ahmet yıldırım wrote:
Dear Justin,
In the first tutorial You said "After we arrive at the correct
temperature (based on kinetic energies), we will apply pressure to the
system until it reaches the proper density." That is, you apply each NVT
and NPT ensembles when you did the position restraints. Would not it
only be sufficient to implement NPT ensemble on the system? Is it
compulsory to apply both the x and y?
For example:
I get proper density and stabilized the temperature of the system though
I implement NPT ensemble on the system (not your tutorial sample).
Do whatever suits your system. The tutorial is just one example, albeit a
common one. Some systems are robust enough to undergo NPT only, but I have seen
cases where the application of pressure coupling to an unequilibrated system has
led to the immediate collapse of the system, whereas NVT + NPT was stable.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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
