[gmx-users] how to run g_tune_pme in cluster?

Hello: Does anybody have any idea how to run g_tune_pme in a cluster? I tried many times with following command: g_tune_pme_d -v -s npt_01.tpr -o npt_01.trr -cpo npt_01.cpt -g npt_01.log -launch -nt 24 > log & but it always failed. Option Type Value Description

[gmx-users] DSSP-last GROMACS 4.5.7 can not use DSSP -please help to solve it

Dear ALL:how to install DSSP in Gromacs4.5.7I followed someone replies mail still can not use do I do right ?DSSP website-miscellaneous-distribution-dsspold-linux distribution then get "dsspcmbi"but Gromacs can not recoginz this index gromacs index is do_dssp ?and DSSPagain , how to install DS

Re: [gmx-users] how to run g_tune_pme in cluster?

Hi, what output does g_tune_pme provide? What is in "log" and in "perf.out"? Can it find the correct mdrun / mpirun executables? Carsten On Apr 26, 2012, at 9:28 AM, Albert wrote: > Hello: > Does anybody have any idea how to run g_tune_pme in a cluster? I tried many > times with following co

Re: [gmx-users] How to choose two atoms at the same time, using g_select selection.dat

On Thu, Apr 26, 2012 at 04:19, mu xiaojia wrote: > e.g, I want to make an "HN" group of both H and N from my 2nd residue, There are multiple ways to achieve what you want with g_select. Probably the easiest is "resnr 2 and name H N", or if you need the atoms in a different order (changing the o

[gmx-users] gromacs 4.5.4 on cygwin cmake

Hi I am having problems installing gromacs on cygwin using autoconf so I used cmake instead. I used the following option with cmake: cmake GMX_PREFER_STATIC_LIBS=ON ../gromacs-4.5.4 followed by make and make install. Gromacs installed finally without complaints. gromacs installs but I get

[gmx-users] GPCR MD Tutorial Using GROMACS

Hi ALL, I have prepared a step-wise tutorial for running a MD simulation of a GPCR protein inserted in a lipid bilayer. I sincerely hope it will help people who are new to such simulations and the GROMACS community in general. This tutorial is adapted from the membrane protein tutorial prepared by

[gmx-users] GPCR MD Tutorial Using GROMACS

Hi ALL, I have prepared a step-wise tutorial for running a MD simulation of a GPCR protein inserted in a lipid bilayer. It can be found at the following URL: https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial I sincerely hope it will help people who are new to such simulations and the

[gmx-users] GPCR MD Tutorial Using GROMACS (URL)

Hi ALL, I have prepared a step-wise tutorial for running a MD simulation of a GPCR protein inserted in a lipid bilayer. It can be found at the following URL: https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial I sincerely hope it will help people who are new to such simulations and the

Re: [gmx-users] how to run g_tune_pme in cluster?

hello: it can find mdrun correctly. and it is only give me the log file as I mentioned in previous thread. thank you very much On 04/26/2012 09:53 AM, Carsten Kutzner wrote: Hi, what output does g_tune_pme provide? What is in "log" and in "perf.out"? Can it find the correct mdrun / mpirun

Re: [gmx-users] GPCR MD Tutorial Using GROMACS (URL)

it seesm to be good. just one pieces of advices, why not use CHARMM36 for this tutorial ? since it is the best FF for lipids currently. On 04/26/2012 11:14 AM, Anirban Ghosh wrote: Hi ALL, I have prepared a step-wise tutorial for running a MD simulation of a GPCR protein inserted in a lipid

Re: [gmx-users] GPCR MD Tutorial Using GROMACS (URL)

Hello Albert, Thanks. Yes, CHARMM36 indeed handles lipids very well. But currently GROMACS 4.5.5 provides only the option for CHARMM27 FF and I found that ff43a1 very well preserves the characters of both the protein as well as the lipids for fairly long simulation time, hence I used that FF in th

Re: [gmx-users] DSSP-last GROMACS 4.5.7 can not use DSSP -please help to solve it

You set the environment variable DSSP to the absolute path to your dssp executable. Then do_sddp can make use of it. Is that clear? Erik 26 apr 2012 kl. 09.33 skrev 李 麗花: > Dear ALL: > how to install DSSP in Gromacs4.5.7 > I followed someone replies mail still can not use > do I do right ? > D

Re: [gmx-users] how to run g_tune_pme in cluster?

