[gmx-users] Membrane Proteins pdb2gmx

Hello Justin, In your membrane protein simulation tutorial after making the topology, you have mentioned that Placing the new gromos53a6_lipid.ff directory in $GMXLIB will allow you to use this force field system-wide. I suppose this is valid only for the proteins (and not membranes) to be

[gmx-users] restart does not automatically use checkpoint?

I attempted to do a restart of an aborted mpirun 4.5.4 simulation with -deffnm but no explicit -cpi. However, the simulation did not restart from the checkpoint but started from 0. Is this a known issue? Do restarts require explicit -cpi flag? (since the workflow I use to extend a run using

[gmx-users] Re: Gromacs 4.5.4 on multi-node cluster

email message attachment Forwarded Message From: Nikos Papadimitriou nik...@ipta.demokritos.gr To: gmx-users@gromacs.org Subject: [gmx-users] Gromacs 4.5.4 on multi-node cluster Date: Wed, 7 Dec 2011 16:26:46 +0200 Dear All, I had been running Gromacs

Re: [gmx-users] Membrane Proteins pdb2gmx

On 2011-12-08 02:43:13AM -0600, Anirban Ghosh wrote: Hello Justin, In your membrane protein simulation tutorial after making the topology, you have mentioned that Placing the new gromos53a6_lipid.ff directory in $GMXLIB will allow you to use this force field system-wide. I suppose this is

Re: [gmx-users] Re: Gromacs 4.5.4 on multi-node cluster

Hi. This is openmpi related. Probably you have active the virbr0 interface with IP 192.168.122.1 on nodes. Stop and disable the libvirtd (and probably libvirt-guests) service if you don't need it. Alternatively, 1. add --mca btl_tcp_if_exclude lo,virbr0 in mpirun flags or 2. add in

Re: [gmx-users] Membrane Proteins pdb2gmx

Hello Peter, Thanks a lot for clarifying my doubt! I have got it right now. Thanks, Anirban On Thu, Dec 8, 2011 at 3:34 PM, Peter C. Lai p...@uab.edu wrote: On 2011-12-08 02:43:13AM -0600, Anirban Ghosh wrote: Hello Justin, In your membrane protein simulation tutorial after making the

[gmx-users] how to set the BASENAME in QMMM simualtions using gromacs/orca

Dear GMX users, Could someone give me some suggestions on how to set the BASENAME file in the QMMM simulations using gromacs/orca? Is the BASENAME file the inp file in orca? Thanks very much! Best Regards, Qinghua -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] No automatic terminus detection

Hi, I try to simulate DNA or better parts of a long DNA double-helix. Therefore, the system I use is not correctly terminated at the ends from chemical point of view with OH-groups but rather cut out the longer helix. Nevertheless, all residues are named correctly, all atoms needed in the

Re: [gmx-users] how to set the BASENAME in QMMM simualtions using gromacs/orca

Dear Qinghua, Yes indeed. It's what you give in the ORCA input file, but without the coordinates, charge, multiplicity, and the Opt or EnGrad keyword. Hope that helps, Christoph On 12/08/2011 11:43 AM, Qinghua Liao wrote: Dear GMX users, Could someone give me some suggestions on how to set

Re: [gmx-users] restart does not automatically use checkpoint?

Peter C. Lai wrote: I attempted to do a restart of an aborted mpirun 4.5.4 simulation with -deffnm but no explicit -cpi. However, the simulation did not restart from the checkpoint but started from 0. Is this a known issue? Do restarts require explicit -cpi flag? (since the workflow I use to

Re: [gmx-users] No automatic terminus detection

On 8/12/2011 9:40 PM, Matthias Ernst wrote: Hi, I try to simulate DNA or better parts of a long DNA double-helix. Therefore, the system I use is not correctly terminated at the ends from chemical point of view with OH-groups but rather cut out the longer helix. Nevertheless, all residues are

Re: [gmx-users] mdrun_mpi error

On 8/12/2011 6:35 PM, aiswarya pawar wrote: Hi users, Am running the mdrun_mpi on cluster with the md.mdp parameters as- ; VARIOUS PREPROCESSING OPTIONS title= Position Restrained Molecular Dynamics ; RUN CONTROL PARAMETERS constraints = all-bonds integrator = md dt =

