[gmx-users] gmx potential for membrane electrostatic potential

Hi gmx users, I am trying to get the electrostatic potential for a simple DMPC lipid bilayer using the following command - gmx potential -f traj.trr -s topol.tpr - n index.ndx -o potential.xvg -sl 1000 --d z -correct Though the electrostatic potential profile that I obtain is similar to those

Re: [gmx-users] Domain decomposition error with -rerun

en if you'd run mdrun without domain decomposition because the > periodicity may not be understood correctly. Find out what was going on and > how the conversion may have worked. > > Mark > > On Sat, Apr 28, 2018, 09:54 Sahithya S Iyer <sah2...@gmail.com> wrote: > >

Re: [gmx-users] Domain decomposition error with -rerun

sure. > > So you have converted the file format using VMD? > > > > On Sat, Apr 28, 2018 at 12:26 PM, Sahithya S Iyer <sah2...@gmail.com> > wrote: > > > Hi, > > > > Thanks for the reply. I am only doing a rerun of a trajectory that has > > a

Re: [gmx-users] Domain decomposition error with -rerun

SURESH <drrahulsur...@gmail.com> wrote: > Hi. > > That indicates a problem with dynamic load balancing. Try to build > different sizes of the box. > > On Sat, Apr 28, 2018 at 11:57 AM, Sahithya S Iyer <sah2...@gmail.com> > wrote: > > > Hi, > >

[gmx-users] Domain decomposition error with -rerun

Hi, I am trying to calculate interaction between specific residues using gmx mdrun -rerun flag. The trajectory was in a dcd format, which I converted to a trr file. I get the following error - Domain decomposition has not been implemented for box vectors that have non-zero components in

Re: [gmx-users] calculating pairwise interactions

tpr for a rerun, but you will not get any > long-range contribution. Neither does any force field that I know of > produce a useful quantity from such a calculation. > > Mark > > On Sun, Apr 15, 2018, 06:46 Sahithya S Iyer <sah2...@gmail.com> wrote: > > > Hi gmx use

[gmx-users] calculating pairwise interactions

Hi gmx users, Can anyone please tell me how to get the values for pairwise interactions from a gromacs trajectory. I would like to get the pairwise energy interaction values (van der waal and electrostatics) for each pair. Thanks in advance, Sahithya. -- Gromacs Users mailing list * Please

[gmx-users] using groups in index for gmx select

Hi gmx users, Can anyone please tell me how to use a group in index file in gmx select. For example - *gmx select -n index.ndx -select 'name "OH2" and within 2 of com of name "P and r 1-36"' -on P-water.ndx -s step7_production.tpr* does not write out anything in the index (P-water.ndx) file. I

Re: [gmx-users] defining two interactions potentials for same pair of atoms

Thanks for the reply Mark. On Wed, Jun 14, 2017 at 4:34 AM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > On Tue, Jun 13, 2017 at 3:26 PM Sahithya S Iyer <sah2...@gmail.com> wrote: > > > Hi gmx users, > > > > Can someone please tell me

[gmx-users] defining two interactions potentials for same pair of atoms

Hi gmx users, Can someone please tell me if it is possible to use two user defined (non-bonded) potentials for the same pair of interaction sites. For instance, if I have beads A and B, I can define non bonded interactions as table_A_A.xvg, table_A_B.xvg, and table_B_B.xvgfor these two sites. But

[gmx-users] gmx sans and gmx saxs

Dear gromacs users, I am trying to calculate static structure factor from the MD trajectory. I want to calculate this from the trajectory and not simply by Fourier transforming g(r). Can someone please tell me how to do this using gromacs ? Can I use gmx sans ? What is gmx saxs ? (are there

[gmx-users] gmx sans and gmx saxs

Dear gromacs users, I am trying to calculate static structure factor from the MD trajectory. I want to calculate this from the trajectory and not simply by Fourier transform of g(r). Can someone please tell me how to do this using gromacs ? Can I use gmx sans ? What is gmx saxs ? (are there

[gmx-users] Invalid order for directive system

Dear gmx users, I am trying to run a martini CG membrane protein system. The required itps are included in the top file -- include "martini_v2.2P.itp" include "Protein.itp" include "martini_v2.0_lipids_all_201506.itp" include "martini_v2.0_ions.itp" The itp file has restrains for protein

[gmx-users] deuterium order parameter and pbc correct

Dear gromacs users, Do we need to need to correct for pbc in order parameter calculations ? (I assume one needs to). Does the code account for this ? Thanks -Sahithya -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

[gmx-users] Scc order parameter

Hi All, Can one calculate Scc order parameter using gmx order ? I have tried the following: gmx order -f ***.xtc -n ***.ndx -s ***.tpr -od ***.xvg This gives me the deuterium order parameter (Scd) . But i am unsure how Scc is calculated. Can someone please help me with this. Thanks ! -

Re: [gmx-users] creating index for first hydration layer water molecules

wrong.. On Tue, Jun 9, 2015 at 5:12 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/9/15 5:11 AM, Sahithya S Iyer wrote: Dear Users, The first hydration layer, to the best of my understanding, is the first minimum in the protein (backbone)-water radial distribution function. How do I create

Re: [gmx-users] which file to use to analyze trajectory using code

/ - I believe one can also write plugins for VMD (in tcl or python) Cheers, Oliver On Tue, Jun 9, 2015 at 3:33 AM, Sahithya S Iyer sah2...@gmail.com wrote: Thanks for the link Eric ! I am unable to open the following link though - ftp://ftp.gromacs.org/pub/contrib/xdrfile-1.1.4

[gmx-users] creating index for first hydration layer water molecules

Dear Users, The first hydration layer, to the best of my understanding, is the first minimum in the protein (backbone)-water radial distribution function. How do I create an index for the water molecules in the first hydration layer? Cheers -- Gromacs Users mailing list * Please search the

Re: [gmx-users] which file to use to analyze trajectory using code

/Programming_Guide/XTC_Library Best, Eric On Mon, Jun 8, 2015 at 9:56 PM, Sahithya S Iyer sah2...@gmail.com wrote: Dear users, If one wanted to analyze the trajectory obtained on production run for a property of the protein that is not already defined in the gromacs programs, which file should

[gmx-users] which file to use to analyze trajectory using code

Dear users, If one wanted to analyze the trajectory obtained on production run for a property of the protein that is not already defined in the gromacs programs, which file should be used for analysis ? If one were to write an external code to analyze this property, .trr, .tpr, .xtc files cannot

Re: [gmx-users] breaking S-S bond using pdb2gmx

Thanks for the reply Justin. yes, i do notice the topology files have the S-H bonds. On Mon, Feb 16, 2015 at 6:10 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/16/15 4:27 AM, Sahithya S Iyer wrote: Deal all, I need to break 1 out of 4 S-S bonds in a protein. While using the pdb2gmx

[gmx-users] breaking S-S bond using pdb2gmx

the break the S-S bonds present in the pdb file ? Thanks in advance. -- Sahithya S Iyer -- 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

[gmx-users] constant pH simulations in GROMACS 4.5

Hi users Have standard methods been developed in Gromacs 4.5 version to perform constant pH simulations ? -- Sahithya -- 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

[gmx-users] regarding generation of a topology file using Topolbuild

of the files attached herein). On running the mol2 file, it gives the following error - Fatal error. Source code file: readmol2.c, line: 765 Atom 3 (CHB) has 2 connections when required to have 3 Can you please guide me as to how this error can be rectified ? Thanks in advance. -- Sahithya S Iyer