Itamar Kass wrote:
Hi Sapna,
It is a good question, but such of personal preferences. I found out
that my simulations tend to crash more often when I am using 4.5.5. It
might be the General-reaction -field I use or something else, I am not
sure. Also, it seems I will not gain much from upgrading, so I stick to
4.0.7.
The general instabilities result from tweaks to the handling of temperature and
pressure coupling. Simply setting nsttcouple and nstpcouple to 1 during the
initial equilibration seems to give stable systems.
I'd say there are many reasons for upgrading. Tons of new features, bug fixes,
etc. But then too, that's my personal preference ;)
-Justin
All this is not to say that 4.5.5 is not a good simulation package. It
is a good and useful MD package, and I highly appreciate all the time
and effort put into it.
Best,
Itamat
PS, there are still people around using 3.3.3 or even 3.2.1, so I am not
that behind.
On 19/10/2011, at 1:14 PM, Sapna Sarupria wrote:
Dear Itamar,
Thank you for your response. Why did you prefer to stick to 4.0.7? Is
there something particularly difficult to transfer from 4.0.7 version
to 4.5 version?
Sapna
On Tue, Oct 18, 2011 at 9:36 PM, Itamar Kass <[email protected]
<mailto:[email protected]>> wrote:
Hi Sapna,
I had the same problem few weeks ago.
Apparently, some parameters are different (eg. nstpcouple).
Cheers,
Itamar
PS I found out that I prefer to stick to 4.0.7.
On 19/10/2011, at 12:08 PM, Sapna Sarupria wrote:
Dear All,
I have a simulation set up for a mixture of carbon dioxide and
water system which runs perfectly on Gromacs 4.0.5 version. I
have run these simulations at different temperatures and
pressures, from the same starting configuration and the
simulation proceeds smoothly in the 4.0.5 version. However, when
I use exactly the same files to run the simulation in 4.5.4
version, the system crashes and writes out several pdb files. I
was wondering if there is anything specific that has been changed
between the two versions. I have pasted the mdp file of the
simulations below. Any input will be much appreciated.
MDP File
title = 100% occupancy CO2 hydrate ; a string
cpp = /lib/cpp ; c-preprocessor
dt = 0.002 ; time step
nsteps = 15000000 ; number of steps
nstcomm = 10 ; reset c.o.m. motion
nstxout = 0000 ; write coords
nstvout = 0000 ; write velocities
nstlog = 25000 ; print to logfile
nstenergy = 500 ; print energies
xtc_grps = OW_HW1_HW2_CO2
nstxtcout = 1000
nstlist = 10 ; update pairlist
ns_type = grid ; pairlist method
coulombtype = PME
rvdw = 1.2 ; cut-off for vdw
rcoulomb = 1.2 ; cut-off for coulomb
rlist = 1.2 ; cut-off
for coulomb
DispCorr = EnerPres
Tcoupl = Nose-Hoover
ref_t = 270
tc-grps = System
tau_t = 0.5
Pcoupl = Parrinello-Rahman
Pcoupltype = semiisotropic ; pressure geometry
tau_p = 1.0 1.0 ; p-coupoling time
compressibility = 4.5e-5 4.5e-5 ; compressibility
ref_p = 30.5 30.5 ; ref pressure
gen_vel = yes ; generate
initial vel
gen_temp = 260 ; initial
temperature
gen_seed = 372340 ; random seed
constraint_algorithm = shake
constraints = all-bonds
-------
Thank you,
Sincerely,
Sapna
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"In theory, there is no difference between theory and practice.
But, in practice, there is." - Jan L.A. van de Snepscheut
===========================================
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376 <tel:%2B61%203%209902%209376>
| Fax: +61 3 9902 9500 <tel:%2B61%203%209902%209500>
| E-mail: [email protected] <mailto:[email protected]>
============================================
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-----
"In theory, there is no difference between theory and practice. But, in
practice, there is." - Jan L.A. van de Snepscheut
===========================================
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: [email protected] <mailto:[email protected]>
============================================
--
========================================
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
========================================
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