ok, but then use ptraj to center/image before looking at the pictures in
vmd.
a.
Pavan G wrote:
> Hello Adrian,
>
> You guessed it right. I am interested in the diffusion constants in the
> system which is the reason why I did not use iwrap=1 and later used ptraj
> for processing the output.
>
> Pavan
>
> On 6/19/07, Adrian Roitberg <roitberg.qtp.ufl.edu> wrote:
>>
>> 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
>>
>> ============================================================================
>>
>>
>> To announce that there must be no criticism of the president,
>> 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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>>
>
--
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
============================================================================
To announce that there must be no criticism of the president,
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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Jun 20 2007 - 06:07:36 PDT