Re: [gmx-users] box vectors

On Thu, Dec 8, 2011 at 12:33 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 8/12/2011 2:54 PM, Chandan Choudhury wrote: Thanks everyone for the responses. I should have framed my question much more precisely. I am trying to use the template.c code of (gmx_4.0.7) and within this, I want

Re: [gmx-users] box vectors

On 9/12/2011 12:00 AM, Chandan Choudhury wrote: On Thu, Dec 8, 2011 at 12:33 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 8/12/2011 2:54 PM, Chandan Choudhury wrote: Thanks everyone for the responses. I should have framed my question much

[gmx-users] Implicit solvent tutorial

Hi gmx_users, is there any tutorial for implicit solvent simulation available? Thanks! -- Gianluca Santoni, Institut de Biologie Structurale 41 rue Horowitz Grenoble _ Please avoid sending me Word or PowerPoint attachments. See

Re: [gmx-users] Implicit solvent tutorial

Gianluca Santoni wrote: Hi gmx_users, is there any tutorial for implicit solvent simulation available? http://www.gromacs.org/Documentation/Tutorials If it's not there, or Google can't find it, the answer is no. -Justin -- Justin A. Lemkul Ph.D.

Re: [gmx-users] No automatic terminus detection

Hi Mark, thanks for your reply. [...] It knows that termini have to be different from mid-chain residues. [...] That answers my question, I think. I wanted to ask if it's possible to just use whatever residue name is given without detection ofend- or midchain residues. I guess you answer

[gmx-users] Postdoc and PhD positions in Denmark

Dear All A PhD and Postdoc position are opening at our center. Following is the advertisement. Starting data: as soon as possible. ––– A PhD position (3 years) and a postdoctoral position (2+ years) in simulations of membranes and membrane proteins are available at the

Re: [gmx-users] box vectors

Hey, On a general note, assuming the frame is read in as a t_trxframe structure called frame, the box is accessible as frame.box and is a matrix instance, which means it's a 3x3 array, containing the triclinic box as a lower triangular matrix. If the code says t_trxframe *frame somewhere, rather

Re: [gmx-users] No automatic terminus detection

On 9/12/2011 12:55 AM, Matthias Ernst wrote: Hi Mark, thanks for your reply. [...] It knows that termini have to be different from mid-chain residues. [...] That answers my question, I think. I wanted to ask if it's possible to just use whatever residue name is given without detection

Re: [gmx-users] Re: Gromacs 4.5.4 on multi-node cluster

Forwarded Message From: Nikos Papadimitriou nik...@ipta.demokritos.gr To: gmx-users@gromacs.org Subject: [gmx-users] Re: Gromacs 4.5.4 on multi-node cluster Date: Thu, 8 Dec 2011 11:44:36 +0200 Forwarded Message From: Nikos Papadimitriou

Re: [gmx-users] Implicit solvent tutorial

On Thu, Dec 8, 2011 at 9:50 PM, Gianluca Santoni gianluca.sant...@ibs.fr wrote: Hi gmx_users, is there any tutorial for implicit solvent simulation available? Hi, I tried it few days ago. 1] pdb2gmx the water model choose none. 2] after editconf, go to energy minimization directly * It's

[gmx-users] Re: gmx-users Digest, Vol 92, Issue 44

Dear Christoph, Thanks very much for your explanation. I will try to figure it out by consulting the manual of orca. Thanks. Best Regards, qinghua Date: Thu, 08 Dec 2011 12:09:03 +0100 From: Christoph Riplinger c...@thch.uni-bonn.de Subject: Re: [gmx-users] how to set the BASENAME in QMMM

Re: [gmx-users] Implicit solvent tutorial

lina wrote: On Thu, Dec 8, 2011 at 9:50 PM, Gianluca Santoni gianluca.sant...@ibs.fr wrote: Hi gmx_users, is there any tutorial for implicit solvent simulation available? Hi, I tried it few days ago. 1] pdb2gmx the water model choose none. 2] after editconf, go to energy minimization

Re: [gmx-users] Implicit solvent tutorial

On Thu, Dec 8, 2011 at 11:26 PM, Justin A. Lemkul jalem...@vt.edu wrote: lina wrote: On Thu, Dec 8, 2011 at 9:50 PM, Gianluca Santoni gianluca.sant...@ibs.fr wrote: Hi gmx_users, is there any tutorial for implicit solvent simulation available? Hi, I tried it few days ago. 1]

Re: [gmx-users] Newbie: How to modify the topology file after adding ions?

