Dear Prof. Case,
Thank you for your reply. I equilibrated the system without restraint
at 298K for 1ns. Since the solvent is ionic in nature, I expect long
range electrostatics and have used a cut off of 15. We have used the
same molecule and its force field parameters for simulation of other
systems (not with DNA though). What should I do now? Should I continue
with dt=0.001 for longer. If the force field is the problem, should'nt
the system have a problem with dt=0.001 also?
Thanks for your help
On 1/17/13, David A Case <case.biomaps.rutgers.edu> wrote:
> On Thu, Jan 17, 2013, DEBOSTUTI GHOSHDASTIDAR wrote:
>>
>> I am simulating DNA in a solvent. After thorough minimization, I
>> heated up the system to 298K keeping the DNA restrained and thereafter
>> performed NPT at 298K keeping the restraints on. However, the system
>> showed a SHAKE error saying "SHAKE cannot be accomplished". So I read
>> out the last few frames just before the error and using VMD saw that a
>> C-H bond of one molecule of the solvent is stretched too much. When I
>> repeated the simulation, the error occured again, this time for a
>> different solent molecule and a N-H bond. During this entire procedure
>> i was using dt=0.002.
>
> I doubt that very many people have experience with simulation of DNA in
> solvents other than water. There may be large forces on the solvent
> molecules, and it is certainly possible that there are problems with
> whatever
> force field parameters you are using for the solvent. Or, you may still
> need
> to equilibrate for longer (you don't say how long the equilibration was...)
> It's not too uncommon to need to use dt=0.001 for the first stages of a
> simulation.
>
>>
>> Here's my input for md
>> &cntrl
>> imin = 0, ntx = 7, irest = 1,
>> ntpr = 1000, ntwx = 1000, ntwe = 0,
>> ntc = 2, ntf = 2,iwrap = 1,nstlim = 500000, dt =0.002,
>> tempi=298.0, temp0 = 298.0, ntt =1, tautp =2.0,
>> cut = 15.0, ntb = 2,ntp = 1,taup = 2.0,pres0 = 1.0
> ^^^^^^^^^^^^
>
> This is way too big....consider using a value in the range of 8-10 Ang.
>
> ...dac
>
>
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--
Debostuti Ghosh Dastidar
PhD Scholar
Computational Biophysics Lab
Department of Biotechnology
Indian Institute of Technology Madras
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Received on Thu Jan 17 2013 - 09:30:03 PST
