Re: [gmx-users] Updating GTX670 PCIE speed from 5GT/s to 8GT/s resulted in about 10% speedup of md_run.

Hi Henk, Thanks for the useful comments! When you run on a single GPU, you do get full timing details both on CPU and GPU - just have a look at the performance tables at the end of the log file. Alternatively you can simply run nvrpof mdrun which will by default give you a nice overview of p

Re: [gmx-users] heating

Hi Kiana, I always heat from 5 K to 300 K with ref_t=300 (ending temp) and gen_temp=5 (starting temp). 5 K is as good as starting at 0 K for my systems. Hope that helps. Regards, On Wed, Dec 4, 2013 at 12:18 PM, kiana moghaddam wrote: > Dear Jastin > > Thanks very much for your reply, when I he

[gmx-users] How to make OPLS forcefield?

Dear Gromacs User, I am the beginner using Gromacs. I have created polyethylene .gro and .top using http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg but in that .top, forcefield is gmx.ff/forcefield.itp. I want to simulate with OPLS forcefield. Please help me how to make or convert to OPLS ff. Th

Re: [gmx-users] out of disk space error

Hi. You can probably try to increase the values of nstxout, nstvout, nstcalcenergy, nstenergy etc. to something like 2000 or 5000 and rerun. 100 seems very small. Amin. On 2013-12-04 12:58, vaani wrote: > nvt.log > > - > t

Re: [gmx-users] GROMACS 4.6.5 is released

Soon enough we will have daily releases :P Mark, can you please elaborate just a tiny bit longer on how relevant were the "GPU-load balancing and GPU-sharing bugs introduced in a bug fix in 4.6.4"? I'm asking this because I just requested the support team at my local cluster to install 4.6.4 and I

Re: [gmx-users] out of disk space error

hi .. thanks for the reply.. but does it has to do something with disk space error ?? amin wrote > Hi. You can probably try to increase the values of nstxout, nstvout, > nstcalcenergy, nstenergy etc. to something like 2000 or 5000 and rerun. > 100 seems very small. > > Amin. > > On 2013-12-

Re: [gmx-users] Atomistic Simulation

Thanks you all for the suggestions. I wil try then... -- View this message in context: http://gromacs.5086.x6.nabble.com/Atomistic-Simulation-tp5012984p5013039.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive a

[gmx-users] reproducing results of an old article from Daura et al.

Dear users, I have been trying to reproduce from Daura et al. (http://www.sciencedirect.com/science/article/pii/S002228369891885X). In this paper the use the gromos43A1 forcefield to study the reversible folding of a beta-heptapeptide. I have use the same forcefield with the PME and LINCS algorit

Re: [gmx-users] out of disk space error

I think so. You are outputting the information too often i.e every 0.2 ps i.e. 5000 times per ns. See this thread http://comments.gmane.org/gmane.science.biology.gromacs.user/32721 Amin. On 2013-12-04 15:11, vaani wrote: > hi .. > thanks for the reply.. > but does it has to do something

[gmx-users] Fwd: Warning while loading .gro generated from .pdb with pdb2gmx

When I convert attached .pdb file to .gro using: pdb2gmx -quiet -ff amber99 -water none -f ${MOL}.pdb -o ${MOL}Initial.gro -i ${MOL}.itp -p ${MOL}.top -ignh the generated .gro file causes vmd (1.9.1) to show this warning while loading it: Warning) Unusual bond between residues: 905 (protein) and

Re: [gmx-users] Warning while loading .gro generated from .pdb with pdb2gmx

Looks like I am unable to attach the offending pdb file because mailing list imposes a size limit of 50 Kb for the whole message (including attachments) and the file is around 1 MB, what way do you prefer for providing the file? Thanks for the info 2013/12/4 Pacho Ramos > When I convert attach

[gmx-users] rcoulomb, rvdw and rlist value

Dear Users I want to use parmbsc0 force field for DNA-ligand interaction. I want some information about value of rcoulomb, rvdw and rlist in mdp file during equilibration & production steps. I set these values 1 nm . Is it correct? Best regards -- Gromacs Users mailing list * Please search the

Re: [gmx-users] Atomistic Simulation

Hello users, After downloading the toluene.pdb file of a toluene molecule and its forcefield tolu.itp from "Automated Topology Builder" and saved in the root /usr/share/gromacs/top/gromos53a6.ff I use the next comand i order to convert the pdb format to .gro : *

[gmx-users] rcoulomb, rvdw and rlist values

Dear Users I want to use parmbsc0 force field for DNA-ligand interaction. I want some information about value of rcoulomb, rvdw and rlist in mdp file during equilibration & production steps. I set these values 1 nm . Is it correct? Best regards -- Gromacs Users mailing list * Please search the

Re: [gmx-users] heating

Honestly, I see no sense in heating from from 0 to 300 K. As long as the system is in the solid state, it is probably not informative to handle it. Thus heating, if any, might start from the freezing point. Moreover, heating from 0 to 300 K over 100 ps is so fulminant that it does not correspond to

Re: [gmx-users] rcoulomb, rvdw and rlist values

the only way to find out, whether it is correct, is to read the paper, where the force field was derived. Dr. Vitaly V. Chaban On Wed, Dec 4, 2013 at 12:17 PM, kiana moghaddam wrote: > Dear Users > I want to use parmbsc0 force field for DNA-ligand interaction. I want some > information about

Re: [gmx-users] rcoulomb, rvdw and rlist values

The values of these cutoffs is specific to each forcefield - it's best not to change them if you can't justify why. It doesn't say in the original paper where they created parmbsc0 as far as I can tell but perhaps you can find a later paper where they do say. Good luck. > Dear Users > I want to us

Re: [gmx-users] heating

Is that really so fulminant? For a gram of water it takes 1.2 kJ. Over 100 ps that requires only a modest laser :) Tsjerk On Wed, Dec 4, 2013 at 12:27 PM, Dr. Vitaly Chaban wrote: > Honestly, I see no sense in heating from from 0 to 300 K. As long as > the system is in the solid state, it is

Re: [gmx-users] constraint in Production

On 12/3/13 11:43 AM, kiana moghaddam wrote: Dear Users I have a problem about production step in MD simulation. Can this step be run with constraints or unconstraints? Whether or not you use constraints depends on whether you need them. It is quite common to constrain at least the bonds

Re: [gmx-users] heating

Hi Kiana, Simulated annealing will take your system temperature distribution to the target temperature. So, I always start at the starting point. Hi Vitaly, Heating slowly (over many ns) from 0K-xK seems to be an important step in crystal simulations performed by other members in my lab...in fact,

Re: [gmx-users] Bug #554: pdb2gmx proton naming compliancy

On 12/3/13 4:51 PM, Kibalchenko, Mikhail wrote: Dear Users, does anyone know what was the resolution of this bug? http://redmine.gromacs.org/issues/554 How does one handle pdb2gmx with PDB files and avoid errors like this? Atom HB3 in residue ASP 2 was not found in rtp entry ASP with 14 atom

Re: [gmx-users] How to make OPLS forcefield?

On 12/4/13 2:59 AM, Pham Kim wrote: Dear Gromacs User, I am the beginner using Gromacs. I have created polyethylene .gro and .top using http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg but in that .top, forcefield is gmx.ff/forcefield.itp. I want to simulate with OPLS forcefield. Please help m

Re: [gmx-users] out of disk space error

On 12/4/13 5:24 AM, a...@imtech.res.in wrote: I think so. You are outputting the information too often i.e every 0.2 ps i.e. 5000 times per ns. See this thread http://comments.gmane.org/gmane.science.biology.gromacs.user/32721 It is unlikely that a few hundred ps of NVT would fill up some

Re: [gmx-users] Fwd: Warning while loading .gro generated from .pdb with pdb2gmx

On 12/4/13 5:33 AM, Pacho Ramos wrote: When I convert attached .pdb file to .gro using: pdb2gmx -quiet -ff amber99 -water none -f ${MOL}.pdb -o ${MOL}Initial.gro -i ${MOL}.itp -p ${MOL}.top -ignh the generated .gro file causes vmd (1.9.1) to show this warning while loading it: Warning) Unusua

Re: [gmx-users] Atomistic Simulation

On 12/4/13 6:15 AM, panzu wrote: Hello users, After downloading the toluene.pdb file of a toluene molecule and its forcefield tolu.itp from "Automated Topology Builder" and saved in the root /usr/share/gromacs/top/gromos53a6.ff I use the next comand i order to convert the pdb format to .gro

