[gmx-users] External electric field applied to water box

box without EF? https://www.dropbox.com/s/zu7vl2wr99sube2/Box%20vectors%20with%20and%20without%20EF.png?dl=0 <https://www.dropbox.com/s/zu7vl2wr99sube2/Box%20vectors%20with%20and%20without%20EF.png?dl=0> Thanks, Nidhin Thomas > On 5/19/19 11:32 PM, Nidhin Thomas wrote: >> Hell

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 181, Issue 45

. But water box without EF did not fail. Could you please help me understand why system with external electric field would behave different from water box without EF? https://www.dropbox.com/s/zu7vl2wr99sube2/Box%20vectors%20with%20and%20without%20EF.png?dl=0 Thanks, Nidhin Thomas > On 5/19

[gmx-users] External electric field applied to water box

actually implemented in GROMACS ? Thanks a lot for your help!. Nidhin Thomas University of Houston -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Su

[gmx-users] Electric field applied to a water box

increased in X and Z direction. Original Size = (4 x 4 x 4) nm Final Size = (4.3 x 2.8 x 4.9) nm I would like to know if I made an error in providing the mdp options and also the origin of the compression of water box in Y direction. Thanks a lot for your help!. Nidhin Thomas University of

[gmx-users] Production Run mdp file for Umbrella Sampling

ial COM distance > 0 Thanks, Nidhin Thomas -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https:/

[gmx-users] Equilibration of Lipid Bilayers created through charmm-gui

ithin 3 Angstrom which I think is within the acceptable range. Also average protein tilt within the lipids is also constant. Could you please tell me what else I can check to confirm if my system is fully equilibrated ? Thanks everyone, Nidhin Thomas -- Gromacs Users mailing list * Please s

[gmx-users] Number of ions in Anionic lipid system- Charmm-GUI

? Thanks, Nidhin Thomas >> Dear GROMACS Users, >> >> I have created a lipid bilayer system (300 POPC + 100 POPG) using CHARMM-GUI. >> I want to include 0.150 M KCl in the system. When I use the option in >> charmm-gui, it gives 98K+ ions and -2 Cl ion. But when

[gmx-users] Number of ions in Anionic lipid system- Charmm-GUI

getting 98 ions. Can anyone tell me what I should do to get the exact number of ions in the system? Would it be correct if I first neutralize the system using 100 K+ ions and then add 0.15 M KCl ions (49 K+ and 49 Cl-) in the system? Thanks a lot!.. Nidhin Thomas -- Gromacs Users mailing list

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 147, Issue 178

o changes. I thought I was doing something wrong in selecting the parameters. https://www.dropbox.com/s/gy85g7wyvavp24v/RDF-2D.png?dl=0 Thanks again! Nidhin Thomas > Message: 6 > Date: Fri, 29 Jul 2016 20:04:24 -0400 > From: Justin Lemkul > To: gmx-us...@gromacs.org > Subject

[gmx-users] Radial Distribution Function of DPPC Bilayer

radial distribution for this system is also provided in the figure. I have also uploaded the part of log files. Could anyone please let me know what am I doing wrong in selecting the parameters? https://www.dropbox.com/sh/hz0ryxeyptf74la/AAD-OKUwauoWO84mlE5_lycha?dl=0 Thank you for the help! Nidhin

[gmx-users] Decreased Area/Lipid of Lipid Bilayer for CHARMM-GUI

. I do not know if 0.61 nm^ APL (from 0.63 nm^2) is an acceptable result for DPPC and I can continue analyze the results further. Thanks a lot for helping me out, Nidhin Thomas University of Houston > -- > > Message: 3 > Date: Tue, 14 Jun 2016 16:51:33

[gmx-users] Decreased Area/Lipid of Lipid Bilayer from CHARMM-GUI

ref_p = 1.0 1.0 ; constraints = h-bonds constraint_algorithm = LINCS continuation = yes ; nstcomm = 100 comm_mode = linear comm_grps = MEMB SOL_ION ; refcoord_scaling = com Thanks, Nidhin Thomas University of Houston > Message: 4 > Date: Mon, 13 Jun 2016 17:51:43 + > From: Christop

[gmx-users] Decreased Area/Lipid for Lipid Bilayer from CHARMM-GUI

ension values. If I provide a non-zero surface tension value, would it change the properties of the system compared to systems simulated using other forces fields? Thanks a lot for the help! Nidhin Thomas Message: 4 > Date: Mon, 13 Jun 2016 17:51:43 + > From: Christopher

[gmx-users] Decreased Area Per Lipid for Lipid Bilayer obtained from CHARMM-GUI

load of the PME mesh part: 0.05 There was 1 note Removing all charge groups because cutoff-scheme=Verlet Thanks a lot for the help! Nidhin Thomas -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * C

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 146, Issue 33

Hi Dr. Wassenaar, I will change insane.py accordingly and give a run. Thanks a lot! Regards, Nidhin Thomas University of Houston > -- > > Message: 4 > Date: Wed, 8 Jun 2016 06:52:27 +0200 > From: Tsjerk Wassenaar > To: Discussion list for GROMAC

Re: [gmx-users] DPPC-DOTAP Mixed Lipid Bilayer

7;CDCC CDCC’ Is this the correct method to create the bilayer and .itp file? Is there anything more that I should do? Thanks a lot for helping me to create the bilayer. Regards, Nidhin Thomas University of Houston -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.

Re: [gmx-users] DPPC-DOTAP Mixed Lipid Bilayer

group. But I don’t know whether this is correct or how to execute this in insane.py. Could you please guid me through the process of creating the template? Thanks, Nidhin Thomas University of Houston > On Jun 7, 2016, at 12:51 AM, > gromacs.org_gmx-users-requ...@maillist.sys.kth.se

[gmx-users] DPPC-DOTAP Mixed Lipid Bilayer

uide me to create these lipid bilayers? It would be great if someone could explain, how to create these mixed bilayers from scratch. Thanks a lot everyone!, Nidhin Thomas University of Houston -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_L

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 145, Issue 111

Hi Tom, Thanks a lot for your input. Cheers! Nidhin Thomas > Message: 7 > Date: Sat, 28 May 2016 00:39:29 +0100 > From: Thomas Piggot > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Lipid Head group Orientation > Message-ID: <5748dab1.5000...@soton.ac.uk> &g

Re: [gmx-users] Lipid Head group Orientation

approaches ? Thanks a lot! Nidhin Thomas PhD Student University of Houston > > Message: 3 > Date: Fri, 27 May 2016 10:33:29 -0400 > From: Chandan Choudhury > To: gmx-users > Subject: Re: [gmx-users] Lipid Head group Orientation > Message-ID: > > Content-Type

[gmx-users] Lipid Head group Orientation

one file? Thanks, Nidhin Thomas University of Houston -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests