Re: [gmx-users] Gromacs 4.5.4 and Gromacs 4.5.5 give different results

the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Sapna Sarupria Assistant Professor, Department of Chemical and Biomolecular Engineering 128 Earle Hall (206 S Palmetto

Re: [gmx-users] Gromacs 4.5.4 and Gromacs 4.5.5 give different results

:16 PM, Sapna Sarupria wrote: Thanks Justin for the response. I thought of that too but was not sure if that could alone be attributed to the crash. There is no obvious reason why it should happen given Gromacs has typically been quite stable. This is quite a straightforward system...but perhaps

Re: [gmx-users] Re: Water spreading on graphene!

-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Sapna Sarupria Assistant Professor Department of Chemical and Biomolecular Engineering 128 Earle Hall Clemson University Clemson, SC 29634 -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] Re: Water spreading on graphene!

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.

Re: [gmx-users] Re: Water spreading on graphene!

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 sp...@xray.bmc.uu.sewrote: On 2013-04-21 18:25, Sapna Sarupria wrote: Dear David and all, Thanks for the suggestions! I did

[gmx-users] Hbond Shake and Gromacs Version Related

; 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 about

Re: [gmx-users] Hbond Shake and Gromacs Version Related

be valid? Thanks, Sapna On Mon, Aug 20, 2012 at 6:54 PM, Mark Abraham mark.abra...@anu.edu.au 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 what is happening. I am

Re: [gmx-users] Hbond Shake and Gromacs Version Related

, Sapna Sarupria wrote: Thanks Mark. I also discovered that if I set the value of nstpcoule = 1 explicitly in my mdp file, it runs with the newer version of Gromacs 4.5.5 which was not the case earlier. Yes, default behaviour of this kind of thing has varied over time. Again, small changes

Re: [gmx-users] Gromacs versions 4.0.5 and 4.5.4

, so I am not that behind. On 19/10/2011, at 1:14 PM, Sapna Sarupria wrote: Dear Itamar, Thank you for your response. Why did you prefer to stick to 4.0.7? Is there something particularly difficult to transfer from 4.0.7 version to 4.5 version? Sapna On Tue, Oct 18, 2011 at 9:36 PM, Itamar

Re: [gmx-users] Gromacs versions 4.0.5 and 4.5.4

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 sapna.sarup

Re: [gmx-users] Gromacs versions 4.0.5 and 4.5.4

, Sapna Sarupria wrote: Hello, I did change nsttcouple and nstpcouple but the simulations that run in 4.0.5 are still crashing in 4.5.4. I think it is related to constraints but I am unable to figure out exactly what is different. I have pasted both my topology and mdp (updated for 4.5.4

[gmx-users] Gromacs versions 4.0.5 and 4.5.4

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

Re: [gmx-users] Gromacs versions 4.0.5 and 4.5.4

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 a mixture of carbon dioxide and water system which runs

[gmx-users] Implementation of Andersen Thermostat

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

[gmx-users] Wrtiing pair interaction energy on the fly

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

Re: [gmx-users] Wrtiing pair interaction energy on the fly

: - Original Message - From: sapna sarupria sapna.sarup...@gmail.com Date: Thursday, September 16, 2010 1:35 Subject: [gmx-users] Wrtiing pair interaction energy on the fly To: Discussion list for GROMACS users gmx-users@gromacs.org Dear all I understand that pair interactions in gromacs

Re: [gmx-users] Speeding up simulation

Thanks for your help. Sapna On Tue, Aug 17, 2010 at 5:29 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu 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

[gmx-users] Speeding up simulation

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

[gmx-users] Re: NPH Simulations

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

Re: [gmx-users] Speeding up simulation

PM, Justin A. Lemkul jalem...@vt.edu 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 per day when a simulation of bulk system

Re: [gmx-users] Speeding up simulation

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 jalem...@vt.edu wrote: sapna sarupria wrote: Hi Justin Thanks for your response. I suspect

Re: [gmx-users] Check V for NVT‏

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 -- Sapna Sarupria Post-doctoral Researcher Princeton University New Jersey 08540 U.S.A. Life isn't about finding yourself. Life is about creating

[gmx-users] NPH Simulations

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

[gmx-users] Exploding box (in one dimension) Semi-isotropic pressure coupling?

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

Re: [gmx-users] Exploding box (in one dimension) Semi-isotropic pressure coupling?

size 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 simulation running for a hydrate (with CO2

Re: [gmx-users] Exploding box (in one dimension) Semi-isotropic pressure coupling?

, 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. Is there then a preference for z-dimension to expand (other than the way

[gmx-users] Semi-isotropic pressure coupling.

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

Re: [gmx-users] Using user-tables for simulations in vacuum

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 PROTECTED] mailto: [EMAIL PROTECTED] Date: Tue, Jul 15, 2008

Re: [gmx-users] Using user-tables for simulations in vacuum

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: Hello, Thanks David for your

[gmx-users] Using user-tables for simulations in vacuum

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

[gmx-users] Different system volumes from gromacs versions 3.2.1 and 3.3.1

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

Re:Re:[gmx-users] Different system volumes from gromacs versions 3.2.1 and 3.3.1

= 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 versions 3.2.1 and 3.3.1

[gmx-users] Different system volumes from gromacs versions 3.2.1 and 3.3.1

to these 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 Dream