[gmx-users] SIMtoEXP spftware

Hi Can anyone guide me on genertaing sim extended file in gromcas to be used in SIMtoEXP software. -- *Best Regards* Shakkira E PhD student INSPIRE Scholar Department of Chemistry sdmdlab.xyz IIT Patna Bihta Patna 801106 -- Gromacs Users mailing list * Please search the archive at

[gmx-users] (no subject)

Dear all I encountered with following error when running the umbrella sampling simulation of a protein. What modification should I make in the pull code to get rid of the error. ERROR 1 [file npt_umbrella.mdp]: When the maximum distance from a pull group reference atom to other atoms in the

[gmx-users] MARTINI forcefield

Hi all Is anyone familiar about electron density profiles using gmx density for lipid bilayer modeled with MARTINI forcefield in gromacs. I am confused with the electrons.dat file to be provided with the calculations. What should be the number of electrons to be provided in the calculations for

[gmx-users] Electron density profile calculation

Hi all Is anyone familiar with Gromacs analysis of MARTINI modeled lipid bilayer systems. -- *Best Regards* Shakkira E PhD student INSPIRE Scholar Department of Chemistry sdmdlab.xyz IIT Patna Bihta Patna 801106 -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] DEFORM option in gromacs

I want to gradually decrease the box along xy direction in my simulation. I m confused what does this six values in the deform options mean? On Sun, Feb 16, 2020 at 6:41 PM Justin Lemkul wrote: > > > On 2/16/20 1:44 AM, shakira shukoor wrote: > > Hi all > > Can anyone he

[gmx-users] DEFORM option in gromacs

Hi all Can anyone help me with the DEFORM option in Gromacs to change the box values? -- *Best Regards* Shakkira E PhD student INSPIRE Scholar Department of Chemistry sdmdlab.xyz IIT Patna Bihta Patna 801106 -- Gromacs Users mailing list * Please search the archive at

[gmx-users] (no subject)

Hi all Can anyone help me with the DEFORM option in Gromacs to change the box values? -- *Best Regards* Shakkira E PhD student INSPIRE Scholar Department of Chemistry sdmdlab.xyz IIT Patna Bihta Patna 801106 -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] problem while calculating order parameter

I guess you have not made your index file correctly. It should contain only the group for which you will calculate the order parameter. On Sat, Feb 15, 2020 at 3:21 PM Devargya Chakraborty < devargyachakraborty@gmail.com> wrote: > i want to calculate the order prameter between two carbon

Re: [gmx-users] (no subject)

which x and v are written to trajectory to ensure exact > restarts. Deformation can be used together with semiisotropic or > anisotropic pressure coupling when the appropriate > compressibilities are set to zero. The diagonal elements can be > used to strain a solid. The off-dia

Re: [gmx-users] Error bar for umbrella sampling?

Error bar will be directly given from gmx wham by bootstrap method. On Tue, Jan 14, 2020 at 8:13 AM Qing Lv wrote: > Thank you Alexander and Quyen. I will try these tools. > > > Qing > > > > > > At 2020-01-14 01:01:31, "Александр Лашков" wrote: > >In pymbar package error estimate directly.

Re: [gmx-users] Which content is in gmx wham -hist output file?

The different columns indicates the counts or probability of different binning distances or the windows you have considered in the simulation. On Fri, Jan 10, 2020 at 1:55 PM 변진영 wrote: > Dear All, > I have tried to run umbrella sampling with GROMACS. > When I tried to analyze the umbrella

Re: [gmx-users] Which content is in gmx wham -hist output file?

her distance length?? > > > > 2020. 1. 10. 오후 5:28, shakira shukoor 작성: > > > > The different columns indicates the counts or probability of different > > binning distances or the windows you have considered in the simulation. > > > > On Fri, Jan 10, 2020 at

[gmx-users] GROMOS forcefields

Hi all Can anyone explain the different code seen in forcefields of GROMOS like 53A6, 54A7, 43a1,. what does these numbers mean? -- *Best Regards* Shakkira E PhD student INSPIRE Scholar Department of Chemistry sdmdlab.xyz IIT Patna Bihta Patna 801106 -- Gromacs Users mailing list * Please

Re: [gmx-users] GROMOS forcefields

ity of Antwerp - Campus Drie Eiken > Universiteitsplein 1 > B-2610 Wilrijk > Belgium > > > > Van: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> namens shakira shukoor > > Verzonden: zate

Re: [gmx-users] Quick question: is TIP3P water model available in GROMOS54a7 force field?

Hi As far as I know tip3p water model is modelled to use in combination with CHARMM force field. However there is nothing wrong in using TIP3P in combination with GROMOS force field. And u will have both the bonded and non bonded parameters of that specific water model in tip3p,itp file itself.

Re: [gmx-users] POPC: Fatal error:

Hi The error states that the number of POPC molecules in your configuration file and that mentioned in your topology files are not same. The number refers to the total number of atoms. On Wed, Apr 29, 2020 at 6:20 PM Dutta, Kunal wrote: > Dear Friends, > I'm trying to learn Tutorial 2: KALP15