On Apr 26, 2012, at 11:37 AM, Albert wrote: > hello: > it can find mdrun correctly. and it is only give me the log file as I > mentioned in previous thread. What files are produced by g_tune_pme? Is there a benchtest.log? Can you cat its contents? Carsten > > thank you very much > > On 04/26/

Re: [gmx-users] GPCR MD Tutorial Using GROMACS (URL)

Hello Anirban: thanks for kind comments. How long did you mean " fairly long simulation time" ? does 1u ns belongs to this range? CHARMM36 ff is available in gromacs website and we can download it and put them into top directory and then it works. It is not need to make any modification by

Re: [gmx-users] how to run g_tune_pme in cluster?

yes, here is the contents for it: :-) G R O M A C S (-: GRowing Old MAkes el Chrono Sweat :-) VERSION 4.6-dev-20120423-25c75 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert v

[gmx-users] Force field for graphene sheet: deformation at the boundaries

Dear colleagues, I came across a puzzling behaviour when simulating graphene sheets (periodic in xy). When running a simulation of just one position restrained graphene sheet in a large vacuum slab with periodic_molecules=yes and pbc=xyz, I found a static deformation of the boundaries of th

Re: [gmx-users] GPCR MD Tutorial Using GROMACS (URL)

Hello Albert, Good to know that! I have carried out simulations using this FF in the range of 600 ns. Regards, Anirban On Thu, Apr 26, 2012 at 3:47 PM, Albert wrote: > Hello Anirban: > > thanks for kind comments. > How long did you mean " fairly long simulation time" ? does 1u ns belongs >

[gmx-users] how to optimize the orientation of the protein in a dodecahedron

Dear GROMACS users, I have noticed that for constant box dimensions the minimum distance from the periodic images of a protein depends on the initial orientation of the protein, whereas the orientation of the dodecahedron relative to the x,y,z axes remains fixed. These are the command lines I use:

[gmx-users] Atom types for phosphate group in OPLS-AA force field

Dear Gromacs users, I am here requesting your help with regards to the editing of the OPLS-AA force field, and more specifically, the choice of the atom types. I have added an entry for the molecule CABP to the .rtp and .hdb files. I can run pdb2gmx, genbox and editconf without getting any e

Re: [gmx-users] GPCR MD Tutorial Using GROMACS (URL)

Hi Anirban: how many ns/day for your simulations? Did you use PME? best Albert On 04/26/2012 12:59 PM, Anirban Ghosh wrote: Hello Albert, Good to know that! I have carried out simulations using this FF in the range of 600 ns. Regards, Anirban -- gmx-users mailing listgmx-users@grom

Re: [gmx-users] Atom types for phosphate group in OPLS-AA force field

On 4/26/12 7:45 AM, Delmotte, Antoine wrote: Dear Gromacs users, I am here requesting your help with regards to the editing of the OPLS-AA force field, and more specifically, the choice of the atom types. I have added an entry for the molecule CABP to the .rtp and .hdb files. I can run pdb2

Re: [gmx-users] GPCR MD Tutorial Using GROMACS (URL)

Hello Albert, On our cluster I usually get around 25-30 ns/day running on 120 cores (system size around 85K atoms) with PME. Regards, Anirban On Thu, Apr 26, 2012 at 5:28 PM, Albert wrote: > Hi Anirban: > how many ns/day for your simulations? Did you use PME? > > best > Albert > > > > On 04

Re: [gmx-users] how to optimize the orientation of the protein in a dodecahedron

Hey Thomas, The rhombic dodecahedron corresponds to the packing of a sphere. Consequently, the difference in the distance between periodic images over the shortest diameter and the longest diameter is pretty small. That means that there isn't really an optimal orientation in a rhombic dodecahedron

[gmx-users] Re: gmx-users Digest, Vol 96, Issue 189

ubject: [gmx-users] Fwd: Error: coordinate file does not match with >the topology file > To: Discussion list for GROMACS users > Message-ID: <4f98cb52.1060...@anu.edu.au> > Content-Type: text/plain; charset="iso-8859-1" > > Please do not make unsolicited

Re: [gmx-users] how to optimize the orientation of the protein in a dodecahedron

Hi, And even if not all orientations are exactly equal in this respect, bare in mind that the solute might rotate during the simulation, taking it out of any optimum. Erik 26 apr 2012 kl. 14.36 skrev Tsjerk Wassenaar: > Hey Thomas, > > The rhombic dodecahedron corresponds to the packing of a

[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

Dear Anirban, Thanks for the tutorial you have created for the newbies like me to follow. I wonder the tutorial is only for the GPCRs not applicable for other membrane proteins? I also have another question about slecting a lipidbilayer, what is the criteria is selecting it, for instance popc, d

Re: [gmx-users] how to optimize the orientation of the protein in a dodecahedron

Hi Tsjerk and Erik, Thanks for the comments. It's strange, because I get different minimum distance for different orientations of the same protein structure using the afore-mentioned command lines. I used a single step energy minimization for speed (em_real.mdp). Below are the outputs of editconf

Re: [gmx-users] how to optimize the orientation of the protein in a dodecahedron

Hi Thomas, Apologies, you are right. I was thinking of the distance to the wall. If the protein is elongated, it will matter in the minimal distance whether the protein major radius is oriented towards a face or towards a corner. In addition, the shape of the protein plays a role. Yet it doesn't r

Re: [gmx-users] Can I equilibrate with Parinello-Rahman?

On 26/04/2012 10:47 PM, PAVAN PAYGHAN wrote: Dear Mark, Thanks a lot for the reply and highlighting the cause of error that I was facing. Still can it be possible to overcome the same error with the available facility. Unfortunately you're forcing me to guess the context for this question.

[gmx-users] MD simulations of covalent bound protein-ligand complex by gromacs

Dear All: I am simulating a complex of protein and ligand, however, the ligand is covalent bound to the protein. I have calculated the charges of the ligand and the non-standard residue by QM method and trying to use the bond parameters in the GROMOS force field. However, I don't know how to ma

[gmx-users] double precision energy minimization show zero pressure in gromacs 4.5.5

Hi all, I am carrying out energy minimization on bulk polymer system (N~2) with integrator = l-bfgs in double precision gromacs 4.5.5. I am using tabulated force-fields for bonded, and non-bonded interactions. In the force field, the coulombic interaction is set to zero, hence, the output is

[gmx-users] FEP

Hello all, This is in reply to Michael shirts a while ago on a FEP of a R-CH3 to an R-H group.  Below is the orignal email. I recently tested out mutating a CH3-CH3-(3dummy atoms) molecule on both sides in order to test out that a peturbation would give you a total of 0. forcefield used was CGen

Re: [gmx-users] Atom types for phosphate group in OPLS-AA force field

Dear Justin, Many thanks for your response. I managed to reduce the number of errors by trying other atom types, by looking at what seemed most likely to be right from the ffnonbonded.itp and ffbonded.itp files. Unfortunately, I did not manage to find a combination that both made some sense,

Re: [gmx-users] MD simulations of covalent bound protein-ligand complex by gromacs

On 4/26/12 10:23 AM, mirc...@sjtu.edu.cn wrote: Dear All: I am simulating a complex of protein and ligand, however, the ligand is covalent bound to the protein. I have calculated the charges of the ligand and the non-standard residue by QM method and trying to use the bond parameters in the GR

Re: [gmx-users] double precision energy minimization show zero pressure in gromacs 4.5.5

On 4/26/12 11:00 AM, Yongchul Chung wrote: Hi all, I am carrying out energy minimization on bulk polymer system (N~2) with integrator = l-bfgs in double precision gromacs 4.5.5. I am using tabulated force-fields for bonded, and non-bonded interactions. In the force field, the coulombic in

Re: [gmx-users] Atom types for phosphate group in OPLS-AA force field

On 4/26/12 11:37 AM, Delmotte, Antoine wrote: Dear Justin, Many thanks for your response. I managed to reduce the number of errors by trying other atom types, by looking at what seemed most likely to be right from the ffnonbonded.itp and ffbonded.itp files. Unfortunately, I did not manage to

Re: [gmx-users] Atom types for phosphate group in OPLS-AA force field

Thank you very much for your answer. This has been very helpful. I think I will follow your advice and try to find similar molecules to find the parameters. Could I just ask you if you know of a database where I could look for the opls parameters which have calculated for other molecules? Be

Re: [gmx-users] Atom types for phosphate group in OPLS-AA force field

On 4/26/12 12:15 PM, Delmotte, Antoine wrote: Thank you very much for your answer. This has been very helpful. I think I will follow your advice and try to find similar molecules to find the parameters. Could I just ask you if you know of a database where I could look for the opls parameters w

Re: [gmx-users] double precision energy minimization show zero pressure in gromacs 4.5.5

On 4/26/12 12:36 PM, Yongchul Chung wrote: Well, actually it has a meaning in the simulation that I am carrying out. Ah, I remember a discussion about this some time ago and was recalling the wrong side of it ;) What you're doing is relying on the virial to dictate the pressure then. The

[gmx-users] Position Restraints

Dear All, I am using CG-MD using MARTINI forcefield. The system contains Protein and lipid bilayer. Although I used: define = -DPOSRES components in system were moving around and interact with each other. Then, I cannot do NVT or NPT equilibration. Could you please let me know how can I control thi

Re: [gmx-users] Position Restraints

On 4/26/12 1:35 PM, Dariush Mohammadyani wrote: Dear All, I am using CG-MD using MARTINI forcefield. The system contains Protein and lipid bilayer. Although I used: define = -DPOSRES components in system were moving around and interact with each other. Then, I cannot do NVT or NPT equilibration

Re: [gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

On 4/26/12 9:35 AM, Bala S wrote: Dear Anirban, Thanks for the tutorial you have created for the newbies like me to follow. I wonder the tutorial is only for the GPCRs not applicable for other membrane proteins? Tutorials present possible workflows. Anirban's tutorial does not significant

[gmx-users] Biasing a dipole vector direction relative to the moment of inertia tensor eigenvectors

Greetings, I am trying to do electrostatics calculations for a protein system which requires knowledge of the average dipole vector for an experimental probe. I've previously obtained this average dipole vector by using umbrella sampling with WHAM over the chi_2 dihedral angle of this probe, h

Re: [gmx-users] Position Restraints

Thanks dear Justin. No, the protein is moving in right direction, but I am going to restrain any changing the position and then monitory these movements during MD run. I could see the Pos. Res. works in md.log file. Regards, Dariush On Thu, Apr 26, 2012 at 1:38 PM, Justin A. Lemkul wrote: > >

[gmx-users] Acpype doubts

I configure Amber1.5 and installed the Acpype compatible (the tests went pretty well) BUT when I tried to submit my own job by the line acpype -i proteinname.mol2 -c user i got the message: == = | ACPYPE

Re: [gmx-users] Position Restraints

On 4/26/12 1:59 PM, Dariush Mohammadyani wrote: Thanks dear Justin. No, the protein is moving in right direction, but I am going to restrain any changing the position and then monitory these movements during MD run. I could see the Pos. Res. works in md.log file. Then I don't understand what

