On 5/13/14, 10:44 AM, ABEL Stephane 175950 wrote:
Hello Justin
Thanks for your reply. I have finally found why I obtained a large drift and
decrease of the temp of my system during the NVE : I stupidly mixed different
cpt and tpr files. If I use the right files and the following parameters below
suggested by M. Shirts in [1] for my tests:
rlist = 1.3
;vdW
vdwtype = Switch
rvdw= 1.1
rvdw_switch = 1.0
; Electrostatics
coulombtype = PME
rcoulomb= 1.3
CHARMM parameters can be very sensitive to the value of rvdw. It's something we
consider as close to an absolute rule as you get, so the settings above should
be modified to read:
rlist = 1.4
rvdw = 1.2
rvdw-switch = 1.0
rcoulomb = 1.4
Or use the settings in my previous message in version 5.0-rc1.
The energy and the temp of my system remain stable during the 100 ps of my
simulation after initial small decrease of the energy and the temp to 295.5 K
(initial temp was 297.904 K)
[1] http://comments.gmane.org/gmane.science.biology.gromacs.user/42686
Please also note that with the parameters for Verlet options you gave I obtain
the following error with 4.6.5 for simulations with NVE,
Temperature coupling is required for calculating rlist using the energy
drift with verlet-buffer-drift 0. Either use temperature coupling or
set rlist yourself together with verlet-buffer-drift = -1
Good to know; I've never had a need to run NVE.
If I add the verlet-buffer-drift = -1 option in my mdp (not sure it is
correct), grompp gives only two notes
NOTE 1 [file run_CH_1_NVE_pot_mod.mdp]:
With Verlet lists the optimal nstlist is = 10, with GPUs = 20. Note
that with the Verlet scheme, nstlist has no effect on the accuracy of
your simulation.
NOTE 2 [file run_CH_1_NVE_pot_mod.mdp]:
rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet
buffer. The cluster pair list does have a buffering effect, but choosing
a larger rlist might be necessary for good energy conservation.
I don't believe the options I provided will work in 4.6.5; they definitely
should in 5.0-rc1, so a test with verlet-buffer-drift = -1 would be potentially
useful.
-Justin
Stéphane
On 5/7/14, 9:05 AM, ABEL Stephane 175950 wrote:
Dear GMX-users
I have done a 90 ns long simulation of a heterogeneous system (SPCE water,
phospholipids and a hydrophobic solvent) in NPT ensemble (298 K at 1 bar) with
GROMACS4.6.5. to compute related dynamical properties, I would like to continue
this simulation in NVE. But I am puzzled to choose the mdp parameters to have a
good energy conservation. Indeed, I have checked the gromacs 2004 JCTC or the
following and follow the advices given in the following threads
http://comments.gmane.org/gmane.science.biology.gromacs.user/42686
https://www.mail-archive.com/gmx-users@gromacs.org/msg60393.html
But I always obtain for my system a large drift and the temp decreases
significantly (20 K) after few dozens of ps (the initial temp was around 297.3
K). For this simulation I used the double precision of gromacs with a timestep
of 1 fs.
Can you provide a full .mdp file so we can look at all your settings? Are these
drifts during NPT or NVE?
More, since I have never used the potential-modifier features, so I not sure
how to setup the correct parameters in the context of CHARMM simulations.
With the caveat that I have NOT thoroughly tested the following, my
understanding of the new Verlet options indicates that these settings should
perform pretty well using CHARMM36:
cutoff-scheme = Verlet
rlist = 1.2
vdwtype = cutoff
vdw-modifier = Potential-switch
rvdw = 1.2
rvdw-switch = 1.0
coulombtype = PME
rcoulomb = 1.2
Again, barely tested on my part, and never tested for NVE.
-Justin
--
==
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==
--
==
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==
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