Re: [gmx-users] Fixing periodicity effects on trajectory file

g the list at > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > >1. Fixing periodicity effects on tra

Re: [gmx-users] Fixing periodicity effects on trajectory file

Dear Justin I have followed your advice but it didn't solve my problem. ​Ligand is still out of binding site. -- Homa Ahmadi Shahed University Faculty of Basic Sciences Alternative email> h.ahm...@shahed.ac.ir -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org

[gmx-users] Fixing periodicity effects on trajectory file

Hi there I'm working with gromacs for ligand-protein interaction simulation. I have run MD for docked complex and now there is a problem with trajectory visualization by VMD. The ligand has left binding site circulating around the protein. I tried to fix the problem by making index and extract the

[gmx-users] trajectory file (xtc) visualization by VMD

Hi guys! I have had a problem with VMD when reads frames on xtc file. It stops suddenly. It seemed VMD is working out of memory so I remove solvent molecules by trjconv command. It went further but still stops before the end. What should I do? Can I remove some frame from the beginning part? H​ow?

[gmx-users] non-glycosilated protein simulation

Can I remove ​carbohydrate part of glycosilated protein from pdb structure then run MD by gromos force field? -- Homa Ahmadi Shahed University Faculty of Basic Sciences Alternative email> h.ahm...@shahed.ac.ir -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org

[gmx-users] How can i install DSSP for gromacs on centos6?

Hi there I tried to execute dssp for gromacs 4.5.7 by following this instruction: #sudo wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64 -O /usr/local/bin