[gmx-users] help about "Inconsistent DD boundary staggering limits"

Hi Guys, I have done the simulation. The total steps is 500. At around 90 steps, the error information appear like the followings. Please give me some suggestions to fix it. Best wishes, Desheng -- Program mdrun, VERSION 4.5.5 Sourc

Re: [gmx-users] double precision energy minimization show zero pressure in gromacs 4.5.5

I suppose I can calculate virial manually ... but thought there might be a glitch in the code when making a transition from 4.0 to 4.5. I sent an e-mail to gmx-developers. Greg On Thu, Apr 26, 2012 at 1:00 PM, Justin A. Lemkul wrote: > > > On 4/26/12 12:36 PM, Yongchul Chung wrote: > >> Well, a

Re: [gmx-users] help about "Inconsistent DD boundary staggering limits"

On 4/26/12 2:52 PM, Desheng Zheng wrote: Hi Guys, I have done the simulation. The total steps is 500. At around 90 steps, the error information appear like the followings. Please give me some suggestions to fix it. Based on the comment that precedes the error call in the code: /*

[gmx-users] gen_pairs to calculate absent 1-4 interactions in CHARMM36c FF

Dear users, In GROMACS, does CHARMM36 ff, calculate eventual 1-4 interactions that are absent from the [pairtypes] section of the ffnonbonded.itp file? I ask this because I'm converting cholesterol parameters from CHARMM36c to gmx format, and several 1-4 values are absent in the last two columns

Re: [gmx-users] help about "Inconsistent DD boundary staggering limits"

On 4/26/12 3:30 PM, Desheng Zheng wrote: Thanks Justin! about the "Software inconsistency error: Inconsistent DD boundary staggering limits!" I still have three concerts. 1. Is it ok, if i use grompp to generate the edr file in gromacs 4.5.5 environmentwith the gro file and top file whic

Re: [gmx-users] How to choose two atoms at the same time, using g_select selection.dat

Thanks for the reply! On Thu, Apr 26, 2012 at 3:28 AM, Teemu Murtola wrote: > On Thu, Apr 26, 2012 at 04:19, mu xiaojia wrote: > > e.g, I want to make an "HN" group of both H and N from my 2nd residue, > > There are multiple ways to achieve what you want with g_select. > Probably the easiest is

RE: [gmx-users] help about "Inconsistent DD boundary staggering limits"

Thanks Justin! about the "Software inconsistency error: Inconsistent DD boundary staggering limits!" I still have three concerts. 1. Is it ok, if i use grompp to generate the edr file in gromacs 4.5.5 environmentwith the gro file and top file which were builed under Gromacs 4.0.7 ? 2. In

RE: [gmx-users] Error in using gromacs for MD simulation

http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu

Re: [gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

Looks I got to the party late (at a conference with limited time to do emails). As a shameless self-plug, we recently published a soup-to-nuts protocol paper for GPCR + POPC + ligand in Gromacs 4.5.x and CHARMM27/36/CGenFF. Our timescales are on the order 100+ns. 20ns/day is possible on 100K ato

Re: [gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

Hello Bala, Yes, exactly as Justin said it represents just a workflow where a GPCR protein (here B2AR) has been taken as an example. I mentioned it as a GPCR tutorial because many often inquire about GPCR MD simulations only in the forum. But it can be adapted for other membrane proteins as well.

[gmx-users] Regarding errors

Respected sir, While i am running the gromacs software i am getting the following error.Kindly tell me how to over come the error. Fatal error: Atom HA in residue LYS 1 was not found in rtp entry LYSH with 15 atoms while sorting atoms. SURYANARAYANA SEERA, PhD student -- gmx-

Re: [gmx-users] Regarding errors

On 27/04/2012 3:53 PM, seera suryanarayana wrote: Respected sir, While i am running the gromacs software i am getting the following error.Kindly tell me how to over come the error. Fatal error: Atom HA in residue LYS 1 was not found in rtp entry LYSH with 15 atoms while sor