[gmx-users] rvdw and DispCorr

Dear gromacs users In a recent paper I found the following protocol of a gromacs simulation: "All simulations were performed with the GROMACS 4.0 [12] compiled in single-precision mode at a constant temperature of 277 K in a periodic box with an edge length of approximately 8.2 nm and the defaul

Re: [gmx-users] solvent group size (12548) is not a multiple of 3

On Fri, May 11, 2012 at 2:18 PM, Sangita Kachhap wrote: > > Hello all > I am runing Gromacs Tutorial KALP-15 in DPPC (I am using POPC) > I am geeting error during addiotion of ions > Fatal error: > Your solvent group size (12548) is not a multiple of 3 > For more information and tips for troublesh

[gmx-users] line longer than 4095 - a bug?

Dear Gmx Users, Many of you probably faced an error: "An input file contains a line longer than 4095 characters, while the buffer passed to fgets2 has size 4095. The line starts with: '20s' " As I noted this error comes from the changes in the topology. Gromacs somehow add " _ " and thus this

Re: [gmx-users] rvdw and DispCorr

On Fri, 2012-05-11 at 10:23 +0200, Bernhard Knapp wrote: > Dear gromacs users > > In a recent paper I found the following protocol of a gromacs simulation: > > "All simulations were performed with the GROMACS 4.0 [12] compiled in > single-precision mode at a constant temperature of 277 K in a p

[gmx-users] Martini mapping for fluorinated alkane

I have a fully fluorinated alkane, and am wondering how to choose the right atom-to-bead mapping. 4 CH2 groups form a C1 bead in Martini. Will CF2-CF2 (6 heavy atoms), also map to a C1 bead type? How does one go about making the right choice? Any suggestions will be so welcome -- Maria G. Techni

[gmx-users] solvent group size (12548) is not a multiple of 3

;> >> ; Include Position restraint file >> #ifdef POSRES >> #include "posre.itp" >> #endif >> >> ; Strong position restraints for InflateGRO >> #ifdef STRONG_POSRES >> #include "strong_posre.itp" >> #endif >> >> ; Inc

[gmx-users] movement in 2 directions - remove one degree of freedom

Dear Gromacs Users, Is there any way in Gromacs which will allow me to contraint some of the atoms in the system to move only in the coordinate X and Z? I do not want some of my atoms to move in Y direction. Do you know how to do this? Steven -- gmx-users mailing listgmx-users@gromacs.org ht

Re: [gmx-users] movement in 2 directions - remove one degree of freedom

11 maj 2012 kl. 14.38 skrev Steven Neumann: > Dear Gromacs Users, > > Is there any way in Gromacs which will allow me to contraint some of the > atoms in the system to move only in the coordinate X and Z? I do not want > some of my atoms to move in Y direction. Do you know how to do this? >

[gmx-users] problem

Hi, Am Anik Sen. AM using GROMACS 3.3.2 for one of my work. I was trying to run the dynamics for some inorganic metal halides solvation in water. A fatal error is comingthat: * Atomtype "CH2r" not found. But in my system I have no such atoms. Only water molecules with tip4p model

Re: [gmx-users] problem

You should paste your topology for you metal halides so that others can help. On Fri, May 11, 2012 at 9:48 PM, Anik Sen wrote: > Hi, Am Anik Sen. AM using GROMACS 3.3.2 for one of my work. > > I was trying to run the dynamics for some inorganic metal > halides solvation in water. A

[gmx-users] Simulation of POPC in water using CHARMM27

Dear gmx users, I'm going to simulate the POPC in water. I downloaded required files in Tielman site and made the .top file. Then included the CHARMM27.ff in the .top file. When I run the grompp I get the fatal error as below: Atomtype CB not found I have done the same with gromos87.ff . But I

Re: [gmx-users] problem

Dear Anik, > Hi, Am Anik Sen. AM using GROMACS 3.3.2 for one of my work. Is there a particular reason you are using such an old version of gromacs? If not then switch to the latest version as there have been many improvements > > I was trying to run the dynamics for some inorganic me

[gmx-users] Create Bond between new residues

Dear Gromacs Users, I created my own residues in aminoacids.rtp which each is formed of one atom. I would like to somehow create bonds between then using standart harmonic potential. Could you please advise how to do this? Stevem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gr

[gmx-users] MPIRUN issue for CHARMM36 FF

Hi ALL, I am trying to simulate a membrane protein system using CHARMM36 FF on GROAMCS4.5.5 on a parallel cluster running on MPI. The system consists of arounf 1,17,000 atoms. The job runs fine on 5 nodes (5X12=120 cores) using mpirun and gives proper output. But whenever I try to submit it on mor

Re: [gmx-users] Simulation of POPC in water using CHARMM27

On Fri, May 11, 2012 at 7:36 PM, Shima Arasteh wrote: > Dear gmx users, > > I'm going to simulate the POPC in water. > I downloaded required files in Tielman site and made the .top file. Then > included the CHARMM27.ff in the .top file. > When I run the grompp I get the fatal error as below: > Ato

Re: [gmx-users] Create Bond between new residues

here is a simple example (for more complex ones see the existing residues in an aminoacids.rtp) assume molecule looks like A-B-C where the -'s are bonds with residues AAA, BBB, CCC containing the corresponding atoms, then the .rtp should contain something like: [ AAA ] [ atoms ] A typeA c

Re: [gmx-users] Simulation of POPC in water using CHARMM27

On Fri, May 11, 2012 at 9:10 PM, Anirban wrote: > > > On Fri, May 11, 2012 at 7:36 PM, Shima Arasteh < > shima_arasteh2...@yahoo.com> wrote: > >> Dear gmx users, >> >> I'm going to simulate the POPC in water. >> I downloaded required files in Tielman site and made the .top file. Then >> included t

Re: [gmx-users] Simulation of POPC in water using CHARMM27

Dear Anirban, No, I have not done. Because I didn't know I need Berger lipids for this simulation. Thanks for you reply, Cheers, Shima From: Anirban To: Shima Arasteh ; Discussion list for GROMACS users Sent: Friday, May 11, 2012 8:10 PM Subject: Re: [gmx

Re: [gmx-users] Simulation of POPC in water using CHARMM27

All right. Thank you From: Anirban To: Shima Arasteh ; Discussion list for GROMACS users Sent: Friday, May 11, 2012 8:11 PM Subject: Re: [gmx-users] Simulation of POPC in water using CHARMM27 On Fri, May 11, 2012 at 9:10 PM, Anirban wrote: > > >On

Re: [gmx-users] Create Bond between new residues

Well, impressive explanation! Thank you very much! Steven On Fri, May 11, 2012 at 4:38 PM, Richard Broadbent < richard.broadben...@imperial.ac.uk> wrote: > here is a simple example (for more complex ones see the existing > residues in an aminoacids.rtp) > > assume molecule looks like > > A-B-C >

[gmx-users] g_mdmat

Dear Gromacs user, I'm trying to calculate de distances between residues in a trajectory with g_mdmat and I'm coming across a problem while trying to restrict only to a smaller number of residues providing an index file. in fact what I get is a matrix as big as if I use all the residues, and the ar

Re: [gmx-users] Simulation of POPC in water using CHARMM27

CHARMM27 or CHARMM36 doesn't make different for me. I just want to get a good output of simulation. Before this, Justin also suggested me for CHARMM36. Ok, I will use CHARMM36. But about the atom types, it's not still clear for me what I need to do. If I use the CHARMM36, am I supposed to build

Re: [gmx-users] Simulation of POPC in water using CHARMM27

On Fri, May 11, 2012 at 10:08 PM, Shima Arasteh wrote: > CHARMM27 or CHARMM36 doesn't make different for me. I just want to get a > good output of simulation. > Before this, Justin also suggested me for CHARMM36. Ok, I will use > CHARMM36. But about the atom types, it's not still clear for me wh

Re: [gmx-users] Simulation of POPC in water using CHARMM27

OK, I'll give it a try. Thank you again! :-) Cheers, Shima From: Anirban To: Shima Arasteh ; Discussion list for GROMACS users Sent: Friday, May 11, 2012 9:22 PM Subject: Re: [gmx-users] Simulation of POPC in water using CHARMM27 On Fri, May 11, 2012

Re: [gmx-users] movement in 2 directions - remove one degree of freedom

Hi, as an alternative of applying position restraints to only the y-component, one can also define a freeze-group only to act on the Y-axis by using: freezedim N Y N see: http://manual.gromacs.org/online/mdp_opt.html#neq freezegrps and freezedim Oliver On Fri, May 11, 2012 at 7:39 AM, Erik Ma

[gmx-users] General amber force field in GROMACS

 Hi Guys Could some one please let me know how to convert general amber force field bond force constents to GROMACS bong function 1 type. Thanks so much Milinda Samaraweera University of Connecticut Department of Chemistry 55 N Eagleville road unit 3060 Storrs CT USA-- gmx-users mailing lis

Re: [gmx-users] General amber force field in GROMACS

On 5/11/12 3:54 PM, Milinda Samaraweera wrote: Hi Guys Could some one please let me know how to convert general amber force field bond force constents to GROMACS bong function 1 type. Bond type 1 is a simple harmonic bond. You need an equilibrium length and force constant in appropriate

[gmx-users] Number of native contacts rho

Hi,   Is there any tool in gromacs that can compute the fraction of native contacts  "rho" ( i,e  the typical parameter that quantifies how close the folding protein is to the native ) ? Thanks Sanku-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-

[gmx-users] editconf and g_editconf confusion

Hi, Can anyone please tell me what is the difference between the commands editconf and g_editconf? If there is no difference then why do some systems recognize g_editconf but not editconf? -- Regards, Nitin Agrawal, Master's Student (Bioinformatics) University of Turku,Finland B.Tech (Biotechnol

Re: [gmx-users] editconf and g_editconf confusion

On 5/11/12 7:40 PM, Nitin Agrawal wrote: Hi, Can anyone please tell me what is the difference between the commands editconf and g_editconf? If there is no difference then why do some systems recognize g_editconf but not editconf? There is no difference. g_editconf is just editconf but with

Re: [gmx-users] editconf and g_editconf confusion

Thank you for your clarification. On Sat, May 12, 2012 at 2:51 AM, Justin A. Lemkul wrote: > > > On 5/11/12 7:40 PM, Nitin Agrawal wrote: > >> Hi, >> >> Can anyone please tell me what is the difference between the commands >> editconf >> and g_editconf? If there is no difference then why do some

Re: [gmx-users] Simulation of POPC in water using CHARMM27

Dear gmx users, Anybody can guide me to some articles which introduces CHARMM36  forcefield? I want to study about this forcefield. Thanks in advance, Shima From: Anirban To: Shima Arasteh ; Discussion list for GROMACS users Sent: Friday, May 11, 2012 9:2

Re: [gmx-users] Simulation of POPC in water using CHARMM27

I would say looking at the CHARMM force field website would be the first thing to do. Google: CHARMM FORCE FIELD, and you should get the relevant pages... The articles are listed on the website... /Jesper On May 11, 2012, at 9:19 PM, Shima Arasteh wrote: > Dear gmx users, > > Anybody can gui

Re: [gmx-users] Simulation of POPC in water using CHARMM27

On Sat, May 12, 2012 at 9:49 AM, Shima Arasteh wrote: > Dear gmx users, > > Anybody can guide me to some articles which introduces CHARMM36 > forcefield? I want to study about this forcefield. > > Have a look at this paper: http://pubs.acs.org/doi/abs/10.1021/jp101759q -Anirban Thanks in advan

[gmx-users] mdrun_mpi issue for CHARMM36 FF

Hi ALL, I am trying to simulate a membrane protein system using CHARMM36 FF on GROAMCS4.5.5 on a parallel cluster running on MPI. The system consists of arounf 1,17,000 atoms. The job runs fine on 5 nodes (5X12=120 cores) using mpirun and gives proper output. But whenever I try to submit it on mor