Re: [gmx-users] MD simulations in the presence of osmolytes

That would be a question for the developers of the force fields. You can start by a google search of the osmolytes and force filed keywords ... > On Nov 19, 2013, at 2:23, Amjad Farooq wrote: > > Hi everyone, > > I am wondering whether it is possible to conduct MD simulations on a > protein

Re: [gmx-users] g_select

Dear justin; As usual, it is of your kindness to explain extensively. I will give it try and let you know. Best regards; semran 2013/11/18 Justin Lemkul > > > On 11/15/13 6:49 AM, SEMRAN İPEK wrote: > >> Dear gromacs users; >> >> I have been trying to find out the waters close to certain res

[gmx-users] ERROR when generated a rtp file with "grompp"

Dear all: I have such error below: Fatal error: number of coordinates in coordinate file (p_wateroil.gro, 55383) does not match topology (topol.top, 55421) it tells that the number of atoms are not same. In my top file: [ molecules ] ; Compound#mols Protein_chain_A 1 DO

Re: [gmx-users] nstlist and performances

Hi, I would be very careful about increasing nstlist for big systems. This can lead to nonphysical phenomena, especially for highly anisotropic systems. Check out http://pubs.acs.org/doi/abs/10.1021/ct3001359 There are other papers too... On Mon, Nov 18, 2013 at 9:50 PM, Mark Abraham wrote: > O

[gmx-users] Cannot write trajectory frame; maybe you are out of disk space?

dear all, i am getting following error on giving command for NVT equilibrations: mdrun -deffnm nvt -v -nt 8 File input/output error: Cannot write trajectory frame; maybe you are out of disk space? i have gromacs 4.6.4 version, 12.04 ubuntu, 7.9GiB memory and 976 GB Disk space, i am simulat

Re: [gmx-users] a query

ok ..thanks - thanks in advance :) -- View this message in context: http://gromacs.5086.x6.nabble.com/a-query-tp5012570p5012623.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Su

Re: [gmx-users] installing latest version of gromacs 4.6.3

can you please suggest me how to get this ..i am using bash shell - thanks in advance :) -- View this message in context: http://gromacs.5086.x6.nabble.com/installing-latest-version-of-gromacs-4-6-3-tp5012529p5012622.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com.

[gmx-users] MD simulations in the presence of osmolytes

Hi everyone, I am wondering whether it is possible to conduct MD simulations on a protein system in the presence of osmolytes such as TMAO and sucrose using an explicit water model. If not, how could this be implemented? Does any of the force fields available in GROMACS support the inclusion of

[gmx-users] How to add motion of center of mass into temperature coupling?

Hello All, I am studying amino acid diffusion in water flow. I first tried to add y direction acceleration to all water molecules while fix center of mass of the system. But found water molecules do not diffuse in the y direction. Then I tried to remove center of mass correction by setting com

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 115, Issue 69

On Mon, Nov 18, 2013 at 11:11 PM, Justin Lemkul wrote: > > > On 11/18/13 5:05 PM, Hari Pandey wrote: > >> Dear Dr. Tsjerk, >> Many many thanks for your help. This makes me some sense but still I am >> confused about that you indicated me to look out the gromacs/share >> directory. In my gromacs

Re: [gmx-users] Average number of salt bridge

Thank you Justin... that's what I was looking for ... On Tue, Nov 19, 2013 at 2:24 AM, Justin Lemkul wrote: > > > On 11/14/13 10:18 PM, bharat gupta wrote: > >> Hi, >> >> How can I calculate the average number of salt bridges between two >> residues >> during the entire simulation ??... >> >> >

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 115, Issue 69

On 11/18/13 5:05 PM, Hari Pandey wrote: Dear Dr. Tsjerk, Many many thanks for your help. This makes me some sense but still I am confused about that you indicated me to look out the gromacs/share directory. In my gromacs, I have following directory tree: gromacs/share/gromacs/top I did not

Re: [gmx-users] about using do_dssp for a few residues

Sounds good! Thank you Justin! Kind regards, Jianqing -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: 18 November 2013 21:51 To: Discussion list for GROMACS users S

Re: [gmx-users] about using do_dssp for a few residues

On 11/18/13 4:08 PM, jianqing wrote: Will appreciate if anyone could provide any suggestions! The only secondary structure that should be affected would be beta-sheets, since their hydrogen bonding patterns are based on non-local interactions. Helices, bends, and turns should show up inde

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 115, Issue 69

Dear Dr. Tsjerk, Many many thanks for your help. This makes me some sense but still I am confused about that you indicated me to look out the gromacs/share  directory.   In my gromacs, I have following directory tree: gromacs/share/gromacs/top I did not found a format. I am wandering what could be

