;
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users>
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>> >
>>>
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==**==
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-u
originated. I hope this clarifies
things.
Again, there are no partial charges on the graphene sheet.
Sapna
On Sun, Apr 21, 2013 at 1:23 PM, David van der Spoel
wrote:
> On 2013-04-21 18:25, Sapna Sarupria wrote:
>
>> Dear David and all,
>>
>>
>> Thanks for the sug
Dear David and all,
Thanks for the suggestions!
I did increase the box size to twice that of the sheet dimensions. The
sheet is 10 x 10 nm^2 and now is place in the center of a 20 x 20 x 20 nm^3
box with the droplet size of about 5 nm (4142 water molecules). I still see
the droplet spreading.
I
ays.
> >
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to
That is a very valid point, Mark! and very well said indeed. Yes, you
are absolutely correct that we were in a rush to get to the
"equilibrium" point but it had to be pushed gently.
Thanks,
Sapna
On Mon, Aug 20, 2012 at 7:29 PM, Mark Abraham wrote:
> On 21/08/2012 9:02 AM, Sapna S
valid?
Thanks,
Sapna
On Mon, Aug 20, 2012 at 6:54 PM, Mark Abraham wrote:
> On 21/08/2012 8:45 AM, Sapna Sarupria wrote:
>>
>> Hello All,
>>
>> I have been having rather bizarre experience with Gromacs and was
>> wondering if any one can shed some light on w
; constraining bonds with H
constraint_algorithm = shake
END MDP FILE ###
Thanks very much,
Sapna
--
Sapna Sarupria
Assistant Professor
Department of Chemical and
Biomolecular Engineering
128 Earle Hall
Clemson University
Clemson, SC 29634
Life isn't about finding yourself. Life is
ote pdb files with previous and current coordinates
Inner product between old and new vector <= 0.0!
constraint #1 atoms 145 and 147
Wrote pdb files with previous and current coordinates
Segmentation fault
@
On Wed, Oct 19, 2011 at 6:19 PM, Mark Abraham wrote:
> On 20/10/2011 8:40 AM, S
1 1.086327913
[ exclusions ]
3 4 5
4 5 3
5 4 3
[ system ]
Hydrate with cages filled with carbon dioxide
[ molecules ]
SOL2944
CO2512
TIP3641
End topology file
On Wed, Oct 19, 2011 at 7:17 AM, Sapna Sarupria wrote:
> D
iate 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,
>
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
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.
Dear All,
I was just wondering if Andersen thermostat is implemented or going to be
implemented in the recent/forthcoming versions of Gromacs.
Is there anyone who has done it otherwise and would be willing to share an
outline of the subroutines that they modified?
Thanks in advance for your help
l Message -
> From: sapna sarupria
> Date: Thursday, September 16, 2010 1:35
> Subject: [gmx-users] Wrtiing pair interaction energy on the fly
> To: Discussion list for GROMACS users
>
> > Dear all
> >
> > I understand that pair interactions in gromacs are calcula
Dear all
I understand that pair interactions in gromacs are calculated through
assembly loops. Can some one guide me to the resources using which I can
write out the interaction energy/force for each pair directly from gromacs
during the simulation (without using the rerun option). The rerun optio
nt to see how others (in the literature)
>> deal with droplet-type simulations.
>>
>> -Justin
>>
>>
>>> Thanks for your help.
>>>
>>> Sapna
>>>
>>> On Tue, Aug 17, 2010 at 5:29 PM, Justin A. Lemkul >> <mailto:jalem...@vt.edu&g
Hi Justin
Thanks for your input. I guess I will do some more literature search and try
to optimize the simulations as much as I can.