Re: [gmx-users] GROMACS 4.6.5 is released

On Wed, Dec 4, 2013 at 10:15 AM, João Henriques wrote: > Soon enough we will have daily releases :P I hope you're not suggesting that we should release less frequently! :) > Mark, can you please elaborate just a tiny bit longer on how relevant were > the "GPU-load balancing and GPU-sharing bugs

Re: [gmx-users] Atomistic Simulation

so How do I convert from .pdb to .gro the ? -- View this message in context: http://gromacs.5086.x6.nabble.com/Atomistic-Simulation-tp5012984p5013058.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://w

Re: [gmx-users] Atomistic Simulation

so How do I convert from .pdb to .gro? -- View this message in context: http://gromacs.5086.x6.nabble.com/Atomistic-Simulation-tp5012984p5013059.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.

Re: [gmx-users] Atomistic Simulation

On 12/4/13 9:06 AM, panzu wrote: so How do I convert from .pdb to .gro the ? You don't technically need one: http://www.gromacs.org/Documentation/File_Formats/Coordinate_File If you prefer to use .gro format, just convert with editconf. The job of pdb2gmx is to produce a topology; the ou

Re: [gmx-users] Atomistic Simulation

You don't need to. Later processing steps such as editconf, genbox and grompp can read .pdb files. > so How do I convert from .pdb to .gro the ? > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Atomistic-Simulation-tp5012984p5013058.html > Sent from the GROMACS Users Foru

Re: [gmx-users] Atomistic Simulation

On Dec 4, 2013, at 3:06 PM, panzu wrote > so How do I convert from .pdb to .gro the ? Use editconf. Carsten -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Sup

Re: [gmx-users] Atomistic Simulation

Hi there, you can use editconf -f file.pdb -o file.gro Cheers, Ricardo. --- Biological Chemistry and Physics Faculty of Pharmaceutical Sciences at Ribeirão Preto University of São Paulo - Brazil - Mensagem original - > De: "panzu" > Para: gmx-us...@gromacs.org > Enviadas: Quar

Re: [gmx-users] Atomistic Simulation

You don't need to. Gromacs accepts pdb, gro and several other coordinate file formats. On 4 Dec 2013 14:30, panzu wrote: so How do I convert from .pdb to .gro? -- View this message in context: http://gromacs.5086.x6.nabble.com/Atomistic-Simulation-tp5012984p5013059.html Sent from the GROMACS

[gmx-users] deformation in cnt

Dear gromacs users My system contains protein + cnt + water molecules (system.gro). cnt is infinite and z dimension of box is equal to the length of the cnt axis. -- em.mdp file is as follows: integrator = steep nstep

Re: [gmx-users] Atomistic Simulation

The thing is when I tray to use the grompp comand: bash >> g_grompp -f grompp.mdp -c tolu.pdb -p topol.top Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5# NOTE 1 [file grompp.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy --

Re: [gmx-users] Atomistic Simulation

On 12/4/13 9:50 AM, panzu wrote: The thing is when I tray to use the grompp comand: bash >> g_grompp -f grompp.mdp -c tolu.pdb -p topol.top Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5# NOTE 1 [file grompp.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setti

[gmx-users] force field for prodrg server

hi dear Justin   You've written the following context in your tutorial:     Force field (GROMOS96.1/GROMOS87): "GROMOS96.1" refers to the first version of the GROMOS96 force field, 43A1. "GROMOS87" refers to the (outdated!) GROMOS87 force field. Choose "GROMOS96.1" to get 43A1 parameters for ou

Re: [gmx-users] force field for prodrg server

On 12/4/13 10:24 AM, Mahboobeh Eslami wrote: hi dear Justin You've written the following context in your tutorial: Force field (GROMOS96.1/GROMOS87): "GROMOS96.1" refers to the first version of the GROMOS96 force field, 43A1. "GROMOS87" refers to the (outdated!) GROMOS87 force field. Choo

[gmx-users] deformation in cnt

Dear Justin Thanks for your reply z dimension of box is exactly equal to the length of the cnt axis. > The box size should be (length of CNT) + (bond length). What value is appropriate for bond length to add length of CNT? So, using freeze is not suitable for my system (neither in the em step

Re: [gmx-users] Fwd: Warning while loading .gro generated from .pdb with pdb2gmx

Thanks for your reply. Anyway, looks like every pdb I convert using above command leads to this warning, for example, when I try with 1TIT: http://www.pdb.org/pdb/explore/explore.do?structureId=1TIT I also get the same kind of warning while loading generated .gro file, telling me that something is

