Re: [gmx-users] syntax for index file in "gmx distance"

Hi http://manual.gromacs.org/documentation/current/user-guide/cmdline.html#command-changes-between-versions Em dom, 17 de fev de 2019 09:22, ZHANG Cheng <272699...@qq.com escreveu: > I think I know now: > > > gmx distance -f dynamic_noPBC.xtc -s dynamic -n index.ndx -select 'group 0 > plus

Re: [gmx-users] Distance COM of two systems

Hi, http://manual.gromacs.org/documentation/current/user-guide/cmdline.html#command-changes-between-versions help? Em qua, 6 de fev de 2019 às 14:48, Antonio PEÓN escreveu: > Hello, > > I would like to calculate the distance from the center of masses (COM) > between two systems. One would be

Re: [gmx-users] g_dist equivalent in Version 5.*

Hi, gmx distance can compute distances of mass center's, right? Im was the same problem and i use: gmx distance -n index.ndx -select 'com of group "A" plus com of group "B"'. A and B can be numbers or words. What did you mean "but it calculates pairwise distances in one selection" ? How is

Re: [gmx-users] COM

Hi I used index.ndx too...but did not work. Thanks Em qua, 23 de jan de 2019 09:07, Quyen VuVan He means, in your first email, your command is using fix.ndx and HAGD group > is in your index.ndx, have you checked it? > > On Tue, Jan 22, 2019 at 7:54 PM laura O. > wrote: > &g

Re: [gmx-users] COM

fix.ndx but you seem to be editing a file > named "index.ndx". > > HTH, > Rui Rodrigues > > > De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> em nome de la

Re: [gmx-users] COM

n be found. Cannot match 'group "MTX"', because no such index group can be found. Em ter, 22 de jan de 2019 às 16:01, Quyen VuVan escreveu: > Hi, > I don't think you need a double quote in your select HAGD > > On Tue, Jan 22, 2019 at 6:32 PM laura O. > wrote: &

Re: [gmx-users] COM

Em ter, 22 de jan de 2019 às 16:01, Quyen VuVan escreveu: > Hi, > I don't think you need a double quote in your select HAGD > > On Tue, Jan 22, 2019 at 6:32 PM laura O. > wrote: > > > Dear Users. > > > > I'm trying to calculate the center of mass distanc

[gmx-users] COM

Dear Users. I'm trying to calculate the center of mass distance between cyclodextrine ( HAGD) and a biological molecule (MTX). I've searched on gromacs documentation in gmx distance I use command line: gmx distance -f fixv1out.xtc -s bcd_mtx_solv_min.tpr -n fix.ndx -oav cmtransv1.xvg -select

[gmx-users] COM

Dear Users. I'm trying to calculate the center of mass distance between cyclodextrine ( HAGD) and a biological molecule (MTX). I've searched on gromacs documentation in gmx distance I use command line: gmx distance -f fixv1out.xtc -s bcd_mtx_solv_min.tpr -n fix.ndx -oav cmtransv1.xvg -select