On 6/5/18 7:02 PM, Eisenhart, Andrew (eisenhaw) wrote:
Here's the link to the files, if there's anything else I can send let me know.
I've been using 5.1.1 for the initial set up and energy minimization, and 5.1.2
for the nvt and npt simulations.
em.mdp is some corrupted binary file. Please upload a corrected version.
-Justin
<https://files.fm/u/c9uef9qh>
https://files.fm/u/c9uef9qh
Thanks
Andrew
________________________________
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul
<jalem...@vt.edu>
Sent: Tuesday, June 5, 2018 12:54:50 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities
On 6/5/18 9:10 AM, Eisenhart, Andrew (eisenhaw) wrote:
Hello again,
I have done a few things since I last updated this list.
I generated a new system of only 1000 water instead of the original 2000, I
used a more careful approach in my energy minimization, minimizing first with
all bonds and angles constrained then again without those hash constraints.
This succeeded in getting the maximum force in my system to below 100kcal
without lincs warnings.
Then I proceeded to equilibrate the temperature as before with no issues, and
finally I attempted to equilibrate the box size using the Berendsen barostat
running for 2ns. The box size increases as before and still does not converge.
The system stays at around 300K, but after a while (~1ns) it seems to fill the
box like its a gas visually at least.
So any ideas that I could try would be appreciated.
If you can assemble a tarball that contains starting coordinates (not
minimized), topology, all .mdp files, and a run script that gives the
exact sequence of what you're doing, and post it somewhere to share, I
will try to take a look at it and see if I can reproduce the behavior.
What version of GROMACS are you using?
-Justin
Thanks,
Andrew
________________________________
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Eisenhart, Andrew
(eisenhaw) <eisen...@mail.uc.edu>
Sent: Thursday, May 31, 2018 1:51:51 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities
Hey,
Thanks for everyone's response.
I have tried using the berendsen barostat, with it I see similar behavior with
the unit cell jumping up in size and then steadily increasing in size. I have
some longer runs using it running now (2-3ns), so I'll be able to see it it
eventually converges.
Nice catch with the particle type being incorrect, but with it corrected I'm
still having the same problems (ie the oscillation of the box size) it has yet
to throw lincs warnings though (even at ts = 2fs) so I'm going to simulate for
a longer amount of time to see if it will converge.
Thanks again for everyone's reply, below is my .itp in its entirety maybe there
is an error in the exceptions(which im still not 100% sure about) or something
else that will stand out.
Andrew
;
[ atomtypes ]
; name bond_type mass charge ptype sigma epsilon
qm1 qm1 0.000 -2.516 V 0.000 0.000
qh1 qh1 0.000 1.258 V 0.000 0.000
[ moleculetype ]
; molname nrexcl
M3 3
[ atoms ]
; id at type res nr residu name at name cg nr charge
1 opls_113 1 M3 OW 1 0.0
2 opls_114 1 M3 HW1 1 0.0
3 opls_114 1 M3 HW2 1 0.0
4 qm1 1 M3 qm 1 -2.516
5 qh1 1 M3 qh1 1 1.258
6 qh1 1 M3 qh2 1 1.258
#ifndef FLEXIBLE
[ settles ]
; OW funct doh dhh
1 1 0.09572 0.15139
#else
[ bonds ]
; i j funct length force.c.
1 2 1 0.09572 502416.0 0.09572 502416.0
1 3 1 0.09572 502416.0 0.09572 502416.0
[ angles ]
; i j k funct angle force.c.
2 1 3 1 104.52 628.02 104.52 628.02
#endif
[ exclusions ]
1 2 3 4 5 6
2 1 3 4 5 6
3 1 2 4 5 6
4 1 2 3 5 6
5 1 2 3 4 6
6 1 2 3 4 5
[ virtual_sites3 ]
; Vsite from funct a b
4 1 2 3 1 0.29869481802 0.29869481802
; Vsite (3fad) funct theta d
5 3 2 1 3 18.06 0.025
6 2 3 1 3 18.06 0.025
________________________________
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark Abraham
<mark.j.abra...@gmail.com>
Sent: Thursday, May 31, 2018 7:54:09 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities
Hi,
If that fixes the issue, then please let us know - we should consider
fixing grompp to check that the inputs have appropriate consistency.
Mark
On Thu, May 31, 2018 at 1:48 PM Justin Lemkul <jalem...@vt.edu> wrote:
On 5/30/18 4:40 PM, Eisenhart, Andrew (eisenhaw) wrote:
Hello all,
I am having an issue with the current systems I am working on. The
system consists of 2000 6point water molecules (3 chargeless masses for Ow,
hw1, and hw2; and 3 massless point charges for the electrostatics). The
three point charges I have implemented as virtual interaction sites using
the section below in my topology file.
[ virtual_sites3 ]
; Vsite from funct a b
4 1 2 3 1 0.29869481802 0.29869481802
; Vsite (3fad) funct theta d
5 3 2 1 3 18.06 0.025
6 2 3 1 3 18.06 0.025
this is loosely based on the tip4p model. Since the two partial charges
off of the hydrogens differ only in location I have them defined as a
single type with sigma and epsilon defined as 0. I have also done this to
the partial charge off of the oxygen. This is all seen below in my
atomtypes and atoms sections.
[ atomtypes ]
; name bond_type mass charge ptype sigma epsilon
qm1 qm1 0.000 -2.516 A 0.000 0.000
qh1 qh1 0.000 1.258 A 0.000 0.000
The particle type for these should be V. This could be the problem - if
you've encoded an incorrect particle type then the update routines will
not propagate them correctly.
-Justin
-----------------------------------
[ atoms ]
; id at type res nr residu name at name cg nr charge
1 opls_113 1 M3 OW 1 0.0
2 opls_114 1 M3 HW1 1 0.0
3 opls_114 1 M3 HW2 1 0.0
4 qm1 1 M3 qm 1 -2.516
5 qh1 1 M3 qh1 1 1.258
6 qh1 1 M3 qh2 1 1.258
The problem I am seeing right now depends on the parameters I use in the
mdp files. During thermostat equlibration nothing is amiss, but once the
volume of the box is allowed to relax the problems show. Using the
parrinello-rahman barostat and 0.002fs timestep I crash with lincs
warnings. Reducing the timestep to 0.001fs stops the lincs warnings, but
the box size never converges It instead expands to around 10x its original
size. So I think that I must have a problem with the implementation of my
virtual sites. Any guidance would be greatly appreciated. Thanks below are
some other parameters I have set in my input files.
Andrew
integrator = md
nsteps = 500000
nstcomm = 100
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 1000
nstenergy = 1000
nstxtcout = 1000
nstlist = 5
ns_type = grid
pbc = xyz
coulombtype = pme
rcoulomb = 0.5
rlist = 0.5
vdw-type = cut-off
rvdw =0.5
constraint_algorithm = lincs
constraints = all-bonds
lincs_iter = 1
lincs_order = 8
fourierspacing = 0.10
pme_order = 6
ewald_rtol = 1e-06
ewald_geometry = 3d
optimize_fft = yes
tcoupl = Nose-Hoover
tc-grps = System
tau_t = 0.4
ref_t = 300
; Pressure coupling is on
pcoupl = parrinello-rahman
pcoupltype = isotropic
tau_p = 2.0
ref_p = 1.0
compressibility = 4.5e-5
refcoord-scaling = com
DispCorr = EnerPres
comm-mode = linear
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
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==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
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--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
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