RE: AMBER: Re: Strange shape in my MD simulations

From: Ross Walker <ross.rosswalker.co.uk>
Date: Wed, 20 Jun 2007 08:27:37 -0700

Hi Pawan,
 
Yes the vacuum bubble should eventually equilibrate out if you just keep
running NPT, but it can take a long time. Potentially nanoseconds. You also
have to realize that you have introduced a huge perturbation to your system
by allowing these bubbles to form in the first place. They are completely
artificial (no experimental equivalent) and are a function of forcing the
system to run as a liquid at a density which does not lie in the liquid
phase for that system. Hence while you can potentially just equilibrate out
the bubbles I would not advise it since you don't know what 'damage' these
bubbles have done in the first place. Instead I would ditch that simulation
and go back to the drawing board and run the NVT fraction for a much shorter
time before switching to NPT.
 
All the best
Ross

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From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
gurpreet singh
Sent: Wednesday, June 20, 2007 00:58
To: amber.scripps.edu
Subject: Re: AMBER: Re: Strange shape in my MD simulations


pawan
i also faced this type of problem some time before. i think if u will carry
out a longer NPT run this will be solved .
tell me if any other queery





On 6/19/07, Pavan G <pavanamber.gmail.com> 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









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Received on Sun Jun 24 2007 - 06:07:09 PDT
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