Hello,
This request is related to python programs used for analyzing gromacs outputs,
not gromacs itself. If there is a more appropriate forum for this question, let
me know and I apologize for posting here.
I have performed a bunch of thermodynamic-integration simulations for liquid
water i
Hello,
I would like to perform some free energy calculations of ice Ic (cubic ice) at
various temperatures. However, I'm having difficulty finding information on how
Gromacs can be used to do this. The goal is to gradually turn off VDW and
Coulomb interactions, just as one would do in a liquid
ut .mdp and.top files, it's hard to say exactly
what is happening.
On Wed, Oct 7, 2015 at 11:08 PM, Nathan K Houtz wrote:
> Thanks for explaining, (and Professor Farais de Moura as well) that makes
> sense.
>
> On a different note, I've noticed a huge difference in p
finding tutorials of
solvation free energies!
On Thu, Oct 1, 2015 at 10:44 PM, Nathan K Houtz wrote:
> Hi everyone,
>
> I would like to use Gromacs to do Thermodynamic Integration (TI) from liquid
> water (TIP4P model) to an ideal gas, to find the relative free energy. To do
&g
from the typical TIP4P
profiles to g(r)=1 for all distances ranging from zero to half of the
smallest box length.
On Thu, Oct 1, 2015 at 11:44 PM, Nathan K Houtz wrote:
> Hi everyone,
>
> I would like to use Gromacs to do Thermodynamic Integration (TI) from
> liquid water (TIP4P model) t
Hi everyone,
I would like to use Gromacs to do Thermodynamic Integration (TI) from liquid
water (TIP4P model) to an ideal gas, to find the relative free energy. To do
this, I believe one generally integrates above the critical point by
increasing the temperature above the critical temperature
Hello everyone,
I am interested in calculating the change in chemical potential between a
metastable liquid, consisting or solvent and solute, and the crystal structure
of the pure solute. For instance, one system I am looking at is tetrolic acid
in CCL4 as my metastable liquid, and one of the
This not a rotation problem, since your crystal is outside the box at
the end. Thus, the box which VMD drew is not the box which gromacs
used during dynamics.
On Fri, Aug 21, 2015 at 9:13 PM, Nathan K Houtz wrote:
> Hello Eric,
>
> Thanks for your reply. I actually had made a mistake
in
Hello Nathan,
Did you set comm-mode and nstcomm
<http://manual.gromacs.org/online/mdp_opt.html#run> in your mdp file?
Best,
Eric
On Thu, Aug 20, 2015 at 3:37 PM, Nathan K Houtz wrote:
> Hello,
>
> I'm sorry to submit a query twice, but I have not received a reply since
>
ls. Thanks!
Regards,
Nathan
- Original Message -----
From: "Nathan K Houtz"
To: "gromacs org gmx-users"
Sent: Thursday, August 13, 2015 10:57:43 PM
Subject: simulations of ice beginning to spin
Hello,
I am simulating two kinds of ice: ice Ih and ice Ic (cubic ice). Both
simu
Hello,
I am simulating two kinds of ice: ice Ih and ice Ic (cubic ice). Both
simulations seem to have developed some rotation spontaneously and I'd like to
know if I can control that somehow. I'm also simulating one in a triclinic box
but the output gro file appears cubic. I'm not sure if I sho
ch to the trajectory, so its heuristics for
guessing where bonds actually are get double-crossed.)
Mark
On Sat, Jul 11, 2015 at 1:15 AM Nathan K Houtz wrote:
> Actually, I think I found the problem. When i looked at the pdb files in
> vmd the first time I missed it, but a colleague had a
g
Sent: Friday, July 10, 2015 5:06:34 PM
Subject: Re: [gmx-users] trouble diagnosing a simulation that's blowing up
(shake not converging --> segmentation fault)
On 7/9/15 9:23 PM, Nathan K Houtz wrote:
> Thanks for your explanations, Dr. Lemkul.
>
> I had already corrected
Lemkul"
To: gmx-us...@gromacs.org
Sent: Thursday, July 9, 2015 7:39:47 AM
Subject: Re: [gmx-users] trouble diagnosing a simulation that's blowing up
(shake not converging --> segmentation fault)
On 7/8/15 8:06 PM, Nathan K Houtz wrote:
> Hello,
>
> I deleted the email and can
acs to generate velocities to start the
simulation, which is incompatible with that command. Is there another way I can
try to start the simulation unconstrained? Or would you suggest another idea to
fix my shake warnings?
Thanks very much for your help,
Nathan
- Original Message -
Hello,
I'm attempting to simulate ice ih in a triclinic box with a rigid tip4p water
model. As the subject says, I get warnings (almost immediately) that "shake
failed to converge in 1000 steps" and then eventually a segmentation fault.
Gromacs documentation suggests that this is a result of my
Hello Gromacs users,
I tried to create a 6.5 nm cubic box of tetrolic acid (otherwise known as
2-butynoic acid), but the density is too low. According to this,
http://www.chemspider.com/Chemical-Structure.61810.html, the density should be
about 0.964 g/mL. Given the molecular weight of tetrolic
Hello all,
I'm wondering if gromacs will allow me to use either a wolf electrostatic
cutoff method or a damp shifted force cutoff method, similar to what is
described by C. J. Fennell (2006). (I think the paper is:
http://scitation.aip.org/content/aip/journal/jcp/124/23/10.1063/1.2206581) If
s
Hello all,
I'm wondering if gromacs will allow me to use either a wolf electrostatic
cutoff method or a damp shifted force cutoff method, similar to what is
described by C. J. Fennell (2006). (I think the paper is:
http://scitation.aip.org/content/aip/journal/jcp/124/23/10.1063/1.2206581) If
s
ary. Is the file outdated, or have I
made a mistake?
Regards,
N.H.
- Original Message -
From: "Justin Lemkul"
To: gmx-us...@gromacs.org
Sent: Monday, November 10, 2014 7:40:58 AM
Subject: Re: [gmx-users] Simulating Multiple Solute Particles
On 11/10/14 3:07 AM, Nathan K H
romacs.org
Sent: Tuesday, November 4, 2014 7:45:39 AM
Subject: Re: [gmx-users] Simulating Multiple Solute Particles
On 11/4/14 12:45 AM, Nathan K Houtz wrote:
> Thanks for your reply. However, I'm still confused. I thought that the
> command:
>
> #include "oplsaa.ff/tip3p.itp
riginal Message -
From: "Justin Lemkul"
To: gmx-us...@gromacs.org
Sent: Monday, November 3, 2014 12:44:52 PM
Subject: Re: [gmx-users] Simulating Multiple Solute Particles
On 11/3/14 12:50 AM, Nathan K Houtz wrote:
> Sorry everybody, I accidentally unsubscribed from the mailing list an
some example file and tried
to make the numbers fit appropriately under the headings. If it's not correct,
why didn't gromacs complain when I solvated it? Doesn't it read in the topology
file then as well?
I'm subscribed again so I won't miss a reply. Thanks again
in for all your help!
N.H.
- Original Message -
From: "Mark Abraham"
To: "Discussion list for GROMACS users"
Sent: Saturday, October 25, 2014 6:10:21 AM
Subject: Re: [gmx-users] Simulating Multiple Solute Particles
On Sat, Oct 25, 2014 at 7:23 AM, Nathan K Houtz wrot
Hello, I apologize for any ignorance but I'm quite new to gromacs and am
confused about a few things.
I want to run some simulations of a small molecule, tetrolic acid
(CH3-C≡C-COOH) dissolved in a box of water. I'm doing this to see if a united
atom approximation on the methyl group is suffic
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