Re: [gmx-users] Build problem with 4.6beta1

On Fri, Nov 30, 2012 at 3:20 AM, Justin Lemkul wrote: > > Hooray for being the first to report a problem with the beta :) > > We have a cluster at our university that provides us with access to some > CPU-only nodes and some CPU-GPU nodes. I'm having problems with getting > 4.6beta1 to build, an

Re: [gmx-users] Build problem with 4.6beta1

On 11/29/12 9:34 PM, Roland Schulz wrote: On Thu, Nov 29, 2012 at 9:20 PM, Justin Lemkul wrote: Hooray for being the first to report a problem with the beta :) We have a cluster at our university that provides us with access to some CPU-only nodes and some CPU-GPU nodes. I'm having proble

Re: [gmx-users] Build problem with 4.6beta1

On Thu, Nov 29, 2012 at 9:20 PM, Justin Lemkul wrote: > > Hooray for being the first to report a problem with the beta :) > > We have a cluster at our university that provides us with access to some > CPU-only nodes and some CPU-GPU nodes. I'm having problems with getting > 4.6beta1 to build, an

[gmx-users] Build problem with 4.6beta1

Hooray for being the first to report a problem with the beta :) We have a cluster at our university that provides us with access to some CPU-only nodes and some CPU-GPU nodes. I'm having problems with getting 4.6beta1 to build, and I suspect the issue is related to GPU detection. Here are s

Re: [gmx-users] How are the charges of the gromos96 forcefiel calculated ?

On 11/29/12 9:06 PM, Tanos Franca wrote: Dear users, I'm trying to find out how the atoms charges in the GROMOS96 force field were calculated but I've not been able to find out in the manual or in the paper I saw so far. I know that the force fields for MM have the atoms charges calcu

[gmx-users] How are the charges of the gromos96 forcefiel calculated ?

Dear users, I'm trying to find out how the atoms charges in the GROMOS96 force field were calculated but I've not been able to find out in the manual or in the paper I saw so far. I know that the force fields for MM have the atoms charges calculated by ab initio mathods but I wonder wit

Re: [gmx-users] Does GPU support ATI card?

On 11/29/12 6:40 PM, Szilárd Páll wrote: Hi Justin, First of all, thanks for the feedback. I find in unfortunate that this information got public in the form of a "by the way". More official wording should follow. I wish it happened differently, but unfortunately things did not come together a

Re: [gmx-users] Does GPU support ATI card?

Hi Justin, First of all, thanks for the feedback. I find in unfortunate that this information got public in the form of a "by the way". More official wording should follow. I wish it happened differently, but unfortunately things did not come together as we thought they would. Dragging along code

Re: [gmx-users] Re: Potential energy from a previous configuration mismatch

On 11/29/12 10:40 AM, escajarro wrote: This is my mdp file for energy minimization: constraints = none ; integration parameters integrator = l-bfgs dt = 0.00 nsteps= 15000 ; center of mass removal nstcomm

Re: Отв: [gmx-users] Hbonds between Adenine and Thymine

On 11/29/12 2:04 PM, Hovakim Grabski wrote: Dear Justin, I only used pdb2gmx when I prepared the DNA which I created with nab. and the command that I used was: make_ndx -f md_0_1.gro -o index.ndx after that then I press r10 and r17 I get : 14 r_10:64 atoms 15 r_17

Re: [gmx-users] query regarding PMF calculation

On 11/29/12 11:55 AM, Timir Hajari wrote: Hi, I am trying to calculate PMF using pull code by freezing two pull groups as I need to calculate PMF for a particular orientation. Is it meaning to use pull code in this condition(freezing two pull groups) ?? I will wait for your helpful suggestions.

Re: [gmx-users] Computing energies using g_energy (is -nmol mandatory?)

On 11/29/12 11:53 AM, André Ferreira wrote: Hello all, I am trying to compute total energies of several systems, but I am not sure if I am doing it the right way. Until now I simply used the command: g_energy -f file.edr -s file.tpr -o ener.xvg But after reading the manual, I found the -nmol

Re: [gmx-users] water mediated hydrogen bond

On 11/29/12 10:18 AM, Raj wrote: Hi all, I would like to measure the water mediated hydrogen bond between the ligand and the protein. When I searched the forum I could able to get the link (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/Scripts/plot_hbmap.txt) for the script with whic

Re: [gmx-users] Does GPU support ATI card?

On 11/29/12 12:51 PM, Albert wrote: On 11/29/2012 06:44 PM, Szilárd Páll wrote: Hi Albert, That claim is false. The current mdrun-opnemm version only supports the CUDA OpenMM plugin and even that is not fully supported as we don't have enough resources to maintain the code. We will make sure

Re: [gmx-users] Does GPU support ATI card?