Re: [gmx-users] about using do_dssp for a few residues

Will appreciate if anyone could provide any suggestions! Thanks a lot!! Jianqing -- View this message in context: http://gromacs.5086.x6.nabble.com/about-using-do-dssp-for-a-few-residues-tp5012521p5012608.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Use

Re: [gmx-users] problems with chain IDs for huge complex

Maybe the answer is to not worry about chain identifiers until analysis stages - you could probably just call everything chain A at the start. You can then create an index entry for each chain. See http://www.gromacs.org/Documentation/How-tos/Multiple_Chains > As far as I remember in pdb format yo

Re: [gmx-users] to study native cluster

Hey, Maybe this is useful: http://md.chem.rug.nl/~mdcourse/molmod2012/analysis.html Hope it helps, Tsjerk On Mon, Nov 18, 2013 at 6:56 PM, Shine A wrote: > Sir, > I did an MD simulation.Now I want to combine the techniques, principal > component (PC) analysis > and clustering, for revealing

Re: [gmx-users] problems with chain IDs for huge complex

Hi Tomek, Process each chain separately with pdb2gmx, rename the moleculetypes and combine them again. This is scriptable, but not entirely trivial. Renaming the moleculetype takes something like sed '/\[ *moleculetype *\]/{p;n;s/^.*$/NEWMOLECULETYPE/p}' itpfile Hope it helps, Tsjerk On Mon

Re: [gmx-users] problems with chain IDs for huge complex

As far as I remember in pdb format you can only use one character for chain id. On Mon, Nov 18, 2013 at 7:05 PM, wrote: > How about naming your chains AA-AZ then BA-BZ? You probably need to change > the chain names in the original structures rather than just renaming the > files. > > > Hi, > >

Re: [gmx-users] problems with chain IDs for huge complex

How about naming your chains AA-AZ then BA-BZ? You probably need to change the chain names in the original structures rather than just renaming the files. > Hi, > > I am preparing simulation of the ribosome and because of it size I am > force > to use A-Z and a-z to name all chains... > With pdb2g

Re: [gmx-users] a query

Try sending your problem in the same way you sent this email. They should be the same. Maybe it hadn't processed your subscription at the time you sent your problem and now it will work. > > > i have posted a problem in gronacs user forum ...but its saying that it > is not accepted by the mailing

[gmx-users] problems with chain IDs for huge complex

Hi, I am preparing simulation of the ribosome and because of it size I am force to use A-Z and a-z to name all chains... With pdb2gmx it is not a problem but with grompp I am ending up with this error (gromacs 4.6.3): Fatal error: moleculetype Protein_chain_b is redefined I figured out that for

[gmx-users] to study native cluster

Sir, I did an MD simulation.Now I want to combine the techniques, principal component (PC) analysis and clustering, for revealing major conformational changes in my protein and for finding native cluster. How can I do this in gromacs? Thanks in advance.

Re: [gmx-users] Membrane is shifted a lot during umbrella sampling

Hi Chris, The lipid of my system is DPPC, which is a neutral. However, the peptide is positively charged polyarginine. The membrane is shifted a lot when the peptide is embedded within it (i,e peptide restrained at the bilayer region). Therefore presence of peptide inside the membrane produces suc

Re: [gmx-users] installing latest version of gromacs 4.6.3

On 11/18/13 11:54 AM, vansh wrote: do i need to source it every time i will use gromacs ?? as this is what happening in my case.. If you don't configure your shell startup scripts to do it for you, yes. Otherwise, the 'source' statement can be added to whatever startup script your shell us

Re: [gmx-users] RF0 and g_energy

On 11/18/13 10:40 AM, Williams Ernesto Miranda Delgado wrote: Hello I made a rerun on a MD simulation using Reaction-Field-zero for electrostatics. When I analyze the *.edr file with g_energy, there appears Coul-SR and Coul-14. How can I get the Coulomb long range term? This is very important f

Re: [gmx-users] setting up simulation with mixed chain (nucleotide + amino acid)

On 11/18/13 8:26 AM, Tomek Wlodarski wrote: Hi, I would like to run simulation of short peptide (nascent chain) bound to tRNA (in amber ff). Do gromacs supports chains which have both protein and nucleic acid components? I have problem with termini of this chain: gromacs is trying to find 3'-

Re: [gmx-users] energy minimization erorr

On 11/18/13 2:36 AM, Archana Sonawani-Jagtap wrote: Hi, I am simulating a peptide in TFE-water system. I am getting following error: 1 particles communicated to PME node 4 are more than 2/3 times the cut-off out o f the domain decomposition cell of their charge group in dimension x. This usual

Re: [gmx-users] help about logfile

On 11/17/13 9:06 PM, cqgzc wrote: Hi Justin: Thanks for your reply. I checked the initial setting and the output file about simulation control (mdout.mdp and .log file) and found that it's ok. There are some strange results related to sample frequency (Statistics over *** steps using *** frames