Re: [gmx-users] GROMACS 4.6.5 is released

I did read it and wasn't very enlightened by it, that's why I kindly requested for further information on the subject. "under certain circumstances (but quite often), a segmentation fault occurs" definitely sounds serious, but it's not very explicit. In any case, I'll request a new install and tel

[gmx-users] atom name - topology

Dear Gmx Users, My molecule contains 2516 atoms made of 5 type of beads: BAS, POL, NON, ACI, GLY and I want to create a topology. Is it possible to make one residue of one [ moleculetype ] with this number of atoms so that: [ moleculetype ] ; Namenrexcl MOL3 [ atoms ] ;

Re: [gmx-users] deformation in cnt

On 12/4/13 10:48 AM, Atila Petrosian wrote: Dear Justin Thanks for your reply z dimension of box is exactly equal to the length of the cnt axis. The box size should be (length of CNT) + (bond length). What value is appropriate for bond length to add length of CNT? Whatever the lengths

Re: [gmx-users] force field for prodrg server

On 12/4/13 11:03 AM, Mahboobeh Eslami wrote: dear Justin thanks for reply I don't find tutorial for ATB and I don't know that which files are used for itp It works much like PRODRG. You can upload coordinates or draw the molecule. and gro files from ATB result, Moreover in gromacs site is

Re: [gmx-users] flags for internal coordinates restraints

LINCS or SHAKE (all atoms) can be used for this? or some better options available? it can be seen as two protein helix interacting with each other as rigid bodies... thanks On Wed, Nov 27, 2013 at 12:35 AM, gromacs query wrote: > Dear All > > I want to simulate two polymer chains as rigid bod

Re: [gmx-users] Fwd: Warning while loading .gro generated from .pdb with pdb2gmx

On 12/4/13 11:22 AM, Pacho Ramos wrote: Thanks for your reply. Anyway, looks like every pdb I convert using above command leads to this warning, for example, when I try with 1TIT: http://www.pdb.org/pdb/explore/explore.do?structureId=1TIT I also get the same kind of warning while loading gener

Re: [gmx-users] atom name - topology

On 12/4/13 11:48 AM, Steven Neumann wrote: Dear Gmx Users, My molecule contains 2516 atoms made of 5 type of beads: BAS, POL, NON, ACI, GLY and I want to create a topology. Is it possible to make one residue of one [ moleculetype ] with this number of atoms so that: [ moleculetype ] ; Name

Re: [gmx-users] force field for prodrg server

dear Justin thanks for reply I don't find tutorial for ATB and I don't know that which files are used for itp and gro files from ATB result, Moreover in gromacs site is mentioned  that PRODRG is used  for GROMOS96 force field, 43A1. can I use ATB for 43A1 force field? On Wednesday, December 4

Re: [gmx-users] Updating GTX670 PCIE speed from 5GT/s to 8GT/s resulted in about 10% speedup of md_run.

Your suspicion is correct, the CPU is waiting >20% of the runtime for the GPU to finish. -- Henk -- View this message in context: http://gromacs.5086.x6.nabble.com/Updating-GTX670-PCIE-speed-from-5GT-s-to-8GT-s-resulted-in-about-10-speedup-of-md-run-tp5012945p5013082.html Sent from the GROMACS U

Re: [gmx-users] out of disk space error

On 12/4/13 5:24 AM, amin@.res wrote: > > > I think so. You are outputting the information too often i.e every 0.2 > ps i.e. 5000 times per ns. See this thread > > http://comments.gmane.org/gmane.science.biology.gromacs.user/32721 > It is unlikely that a few hundred ps of NVT would fill up someone

Re: [gmx-users] out of disk space error

If none of the earlier suggestions worked then, it could be a simple problem of power port from which you have connected your hard disk. Try reconnecting the hard disk and and retry running the mdrun. Posting the exact commands used while writing the output during mdrun, may help to trace the prob

Re: [gmx-users] GROMACS 4.6.5 is released

The first update on the redmine page does describe the source of the issue - although perhaps not in the most user-friendly manner. Translating it to a simple example, if you have dual-socket 8c nodes and 2 GPUs per node: mpirun -np 4 mdrun -ntomp 4 -gpu_id 0011 #single node 4 ranks per node, 2-w