Yanmei Song wrote:
Dear Justin:
Thank you for your suggestions. using shift for vdwtype helps a lot.
Can I ask you another question? The density of my system is about 8%
larger than the experimental value. Do you have any suggestions on how
to reduce the density of the system. Or once the force field and all the
parameters are fixed, the density is independent of the MD procedure? I
am using NPT ensemble with the mdp I mentioned before with added vdwtype
= shift.
Output like density, pressure, energy conservation, etc. are a consequence of
both the force field parameters and their proper use. Look into the primary
literature for the force field you are using and see how well the parameters are
expected to behave. A difference of 8% doesn't sound that unreasonable to me,
but the primary literature will be the judge.
-Justin
On Thu, May 14, 2009 at 4:35 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Yanmei Song wrote:
Dear Justin:
Thanks for your response. Here is the complete my .mdp file:
title = pdm
cpp = /lib/cpp
constraints = all_bonds
integrator = md
dt = 0.004 ; ps !
nsteps = 2500000 ; total 10ns.
nstcomm = 1
nstxout = 50000
nstvout = 50000
nstfout = 0
nstlog = 5000
nstenergy = 5000
nstxtcout = 25000
nstlist = 10
ns_type = grid
pbc = xyz
coulombtype = PME
rlist = 1.4
rcoulomb = 1.4
rvdw = 1.4
fourierspacing = 0.20
pme_order = 4
ewald_rtol = 1e-5
; Berendsen temperature coupling is on in one groups
Tcoupl = berendsen
tc_grps = PDM
tau_t = 0.1
ref_t = 300
; Energy monitoring
energygrps = PDM
; Isotropic pressure coupling is now on
Pcoupl = berendsen
pcoupltype = isotropic
;pc-grps = PDM
tau_p = 1.0
ref_p = 1.0
compressibility = 4.5e-5
; Generate velocites is off at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 100000
The problem you're seeing could be an artifact of the shorter
cutoff. Have you tried using DispCorr = EnerPres? Or what about
using a Shift function for vdwtype? You might see better energy
conservation in that case compared to a plain cutoff.
-Justin
On Thu, May 14, 2009 at 4:06 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
Yanmei Song wrote:
Dear All:
I have question about the pressure coupling. I have done
a 10ns
simulation with 19800 atoms for 120 large molecules using the
following pressure coupling.
Tcoupl = berendsen
tc_grps = PDM
tau_t = 0.1
ref_t = 300
Pcoupl = berendsen
pcoupltype = isotropic
;pc-grps = PDM
tau_p = 1.0
ref_p = 1.0
compressibility = 4.5e-5
Then I did g_energy for the last 3ns and got the results:
Energy Average RMSD Fluct.
Drift Tot-Drift
-------------------------------------------------------------------------------
Potential -98061 0 0
0.61668 1850.04
Temperature 303.561 109.602 109.602
0.000181791 0.545372
Pressure (bar) 4.4884 11110.8 11109.8
-0.169835 -509.506
For such a long run the pressure drift is still too much and
seem hasn't approached 1bar. Does it mean the system hasn't
reach equilibrium yet. I did a similar system by using
the same
method. it just take 2 or 3ns to reach the equilibrium.
and the
pressure is around 1.01after the run. The only difference
is the
cutoff changing from 1.2 to 1.4. Does the cufoff of 1.4
is too
large to make the system running slower. Or the pressure
coupling method is not working well. Anyone can give me any
suggestions?
I think it will depend on the interplay of other parameters
as well.
Posting a complete .mdp file may be more helpful.
-Justin
-- Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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
<mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>.
Can't post? Read
http://www.gromacs.org/mailing_lists/users.php
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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
<mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