Hi Jose, You're not the first one to follow the tutorial, it does state which version to use (4.5, see introduction), and it does state how to fix the topology: editing the file, adding the lines, using the appropriate names. This tutorial is made to be read and to be thought over. Of course

[gmx-users] freezing grps during em

Dear Users, Sorry for maybe naive question. I am new user of gmx. I like to fix the positions of three atoms in three neighboring residues (not connected) with respect to each other. These atoms are very close to each others and van der waals interaction makes the distance larger after em.

[gmx-users] Re:Newbie: How to modify the topology file after adding ions?

Message: 6 Date: Wed, 7 Dec 2011 11:38:58 -0500 From: Jose Borreguero borregu...@gmail.com Subject: Re: [gmx-users] Newbie: How to modify the topology file after addingions? To: jalem...@vt.edu, Discussion list for GROMACS users gmx-users@gromacs.org Message-ID:

[gmx-users] Aminoacids.hdb problem

*Dear gmx-users, I am trying to insert a custom residue (a phosphoserine) in Gromacs using force field Amber ff99sb-ildn. I created a new .rtp entry named SEP like this:* [SEP] [ atoms ] NN -0.49370 1 HH0.30180 2 CA CT -0.23800

Re: [gmx-users] Aminoacids.hdb problem

Alberto Arrigoni wrote: *Dear gmx-users, I am trying to insert a custom residue (a phosphoserine) in Gromacs using force field Amber ff99sb-ildn. I created a new .rtp entry named SEP like this:* [SEP] [ atoms ] NN -0.49370 1 HH0.30180 2

[gmx-users] REST simulation

Dear gromacs users, Recently I stumbled over following paper: T. Terakawa, T. Kameda, and S. Takada, On Easy Implementation of a Variant of the Replica Exchange with Solute Tempering in GROMACS. Journal of Computational Chemistry 32 (2011) 1228-1234. The authors suggested an easy way to run this

[gmx-users] Re:Re:Re: MSD normalization

Hi! Thanks Mark for reply. When I calculated fractional diffusion constant from mass weighted MSD of long simulation I get sth about 0.05. But when I do the same for centre of mass, considering that MSD is expressed in nm^2, the result is 1.35. When I look into xvg file MSD of centre of mass

Re: [gmx-users] Newbie: How to modify the topology file after adding ions?

Hi Jose, The references to NA+ and CL- have been changed, you can reload the page in your browser if you care to continue. Now I still think your statement was rather rude and showing disrespect to the time I put in the tutorial. Apart from the reference to NA/CL you're also factually incorrect

Re: [gmx-users] Newbie: How to modify the topology file after adding ions?

Dear Tsjerk, I never thought I was being rude, probably because I was upset at the time. I apologize. Unfortunately, I believe you'll get more of the same in the future if you don't spend more time updating your page. Devilish details like Na or Na+ have no place in a tutorial. There will be

Re: [gmx-users] Re:Re:Re: MSD normalization

On 9/12/2011 5:37 AM, Sławomir Stachura wrote: Hi! Thanks Mark for reply. When I calculated fractional diffusion constant from mass weighted MSD of long simulation I get sth about 0.05. But when I do the same for centre of mass, considering that MSD is expressed in nm^2, the result is 1.35.

[gmx-users] diffusion coefficient

I want to calculate the diffusion coefficient of a small polypeptide with g_msd (see here http://www.gromacs.org/Documentation/How-tos/Diffusion_Constant) because of periodic boundary condition, when the peptide goes out of the right side it comes in from left side, which leads to an artificial

Re: [gmx-users] diffusion coefficient

On 9/12/2011 5:53 PM, Ruhollah Moussavi-Baygi wrote: I want to calculate the diffusion coefficient of a small polypeptide with g_msd (see here http://www.gromacs.org/Documentation/How-tos/Diffusion_Constant) because of periodic boundary condition, when the peptide goes out of the right side

Re: [gmx-users] diffusion coefficient

On 2011-12-09 08:34, Mark Abraham wrote: On 9/12/2011 5:53 PM, Ruhollah Moussavi-Baygi wrote: I want to calculate the diffusion coefficient of a small polypeptide with g_msd (see here http://www.gromacs.org/Documentation/How-tos/Diffusion_Constant) because of periodic boundary condition, when