AMBER Archive (2007)

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

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Jun 19 2007 - 10:42:08 CDT

Dear Pavan,
 
The image you show is indicative of having vacuum bubbles present in your
simulation. You can see this clearly if you open the trajectory or restrt
file in VMD and then under graphical representations select periodic and
turn on the periodic images. Then you will see the bubbles crossing the edge
of the box.
 
This occurs because the initial density of the system is too low - required
for stability initially. You then run with NVT for too long and the system
forms these vacuum bubbles that can take an extremely long time to
equilibrate out.
 
I suggest you try the following protocol:
 
1) Minimize
 
2) NVT 0 to 100K (20ps or so)
 
3) NPT 100 to 300K (100ps or so) - density should equilibrate around 1.
 
4) Continue with NPT, NVT or NVE, your choice.
 
All the best
Ross
 

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From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Pavan G
Sent: Tuesday, June 19, 2007 07:35
To: amber_at_scripps.edu
Subject: Re: AMBER: Re: Strange shape in my MD simulations

Yeah, the picture attached is what I got after imaging the protein to the
center of the box. My ptraj input was

trajin mdcrd
image familiar
center :1-420
trajout reimg.mdcrd

Pavan

On 6/19/07, Adrian Roitberg <roitberg_at_qtp.ufl.edu> wrote:

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_at_qtp.ufl.edu
<mailto:roitberg_at_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_at_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_at_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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