The fact that you are getting vlimit errors suggests that your
previous minimization scheme was not adequate. However, without
knowing more details about your system and what minimization you have
already tried to do to, it's difficult to make further suggestions. I
see that you're running with PBC off (ntb=0) and no implicit solvent
model (igb=0) - is there a particular reason for that?
-Dan
On Tue, Oct 9, 2012 at 5:18 AM, Jitesh Doshi <dosjitesh.gmail.com> wrote:
> Hi all,
> can anyone help me out with the error discussed above? Still not through
> with it..
>
> On Fri, Oct 5, 2012 at 5:41 PM, Jitesh Doshi <dosjitesh.gmail.com> wrote:
>
>> yes.. i have run minimization in two steps.. restrained and then freeing
>> all the atoms. I am not sure as to how exactly I should start dissecting
>> the problem. Whatever i know about amber, things seems fine except I don't
>> know if something is wrong with the input file for the run which is:
>>
>> Initial heating and equilabration
>> &cntrl
>> imin=0, irest=0, ntx=1,ig=-1,
>> nstlim=100000, dt=0.001, ntc=1,
>> ntpr=100, ntwx=10,
>> ntr=1, restraint_wt=1, restraintmask=':1-356',
>> cut=16, ntb=0, igb=0,
>> ntt=3, gamma_ln=1.0,
>> tempi=0.0, temp0=300.0,
>> /
>>
>> On Fri, Oct 5, 2012 at 5:28 PM, David A Case <case.biomaps.rutgers.edu>wrote:
>>
>>> On Fri, Oct 05, 2012, Jitesh Doshi wrote:
>>>
>>> > first occurrence of vlimit exceeds appears at step 159, so it runs
>>> properly
>>> > till 158 steps.
>>>
>>> This ain't necessarily so. It may just mean the problems with the setup
>>> don't
>>> become severe enough until then to trigger the warning.
>>>
>>> > My temperature limits are 0 to 300. and i observe that in all those
>>> steps
>>> > where vlimit exceeds, temperature blows off beyond 300. Could this be
>>> the
>>> > reason for vlimit exceeding?
>>>
>>> It's the other way around: bad forces or collisions are leading to large
>>> local
>>> velocities. This is turn results in high temperatures. All these are
>>> just
>>> symptoms....you need to examine your simulation carefully to look for what
>>> might be causing the problem. Did you indeed run energy minimization
>>> first?
>>>
>>> ...dac
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>>
>> --
>> Jitesh V. Doshi
>> Research Associate,
>> Bioinformatics Centre,
>> University of Pune.
>>
>>
>
>
> --
> Jitesh V. Doshi
> Research Associate,
> Bioinformatics Centre,
> University of Pune.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Tue Oct 09 2012 - 09:30:07 PDT