Thanks,
Sapna
On Tue, Aug 17, 2010 at 5:36 PM, Justin A. Lemkul wrote:
>
>
> sapna sarupria wrote:
>
>> Hi Justin
>> Thanks for your res
PM, Justin A. Lemkul wrote:
>
>
> sapna sarupria wrote:
>
>> Hi all,
>>
>> I am running (NVT) simulations of a drop of water (~5 nm in radius) in a
>> big box (~25 nm) in a box and find that the simulations are rather slow. I
>> am getting about 0.8 ns p
Hi all,
I am running (NVT) simulations of a drop of water (~5 nm in radius) in a big
box (~25 nm) in a box and find that the simulations are rather slow. I am
getting about 0.8 ns per day when a simulation of bulk system of equivalent
number of waters will be much faster. The number of waters is ~
Hi all,
I am running (NVT) simulations of a drop of water (~5 nm in radius) in a big
box (~25 nm) in a box and find that the simulations are rather slow. I am
getting about 0.8 ns per day when a simulation of bulk system of equivalent
number of waters will be much faster. The number of waters is ~
://www.gromacs.org/mailing_lists/users.php
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe request
Hi All,
I was wondering if there is a way to run simulations in the NPH ensemble in
Gromacs. Does any one have experience doing this?
Thank you
Sapna
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gro
7;re describing will always happen, and with a small number of
> particles (i.e. less than you can see with the naked eye) it will happen
> sooner rather than later.
>
> Sander
>
>
> On Mar 30, 2010, at 18:00 , sapna sarupria wrote:
>
> Hi Sander
> Thanks for your response
> in one coordinate with a concomitant decrease in the other coordinates, so
> eventually this should happen (unless I misunderstand the nature of your
> system).
>
> Sander
>
>
> On Mar 30, 2010, at 17:47 , sapna sarupria wrote:
>
> Hello all,
>
> I have a si
Hello all,
I have a simulation running for a hydrate (with CO2) and water in contact
with each other. I run the simulation at 280K at which the hydrate melts and
finally the system is just liquid water with CO2 in it. However, as the
simulation proceeds the box begins to expand in the z-direction
Hello all,
I have a simulation running for a hydrate (with CO2) and water in contact
with each other. I run the simulation at 280K at which the hydrate melts and
finally the system is just liquid water with CO2 in it. However, as the
simulation proceeds the box begins to expand in the z-direction
= POL
energygrp_table = POL POL
The commands I use are as follows:
grompp -f em.mdp -p 25mer_wca_vac.top -c 3.5ns.gro
mdrun -s topol.tpr -table table.xvg
Regards
Sapna
On Wed, Jul 16, 2008 at 10:08 AM, David van der Spoel <[EMAIL PROTECTED]>
wrote:
> sapna sarupria wrote:
>
be the
problem.
Thanks a lot for your help.
Regards
Sapna
On Wed, Jul 16, 2008 at 9:23 AM, David van der Spoel <[EMAIL PROTECTED]>
wrote:
> sapna sarupria wrote:
>
>>
>>
>> -- Forwarded message --
>> From: *sapna sarupria* <[EMAIL PROTEC
-- Forwarded message --
From: sapna sarupria <[EMAIL PROTECTED]>
Date: Tue, Jul 15, 2008 at 9:16 AM
Subject: Using user-tables for simulations in vacuum
To: Discussion list for GROMACS users
Hello users,
I am trying to do a simulation of a polymer chain (which is simply
Hello users,
I am trying to do a simulation of a polymer chain (which is simply a bead of
unified methane molecules) in vacuum using user-defined tables. The
interactions are Weeks-Chandler-Andersen instead of Lennard-Jones. However,
when I run the simulations, mdrun gives me a segmentation fault.
emp = 300 ; initial temperature
gen_seed = 2432384243 ; random seed
Date: Tue, 18 Dec 2007 08:28:52 -0500
> From: "sapna sarupria" <[EMAIL PROTECTED]>
> Subject: [gmx-users] Different system volumes from gromacs vers
was wondering if someone could tell me why this happens?
Has there been a modification in the pressure virial calculation or
something related to the same that leads to these differences?
Thank you
Regards
Sapna
--
Sapna Sarupria
Ph.D. Student - Chemical Engineering
Rensselaer Polytechnic
differences?
Thank you
Regards
Sapna
--
Sapna Sarupria
Ph.D. Student - Chemical Engineering
Rensselaer Polytechnic Institute
Troy, New York 12180
U.S.A.
Ph#: (518)276-3031
Life isn't about finding yourself. Life is about creating yourself.
George Bernard Shaw.
Dare to
34 matches
Mail list logo
