation? If so I'm not entirely sure
> how one can
> do this, with periodic boundaries you can do it by using center
> in ptraj to
> center the coordinates on say your protein, but without periodic
> boundaries
> I think you might need to write a script to go through the output
> and add
> the RE_POSITION changes to the mdcrd file each time it comes up.
> You could
> also set nscm=0 to force sander to not make the shift but in gas
> phase you
> will eventually end up with your system diffusing a long way from
> the
> origin. Maybe others can comment some more here.
>
> All the best
> Ross
>
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk | |
> http://www.rosswalker.co.uk | PGP Key available on request |
>
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--
Wang,Ying
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Received on Sun Aug 31 2008 - 06:08:20 PDT