Re: [gmx-users] how to pull both side

On 11/17/13 8:48 AM, Tom wrote: Dear All, Can gromacs pull both sides (end) of a body way? for example pulling two end of a cylinder unitl it breaks. I knew Gromacs can pull two bodies (A and B) objects away. Can someone inform about this functionality of pulling (both sides/end of a same bo

Re: [gmx-users] membrane protein tutorial

On 11/15/13 10:04 AM, leila karami wrote: Dear Justin I am using your tutorial (membrane protein) for my system. I inserted my peptid into lipid bilayer. Now I want to solvate with water using genbox tool. To remove those water molecules are into lipid bilayer, I want to use keepbyz.pl script

Re: [gmx-users] g_select

On 11/15/13 6:49 AM, SEMRAN İPEK wrote: Dear gromacs users; I have been trying to find out the waters close to certain residue. Here is my selection dat: waterO = name "OW"; close = waterO and within 0.35 of resnr 334; close ** I have been using the comma

Re: [gmx-users] Average number of salt bridge

On 11/14/13 10:18 PM, bharat gupta wrote: Hi, How can I calculate the average number of salt bridges between two residues during the entire simulation ??... Unless you've got some wildly noncanonical residues, this is a binary function. Either the salt bridge exists (1) or does not (0).

Re: [gmx-users] installing latest version of gromacs 4.6.3

do i need to source it every time i will use gromacs ?? as this is what happening in my case.. - thanks in advance :) -- View this message in context: http://gromacs.5086.x6.nabble.com/installing-latest-version-of-gromacs-4-6-3-tp5012529p5012586.html Sent from the GROMACS Users Forum mailing

Re: [gmx-users] nstlist and performances

On Mon, Nov 18, 2013 at 3:58 PM, Riccardo Concu wrote: > Dear all, > I'm running a simulation of a quite big system and is running very low > 2ns/day. I need to boost-up the simulation speed but i don't know how. I > tried to use nstlist=10 but the system crash due to too many lincs > warning. Pr

Re: [gmx-users] Membrane is shifted a lot during umbrella sampling

Hi All, Thank you very much for your kind reply. But obviously, if I put some position restraints on membrane then there will be some artifacts. Also, Chris has mentioned that it is a kind of bug in gromacs. please help me how do I resolve this issue sudipta On Fri, Oct 4, 2013 at 9:33 PM, Ju

Re: [gmx-users] RF0 and g_energy

Hello I made a rerun on a MD simulation using Reaction-Field-zero for electrostatics. When I analyze the *.edr file with g_energy, there appears Coul-SR and Coul-14. How can I get the Coulomb long range term? This is very important for making LIE calculations. I used AMBER99SB FF and rlist = 1.2 rc

Re: [gmx-users] (no subject)

On Mon, Nov 18, 2013 at 2:28 PM, Shima Arasteh wrote: > Dear gmx users, > > > My simulated system contains is composed of lipid, protein and water > molecules. > The NPT and NVT steps were done with position restraints on protein atoms. > Then I removed the position restraints by line ";define =

Re: [gmx-users] Windows/x64, VCVS2012 compiled, crash on checkpoint writing

On Fri, Nov 15, 2013 at 6:43 PM, Mirco Wahab < mirco.wa...@chemie.tu-freiberg.de> wrote: > Gromacs 4.6.4 compiles (and links) perfectly w/VS2012 > and nvcc from CUDA 5.5 on windows/x64 > (MSVC 2012 Version 11.0.60610.01 Update 3). > > But -- when compiled with VS2012 (because of linking > against

[gmx-users] nstlist and performances

Dear all, I'm running a simulation of a quite big system and is running very low 2ns/day. I need to boost-up the simulation speed but i don't know how. I tried to use nstlist=10 but the system crash due to too many lincs warning. Previously I minimized the system, then annealed and now i need to ru

Re: [gmx-users] GROMACS-4.6.3 CUDA version on multiple nodes each having 2 GPUs

On Mon, Nov 18, 2013 at 12:06 PM, Prajapati, Jigneshkumar Dahyabhai < j.prajap...@jacobs-university.de> wrote: > Hi Carsten, > > Thanks for reply. Everything is working fine on single node. The problem > starts when I move to two nodes. > > I have tried with the option that you have mentioned earl

[gmx-users] position restraint term

Dear gmx users, My simulated system contains is composed of lipid, protein and water molecules. The NPT and NVT steps were done with position restraints on protein atoms. Then I removed the position restraints by line ";define  = -DPOSRES_LIPID -DPOSRES". But I still see the position restrai

