Hi,
On Sun, Jul 21, 2013 at 12:30 PM, John Travers <jtravers70.yahoo.com> wrote:
> Yes, I am talking about tutorial B1, step 5.1.5 but with the molecule of
> mine.
The tutorials are meant as guidelines only, not as templates for how
to do minimization, equilibration, etc. The fact that your kinetic
energy goes all NaN within a few steps indicates that your previous
minimization/equilibration was inadequate. Without knowing more
details of your system I can only make general recommendations, but
for an explicitly solvated system I usually follow a 9 step initial
minimization/equilibration scheme:
1) 1K step Steepest Descent Minimization with strong (5
kcal/mol*Ang^2) restraints on heavy atoms, no shake.
2) NTV MD with strong restraints on heavy atoms and shake, dt=.001, 15 ps.
3) 1K step Steepest Descent Minimization with relaxed (2
kcal/mol*Ang^2) restraints on heavy atoms, no shake.
4) 1K step Steepest Descent Minimization with minimal (0.1
kcal/mol*Ang^2) restraints on heavy atoms, no shake
5) 1K step Steepest Descent Minimization with no restraints, no shake.
6) NTP MD with shake and low (1.0 kcal/mol*Ang^2) restraints on heavy
atoms, 5 ps dt=.001.
7) NTP MD with shake and minimal (0.5 kcal/mol*Ang^2) restraints on
heavy atoms, 5 ps dt=.001.
8) NTP MD with shake and minimal restraints on backbone atoms, dt=0.001, 10 ps
9) NTP MD with shake and no restraints, dt=0.002, 10 ps.
For every MD step temp0 is always set to the temperature of choice,
and I use a Berendsen thermostat/barostat. Of course, all restraints
are applied to the solute molecule only. This procedure is usually
good enough to get you on your way - I generally run out step 9 until
the density (among other things) seems well-behaved before even
considering a production run. For steps 1-4 I use as reference
structure the initial coordinates for that step, and for steps 6-8 I
use the final structure from step 5. Others probably have their own
minimization schemes but this is one that works for me on most
systems.
Hope this helps,
-Dan
>
> Best
>
> JT
>
> ________________________________
> From: Daniel Roe <daniel.r.roe.gmail.com>
> To: John Travers <jtravers70.yahoo.com>; AMBER Mailing List
> <amber.ambermd.org>
> Sent: Saturday, July 20, 2013 6:17 PM
> Subject: Re: [AMBER] problem on heating with restraints on the solute
>
> Hi,
>
> Are you talking about tutorial B1, step 5.1.5? Are you using the files
> provided from the website ( polyAT_wat_md1.in, polyAT_wat.prmtop,
> polyAT_wat_min2.rst)?
>
> -Dan
>
> On Sat, Jul 20, 2013 at 2:21 PM, John Travers <jtravers70.yahoo.com> wrote:
>> Dear Amber experts
>>
>> I am a new user of AMBER. I am trying to run a MD simulation following the
>> tutorial on simulating a DNA polyA-polyT Decamer. I got a problem at the
>> heating stage. I used the SHAKE algorithm (the same as in the tutorial), but
>> the MD only ran for 7 steps (stepsize 1fs) and stopped with the error
>> message of segmentation fault. At the step 7, the kinetic energy term
>> becomes NaN. On the other hand, if I don't use the SHAKE algorithm (ntc=1,
>> ntf=1, time step=0.2 fs) the MD ran normally. Any hints on this?
>>
>> I also check the 6 step MD results using VMD, it seemed only a small part
>> of the whole water was moving. I followed strictly the tutorial. The partial
>> and full minimization went smoothly. I compared the structures before and
>> after minimization, they looked just fine.
>>
>> Thanks!
>>
>> Best wishes
>>
>> JT
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Sun Jul 21 2013 - 12:00:02 PDT
