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
>>
>>
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>>
>
>
>
> --
> Jitesh V. Doshi
> Research Associate,
> Bioinformatics Centre,
> University of Pune.
>
>
--
Jitesh V. Doshi
Research Associate,
Bioinformatics Centre,
University of Pune.
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Received on Tue Oct 09 2012 - 04:30:03 PDT