On 11/29/2012 06:44 PM, Szilárd Páll wrote: Hi Albert, That claim is false. The current mdrun-opnemm version only supports the CUDA OpenMM plugin and even that is not fully supported as we don't have enough resources to maintain the code. We will make sure to get the false claim of ATI GPU supp

Re: [gmx-users] Does GPU support ATI card?

Hi Albert, That claim is false. The current mdrun-opnemm version only supports the CUDA OpenMM plugin and even that is not fully supported as we don't have enough resources to maintain the code. We will make sure to get the false claim of ATI GPU support removed from the OpenMM website. Cheers,

Re: [gmx-users] Does GPU support ATI card?

tha't strange, from the link: https://simtk.org/project/xml/downloads.xml?group_id=161 we can see, it said: The current release of OpenMM and OpenMM-accelerated GROMACS enables acceleration of molecular dynamics on specific NVIDIA and ATI GPU cards. I've got ATI-Radeon HD5770, I tried both

[gmx-users] Re: Potential energy from a previous configuration mismatch

This is my mdp file for energy minimization: constraints = none ; integration parameters integrator = l-bfgs dt = 0.00 nsteps= 15000 ; center of mass removal nstcomm = 10 comm_mode = Linear ; ne

[gmx-users] water mediated hydrogen bond

Hi all, I would like to measure the water mediated hydrogen bond between the ligand and the protein. When I searched the forum I could able to get the link (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/Scripts/plot_hbmap.txt) for the script with which we can get the above mentioned obje

[gmx-users] Computing energies using g_energy (is -nmol mandatory?)

Hello all, I am trying to compute total energies of several systems, but I am not sure if I am doing it the right way. Until now I simply used the command: g_energy -f file.edr -s file.tpr -o ener.xvg But after reading the manual, I found the -nmol (number of molecules in your sample) flag.

Re: [gmx-users] Does GPU support ATI card?

No. -- Szilárd On Thu, Nov 29, 2012 at 5:15 PM, Albert wrote: > hello: > > I am just wondering does Gromacs GPU accerlation suppport ATI card? > > THX > > Albert > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users

[gmx-users] Does GPU support ATI card?

hello: I am just wondering does Gromacs GPU accerlation suppport ATI card? THX Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Pl

Re: [gmx-users] segmentation fault

On 11/29/12 10:44 AM, Shine A wrote: Sir, I have one more doubt. During NVT equilibration mdrun giving segmentation fault and not generating any gro files and generating two pdb files. The message is like this Wrote pdb files with previous and current coordinates Warning: 1-4 int

[gmx-users] segmentation fault

Sir, I have one more doubt. During NVT equilibration mdrun giving segmentation fault and not generating any gro files and generating two pdb files. The message is like this Wrote pdb files with previous and current coordinates Warning: 1-4 interaction between 485 and 490 at distance 3.8

Re: [gmx-users] About Diffusion of Water towards Protein in ceter of box

On 11/29/12 10:09 AM, vidhya sankar wrote: Dear Justin, Thank you for your Previous Reply To avoid the Diffusion of Water You Suggested me s follows The better approach would be a position restrain along the z-axis only, allowing the lipids to perhaps re-orient and pack a

Re: [gmx-users] Potential energy from a previous configuration mismatch

On 11/29/12 9:59 AM, juan-manuel.casti...@mv.uni-kl.de wrote: Dear Gromacs friends, I am running some simulations of a hexane/ethanol mixture in a box, using a United-Atom OPLS model. My Gromacs version is the 4.5.5. I fill the simulation box with genbox (I have also used an equilibrated pdb

[gmx-users] About Diffusion of Water towards Protein in ceter of box

Dear Justin,    Thank you for your Previous Reply To avoid the Diffusion of Water You Suggested  me s follows The better approach would be a position restrain along the z-axis only, allowing the lipids to perhaps re-orient and pack a bit better, followed by NVT equilibration i

Re: [gmx-users] g_tune_pme for multiple nodes

Hi Chandan, On Nov 29, 2012, at 3:30 PM, Chandan Choudhury wrote: > Hi Carsten, > > Thanks for your suggestion. > > I did try to pass to total number of cores with the np flag to the > g_tune_pme, but it didnot help. Hopefully I am doing something silliy. I > have pasted the snippet of the PBS

[gmx-users] Potential energy from a previous configuration mismatch

Dear Gromacs friends, I am running some simulations of a hexane/ethanol mixture in a box, using a United-Atom OPLS model. My Gromacs version is the 4.5.5. I fill the simulation box with genbox (I have also used an equilibrated pdb file generated by other simulation code), and I run a energy

AW: [gmx-users] g_tune_pme for multiple nodes

> -Ursprüngliche Nachricht- > Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- > boun...@gromacs.org] Im Auftrag von Chandan Choudhury > Gesendet: Donnerstag, 29. November 2012 15:31 > An: Discussion list for GROMACS users > Betreff: Re: [gmx-users] g_tune_pme for multiple nodes > > H

Re: [gmx-users] g_tune_pme for multiple nodes

Hi Carsten, Thanks for your suggestion. I did try to pass to total number of cores with the np flag to the g_tune_pme, but it didnot help. Hopefully I am doing something silliy. I have pasted the snippet of the PBS script. #!/bin/csh #PBS -l nodes=2:ppn=12:twelve #PBS -N bilayer_tune .

