[gmx-users] documentation error?

Hi All, Though am naive, and much appreciate the efforts required to put things altogether but I think I found few things confusing or wrong by mistake or repeated here: http://manual.gromacs.org/documentation/2016/user-guide/mdrun-performance.html The replaced corrections are in [CAPITAL]

Re: [gmx-users] what is the difference between gmx mdrun and gmx tune_pme

Hi, They do somewhat different things. See parts of http://manual.gromacs.org/documentation/2016.4/user-guide/mdrun-performance.html#running-mdrun-on-more-than-one-node Mark On Fri, Sep 15, 2017 at 5:50 PM Peter Stern wrote: >

Re: [gmx-users] what is the difference between gmx mdrun and gmx tune_pme

http://manual.gromacs.org/programs/gmx-tune_pme.html -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Vidya R Sent: Friday, September 15, 2017 6:42 PM To: gmx-us...@gromacs.org Subject:

[gmx-users] what is the difference between gmx mdrun and gmx tune_pme

Hi gromacs users, What is the difference between gmx mdrun and gmx tune_pme? Which is better to use in a cluster (especially when we submit our jobs through qsub command?) Also, what is the purpose of -np option in gmx tune_pme? Can someone elucidate? Thanks, Viday.R -- Gromacs Users

Re: [gmx-users] Binary mixture

On 9/15/17 11:14 AM, sp...@iacs.res.in wrote:  - Message from Justin Lemkul -     Date: Fri, 15 Sep 2017 11:12:37 -0400     From: Justin Lemkul Reply-To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Binary mixture       To:

Re: [gmx-users] Binary mixture

- Message from Justin Lemkul -     Date: Fri, 15 Sep 2017 11:12:37 -0400     From: Justin Lemkul Reply-To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Binary mixture       To: gmx-us...@gromacs.org On 9/15/17 10:59 AM, sp...@iacs.res.in wrote:

[gmx-users] GROMACS 2016.4 released

Hi GROMACS users, The official release of GROMACS 2016.4 is available! This release fixes several issues found since 2016.3, including disabling the broken support for automatic PME tuning in mdrun for group-scheme simulations, and various other fixes. It also implements production-ready support

Re: [gmx-users] Binary mixture

On 9/15/17 10:59 AM, sp...@iacs.res.in wrote: Hi all I want to prepare a  cubic box of 6M urea. How many molecules of urea and how many water molecules should be added to the simulation box? How to calculate these numbers? Please help me to solve this. Everything depends on the size of the

Re: [gmx-users] Doubts about rtp, itp and how to modify force fields

On 9/15/17 10:57 AM, Elisa Pieri wrote: Dear Gromacs users, I'm trying to simulate a system in a membrane. My protein is a rhodopsin (which contains the RET chromophore); I already have a forcefield to treat the retinal, i.e. a modified version of an Amber94 forcefield. Now, I added the

[gmx-users] Doubts about rtp, itp and how to modify force fields

Dear Gromacs users, I'm trying to simulate a system in a membrane. My protein is a rhodopsin (which contains the RET chromophore); I already have a forcefield to treat the retinal, i.e. a modified version of an Amber94 forcefield. Now, I added the membrane in my initial PDB file. I chose

[gmx-users] Binary mixture

Hi all I want to prepare a  cubic box of 6M urea. How many molecules of urea and how many water molecules should be added to the simulation box? How to calculate these numbers? Please help me to solve this. Thanks Sunipa -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] *** Spam ? ***Re: Changing position restraints force in GMX

Sounds complex! Thanks Justin Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab  ] | [

Re: [gmx-users] Changing position restraints force in GMX

On 9/15/17 4:14 AM, Sergio Manzetti wrote: Hi, has anyone experience with changing position restrains for DNA in GMX? In case, is it only to change the figure "1" to "0.75" for instance in the itp file? If you want to change the magnitude of the restraints, you need to generate a new

Re: [gmx-users] Ionic liquid simulation problem

I answered this the other day: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2017-September/115865.html -Justin On 9/14/17 9:55 AM, Agatha Faria wrote: Dear GROMACS Community, I am very new with GROMACS I am trying to run a simulation of an ionic liquid

Re: [gmx-users] gmx error

Hi, I can't tell what you think the error is Mark On Fri, 15 Sep 2017 13:46 Rana Rehan Khalid wrote: > Hi everybody > > I am facing this error kindly guide me > > hecking for duplicate atoms > Generating any missing hydrogen atoms and/or adding termini. > Now there are

[gmx-users] gmx error

Hi everybody I am facing this error kindly guide me hecking for duplicate atoms Generating any missing hydrogen atoms and/or adding termini. Now there are 324 residues with 5193 atoms Chain time... Making bonds... Number of bonds was 5261, now 5260 Generating angles, dihedrals and pairs...

[gmx-users] gmx tune_pme

Hi gromacs users, When i tried using, gmx tune_pme -np 8 -s eql2.tpr -launch Got this error.. How to fix it? [compute-0-3.local:28193] [[20294,1],0] ORTE_ERROR_LOG: A message is attempting to be sent to a process whose contact information is unknown in file rml_oob_send.c at line 105

[gmx-users] how to fix pme number

Hi gromacs users, In this command, gmx mdrun -ntmpi 1 -ntomp 8 -v -deffnm eql2 how to determine the value of pme.. I want to include -npme... Please help Thanks, Vidya.R -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] problem with dihedral restraints in gromacs 5.1.4.

Hi, This approach to dihedral restraints was removed in 4.6, and removed from the documentation in 5.0. In such versions, you need to implement such restraints wholly in the topology file. See PDF reference manual for details. Mark On Fri, Sep 15, 2017 at 7:22 AM minky son

[gmx-users] Changing position restraints force in GMX

Hi, has anyone experience with changing position restrains for DNA in GMX? In case, is it only to change the figure "1" to "0.75" for instance in the itp file? Thanks Sergio Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [