[gmx-users] Re: eg compilation problem in Mopac gromacs (vidhya sankar)

am expecting your reply > also when i use ./configure --without-qmmm-mopac --disable-float it compiles > successfully > > -- next part -- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20100908/a45d777d

[gmx-users] Problem about thread based MPI in Gromacs-4.5.1

Hi all In Gromacs-4.5 new features, there're "Running on a multi-core node now uses thread-based parallelization to automatically spawn the optimum number of threads in the default build. MPI is now only required for parallelization over the network. " And in Gromacs-4.5 manual, mdurn options h

Re: [gmx-users] Problem about thread based MPI in Gromacs-4.5.1

Hi, > But when use "mdrun -h", the -nt does not exist. > So can the -nt option be used in mdrun? Just checked and If you have threads turned on (!) when building gromacs then on the help page (mdrun -h) -nt does show up! Otherwise, it's easy to check if you have thread-enabled build or not: just

[gmx-users] energygrps

Hi, I have completed membrane protein simulations. I want to do some free energy calculations but haven't included energygrps in the mdp file. Please can someone suggest me if theres a way to generate separate energygrps for my protein and lipid now as I carried out simulations without having

Re: [gmx-users] Alanine dipeptide simulations

Did you do any form of equilibration prior to the production run? If so, what? In my experience, an incompletely (or improperly) equilibrated system that is passed to the P-R barostat can lead to undesired pressures. As long as there are no systematic influences on your pressure (i.e., tren

Re: [gmx-users] energygrps

Poojari, Chetan wrote: Hi, I have completed membrane protein simulations. I want to do some free energy calculations but haven't included energygrps in the mdp file. Please can someone suggest me if theres a way to generate separate energygrps for my protein and lipid now as I carried out

Re: [gmx-users] restraining atoms to the plane at the bilayer center: pull code ?

Dear Chris, Thank you for the code. I did check out pull_pbcatomN, and thank you for the heads up that it is a global index. I used a central atom in the box for each of the two groups as pull_pbcatom. After using the code below with a rate constant of ~ 5500 for about 100 ps, I realized that the

Re: [gmx-users] hessian.mtx----> readable format

Thanks Justin On Tue, Sep 7, 2010 at 5:14 PM, Justin A. Lemkul wrote: > > > Vishal Agarwal wrote: > >> Dear Gromacs Users, >> Is there a way to convert the hessian.mtx file into a readable format >> using any of the gromacs utilities? >> > > gmxdump -mtx > g_nmeig > > -Justin > > > Any

[gmx-users] restraining atoms to the plane at the bilayer center: pull code ?

Maria, I highly doubt that you are correct. If you want more help, please copy and paste your commands and some relevant output back to the list. Chris. --original message -- Message: 4 Date: Wed, 8 Sep 2010 15:07:15 +0200 From: maria goranovic Subject: Re: [gmx-users] restraining atoms to

[gmx-users] How to select atoms dynamically

Hi,  I want to analyze the local density of water in CNT,but the water in CNT are not static,in one frame, it is in the CNT,but in another frame, it is may not ,how to select the waters in CNT DYNAMICALLY?Zhongjin He -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs

Re: [gmx-users] How to select atoms dynamically

zhongjin wrote: Hi, I want to analyze the local density of water in CNT,but the water in CNT are not static,in one frame, it is in the CNT,but in another frame, it is may not ,how to select the waters in CNT DYNAMICALLY? There is a new tool in the 4.5 release called g_select. It may suit

Re: [gmx-users] How to select atoms dynamically

On Wed, Sep 8, 2010 at 11:23 AM, zhongjin wrote: > > Hi, >   I want to analyze the local density of water in CNT,but the water in CNT > are not static,in one frame, it is in the CNT,but in another frame, it is may > not ,how to select the waters in CNT DYNAMICALLY? > Zhongjin He Hello, zhongjin

[gmx-users] dihedrals potential as a expansion of cosine funtions

Hi all. I am a bit confused about how GROMACS handles multiply defined interactions in the top file. Concretely, I see from the lipid parameters (POPC) from Kukol (JCTC, 5:615, updated in http://lists.gromacs.org/pipermail/gmx-users/2010-May/050647.html ) that when defining several times an i

[gmx-users] g_rdf between bonded and nonbonded groups

I would like to calculate the inter- and intra-molecular radial distribution functions separately. I have read through g_rdf -h many times and I have a few questions: 1. I think that I may have to modify a trp file (and not use it for the simulations) by setting the nrexcl to the number of bonds

Re: [gmx-users] g_rdf between bonded and nonbonded groups

Emily Curtis wrote: I would like to calculate the inter- and intra-molecular radial distribution functions separately. I have read through g_rdf -h many times and I have a few questions: 1. I think that I may have to modify a trp file (and not use it for the simulations) by setting the

Re: [gmx-users] dihedrals potential as a expansion of cosine funtions

- Original Message - From: Javier Cerezo Date: Thursday, September 9, 2010 3:17 Subject: [gmx-users] dihedrals potential as a expansion of cosine funtions To: gmx-users@gromacs.org > Hi all. > > I am a bit confused about how GROMACS handles multiply defined > interactions in the top f

Re: [gmx-users] g_rdf between bonded and nonbonded groups

Hi Justin, Thank you for your help. I will edit the topology file. I am running GROMACS 4.0.7. I can download the latest version. The command line I was using was: g_rdf -n index -rdf res_com -s full -surf -o rdf08SEPT10.xvg Emily On Wed, Sep 8, 2010 at 5:31 PM, Emily Curtis wrote: > Hi

Re: [gmx-users] g_rdf between bonded and nonbonded groups

Emily Curtis wrote: Hi Justin, Thank you for your help. I will edit the topology file. I am running GROMACS 4.0.7. I can download the latest version. The command line I There's your problem. The -surf option only appears as of version 4.5. was using was: g_rdf -n index -rdf res_com

[gmx-users] Overflow problem with test-particle insertion

Hello Gromacs users, I sent a message to the list in June describing what appeared to be a float overflow issue with the energy calculation for test-particle insertions: http://lists.gromacs.org/pipermail/gmx-users/2010-June/052213.html. I have recently tried the test-particle insertion mode in G

[gmx-users] Re: multiplication of lambda constant with LJ potential affecting only solvent.

Hi all I want to change LJ potential for water only by multiplying a factor lambda. Can anybody help me that it affect only water not protein. Thanks in advance. -- Navjeet Ahalawat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please se