[gmx-users] Re:Energy landscapes

Dear All, I remember a post in the last couple months but cant find it. In any case, by searching through van der groot et alls. papers, the -xmin, -xmax, -dim and -ngrid options third point, example: -xmin 3 3 3 -xmax 3 3 3 is for reading in the output 3d (projections on V1, V2, V3 or first

Re: [gmx-users] Electrostatic field in atoms - GROMACS is not reading table interaction functions for bonded interactions

On 11/29/12 8:18 AM, Ariana Torres Knoop wrote: Dear GROMACS users, We are trying to determine the electric fields at the C and N atoms in a protein. To do so, we thought of performing a one step energy minimization with the Lennard-Jones as well as the bonded interactions turned off, in ord

[gmx-users] Electrostatic field in atoms - GROMACS is not reading table interaction functions for bonded interactions

Dear GROMACS users, We are trying to determine the electric fields at the C and N atoms in a protein. To do so, we thought of performing a one step energy minimization with the Lennard-Jones as well as the bonded interactions turned off, in order to get only the coulomb forces. For that, accord

Re: [gmx-users] error during mdrun

On 11/29/12 7:49 AM, Shine A wrote: Sir, I am studying the dynamics of membrane proteins using KALP-15 in DPPC. Now doing nvt equilibration.During mdrun (mdrun -deffnm nvt) getting error like this Fatal error: 6 particles communicated to PME node 1 are more than 2/3 times the cut-off ou

[gmx-users] error during mdrun

Sir, I am studying the dynamics of membrane proteins using KALP-15 in DPPC. Now doing nvt equilibration.During mdrun (mdrun -deffnm nvt) getting error like this Fatal error: 6 particles communicated to PME node 1 are more than 2/3 times the cut-off out of the domain decomposition cell of thei

Re: [gmx-users] MM-GB/SA analysis in Gromacs

Dear all, I would like to bring to your attention this paper http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0046902 in which we made a tool to perform MM/PBSA binding free energy calculation in automatic fashion, using torque/pbs parallel system implemented in most clusters

Re: [gmx-users] Hbonds between Adenine and Thymine

Please keep the discussion on the gmx-users list. On 11/29/12 6:12 AM, Hovakim Grabski wrote: Dear Justin, When I try to select 10DA residue from one strand and 17DT from the other strand,I type r10 and r17 and both select 64 atoms, after r26 it selects water molecules. You can easily check

Re: [gmx-users] gromacs 4.5.5 Do_dssp segment fault

Thanks for your help!I will try .   -- xiaohong     -- Original -- From:  "Justin Lemkul"; Date:  Thu, Nov 29, 2012 10:43 AM To:  "Discussion list for GROMACS users"; Subject:  Re: [gmx-users] gromacs 4.5.5 Do_dssp segment fau

Re: [gmx-users] error during nvt equilibration

On 11/29/12 12:40 AM, Shine A wrote: Sir, I am studying the dynamics of membrane proteins using KALP-15 in DPPC. Now doing nvt equilibration and created index.ndx by using make_ndx. During this step I selected "16/14" and "1/13".The next step (grompp -f nvt.mdp -c em.gro -p topol.top -n in

Re: [gmx-users] Hbonds between Adenine and Thymine

Hi, A general note: make_ndx and index files are not magical in any way. You can usually construct an index group from e.g. a pdb file with awk. It's just lists of atom indices. Best, Erik 28 nov 2012 kl. 22.33 skrev Justin Lemkul: > > > On 11/28/12 3:43 PM, Hovakim Grabski wrote: >> Dear

[gmx-users] MM-GB/SA analysis in Gromacs

Dear gmx-users, I ran several MD simulations using Gromacs 4.5.4 version, and now I'd need to calculate binding free energies using the MM-GBSA method. I searched through the manual and through the gmx-users archive, but I didn't find a way to do it. I found an old post in which it appeared t

Re: [gmx-users] what does it mean by 'started mdrun on node 0'

Hi Yihua Zhou, Step Time Lambda > 00.00.0 > >Energies (kJ/mol) >Bond G96AngleProper Dih.LJ (SR) Coulomb (SR) > 4.19801e+051.40206e+033.49599e+038.36580e+208.17307e+04 >