On 5/17/13 7:16 AM, Shima Arasteh wrote:
Thanks for your reply.
It' s around 5 nano seconds that I ran equilibration time on the system, and
the average pressure I see as a result, seems sensible. However I am not sure
if this criteria is sufficient? Others suggest to evaluate the box-dimension
changes using g_energy code to judge of sufficient equilibration time.
The box vectors won't tell you anything more than the pressure will since
they're related quantities.
The better question is, "What is a suitable starting structure for the system of
interest?" The umbrella sampling tutorial (which everyone seems to take at
literal face value as the only way to do things, which it is decidedly not)
presents a simple, easy-to-understand method. In the paper I did (upon which I
based the tutorial), I simulated the protofibril structures for 100 ns before I
was confident they were suitably stable and representative of viable structures
for doing SMD and US. Your mileage will vary and depends on the quality of the
starting structure and what it is that you hope to determine. There is no magic
recipe that is universal.
-Justin
I appreciate your suggestion.
Sincerely,
Shima
----- Original Message -----
From: Thomas Schlesier <schl...@uni-mainz.de>
To: gmx-users@gromacs.org
Cc:
Sent: Friday, May 17, 2013 3:30 PM
Subject: [gmx-users] Re: Running Pull Code
The three steps (EM, NVT and NPT) are to equilibrate the system. How
much time these steps need depends on the system. But i would assume a
ouple of nanosecounds are sufficient for most systems. You could look
into the literature, how long other people equilibrate systems which are
similar to ours.
If the system is equilibrated, you an start to perform the pulling
simulation to obtain the individual structure for the later umbrella
sampling.
Greetings
Thomas
Am 17.05.2013 07:46, schrieb gmx-users-requ...@gromacs.org:
Hi,
I have a system composed of POPC/peptide/water/ions. I aim to study ion
conduction through the peptide using umbrella sampling.
I built the system and ran EM, NVT, NPT successfully, but have not run md yet.
I' d like to know if the system is required of passing a few nanoseconds md? Or
I might be able to go to Umbrella Sampling straight after NPT?
As I studied in Justin's tutorial, running pull code is done after some typical
steps of every simulation ( EM, NVT, NPT). But I dont know if is correct
generally for other systems as well?
Would you please give me any suggestions?
Thanks in advance.
Sincerely,
Shima?
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
