Pavan,
First guess is that you need to center/image your MD run (using ptraj).
It is always wise to use iwrap=1 in your md runs, unless you are really
interested in diffusion properties.
Adrian
Pavan G wrote:
> Hello All!
>>
>> Following are the input files I used to study a system of protein
>> surrounded by drugs (parameterized using antechamber).
>>
>> ==============
>> First I minimized the system with restraints on residues 1-420 which were
>> picked from a previous simulation which was stabilized over a few
>> nanoseconds at 312 K. This part (1-420) was picked and surrounded with
>> more
>> water and drugs.
>> ==============
>> minmization
>> &cntrl
>> imin = 1,
>> maxcyc = 5000,
>> ntpr = 100,
>> ncyc = 500,
>> ntr = 1,
>> restraint_wt = 2.0,
>> restraintmask = ':1-420'
>> /
>> ================
>> Then I heated the system from 250K to 400K again with the first 420
>> residues restrained.
>> ==============
>> 500ps heating with NVT
>> &cntrl
>> imin = 0,
>> irest = 0,
>> nstlim = 500000,
>> dt = 0.001,
>> tempi = 250,
>> temp0 = 400,
>> cut = 8,
>> ntb = 1,
>> ntt = 1,
>> ntf = 2,
>> ntc = 2,
>> ntpr = 1000,
>> ntwr = 1000,
>> ntwx = 1000,
>> ntwe = 1000,
>> ntr = 1,
>> restraint_wt = 2.0,
>> restraintmask =':1-420'
>> /
>> =========================
>> Cooling the system to 312K with restraints on first 420 residues
>> =========================
>> 100ps cooling with NVT
>> &cntrl
>> imin = 0,
>> irest = 1,
>> ntx = 5,
>> nstlim = 100000,
>> dt = 0.001,
>> tempi = 402.37,
>> temp0 = 312,
>> cut = 8,
>> ntb = 1,
>> ntt = 1,
>> ntf = 2,
>> ntc = 2,
>> ntpr = 1000,
>> ntwr = 1000,
>> ntwx = 1000,
>> ntwe = 1000,
>> ntr = 1,
>> restraint_wt = 2.0,
>> restraintmask =':1-420'
>> /
>> ==========================
>> NPT at 312K on the whole system. No restraints on any part of the system
>> ==========================
>> 200ps NPT
>> &cntrl
>> imin = 0,
>> irest = 1,
>> ntx = 5,
>> nstlim = 200000,
>> dt = 0.001,
>> tempi = 312,
>> temp0 = 312,
>> cut = 8,
>> ntb = 2,
>> ntp = 1,
>> taup = 2.0,
>> ntt = 1,
>> ntf = 2,
>> ntc = 2,
>> tautp = 1,
>> ntpr = 1000,
>> ntwr = 1000,
>> ntwx = 1000,
>> ntwe = 1000,
>> /
>> ==========================
>>
>> All the plots, temperature, Etot, etc. don't have any major fluctuations.
>> The Ewald error estimate for NPT had a mean of 5*10^(-5) and a standard
>> deviation of 3*10(-5). Should this be a cause for alarm?
>> When I imaged the frames to center the initial 420 residues I ended up
>> with a system which was fine when looked at two planes (rectangular).
>> However when viewed it along the third plane, it looked like a plus
>> symbol.
>> (Figure attached).
>> Could you please comment on why it turned out that way. I don't see a
>> reason why it should have the edges filletted and even if should, why
>> only
>> in one direction?
>> Please let me know if you want any additional information.
>>
>> Thank you,
>> Pavan K. Ghatty
>>
>>
>
>
> ------------------------------------------------------------------------
>
--
Dr. Adrian E. Roitberg
Associate Professor
Quantum Theory Project and Department of Chemistry
University of Florida PHONE 352 392-6972
P.O. Box 118435 FAX 352 392-8722
Gainesville, FL 32611-8435 Email adrian.qtp.ufl.edu
============================================================================
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or that we are to stand by the president right or wrong,
is not only unpatriotic and servile, but is morally treasonable
to the American public."
-- Theodore Roosevelt
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Received on Wed Jun 20 2007 - 06:07:36 PDT