[gmx-users] position restraint term

Dear gmx users, My simulated system contains is composed of lipid, protein and water molecules. The NPT and NVT steps were done with position restraints on protein atoms. Then I removed the position restraints by line ";define  = -DPOSRES_LIPID -DPOSRES". But I still see the position restra

[gmx-users] (no subject)

Dear gmx users, My simulated system contains is composed of lipid, protein and water molecules. The NPT and NVT steps were done with position restraints on protein atoms. Then I removed the position restraints by line ";define  = -DPOSRES_LIPID -DPOSRES". But I still see the position restraint

[gmx-users] setting up simulation with mixed chain (nucleotide + amino acid)

Hi, I would like to run simulation of short peptide (nascent chain) bound to tRNA (in amber ff). Do gromacs supports chains which have both protein and nucleic acid components? I have problem with termini of this chain: gromacs is trying to find 3'- terminus of RNA - but it can't because terminus

Re: [gmx-users] can not write coordinate file when running ibi

Dear Zhichen, This is not the appropriate forum for your query. It seems you are using votca for coarse grained simulations. Please post at votca@googlegroups.comrelating all your votca queries. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Mon, Nov 18, 2013 at 10:49 AM, cqgzc wrote:

Re: [gmx-users] Cannot write trajectory frame; maybe you are out of disk space?

Run somewhere where you have write permissions, like your home directory. Don't run in root file space, or as root! Mark On Nov 18, 2013 1:04 PM, "vansh" wrote: > dear all, > i am getting following error on giving command: mdrun -deffnm nvt -v -nt 8 > File input/output error: > Cannot write tra

Re: [gmx-users] Replicating triclinic unit cells

genconf can't replicate the triclinic cell that you gave it (e.g. created with editconf)? Mark On Sun, Nov 17, 2013 at 9:04 PM, Eudes Fileti wrote: > Hi GMX users > I need replicate a triclinic unit cell. However, both > genconf and topotools (VMD plugin) generate only > orthorrombic cells. An

Re: [gmx-users] installing latest version of gromacs 4.6.3

Your system is configured such that it recognizes the (old) version of GROMACS you could get with the command it lists. Since you want the latest version (which is no longer 4.6.3!) do what you've done and make sure you finish reading http://www.gromacs.org/Documentation/Installation_Instructions#4

Re: [gmx-users] GROMACS-4.6.3 CUDA version on multiple nodes each having 2 GPUs

Hi Szilárd, My apologies for misunderstanding. The old thread I mentioned is not mine, I just found it on website. Unlike that thread, our nodes have homogeneous hardware. I tried all the options and everything looks perfect on a single node. I started to face problems when I switched to tw

Re: [gmx-users] installing latest version of gromacs 4.6.3

Try: source /usr/local/gromacs/bin/GMXRC and read 4.11. Getting access to GROMACS after installation ​on page http://www.gromacs.org/Documentation/Installation_Instructions On 17 November 2013 09:30, vansh wrote: > > hello all, > > I followed below mentioned instructions on how to install late

Re: [gmx-users] restart failed

On Sat, Nov 16, 2013 at 10:46 AM, xiao wrote: > Hi all gromacs users, > > My simulation crashed, and i try to restart it by using the following > command: mdrun -s topol.tpr -cpi state.cpt > Not using -deffnm means mdrun expects to write traj.trr, traj.xtc, ener.edr... > The version of the so

Re: [gmx-users] GROMACS-4.6.3 CUDA version on multiple nodes each having 2 GPUs

Hi Carsten, Thanks for reply. Everything is working fine on single node. The problem starts when I move to two nodes. I have tried with the option that you have mentioned earlier and this is the error I got , mpirun -np 4 mdrun mismatching number of PP MPI processes and GPUs per node. mdrun wa

Re: [gmx-users] GROMACS 4.6.4 is released

Thanks Mark. On 14 Nov 2013, at 10:20, Mark Abraham wrote: > Hi, > > Good question. That is our hope, from the way we have selected and > implemented the changes in 4.6.x series. Except actual bug fixes, of > course! The idea is that the new patch release implements the same physics, > so a res

[gmx-users] test gmx-users, please ignore

-- gromacs.org_gmx-users mailing listgromacs.org_gmx-users@maillist.sys.kth.se https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to t

[gmx-users] energy minimization erorr

Hi, I am simulating a peptide in TFE-water system. I am getting following error: 1 particles communicated to PME node 4 are more than 2/3 times the cut-off out o f the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. bel

[gmx-users] a query

i have posted a problem in gronacs user forum ...but its saying that it is not accepted by the mailing list yet.. althuogh i am already a subscriber to it.. please suggest -- VANDNA JRF C/O Dr. Girish Sahni Protein Science lab Phone No. 0172-2690830 Institurte of Microbial Technology (IMT

[gmx-users] can not write coordinate file when running ibi

Hi: When I am running the ibi procedure, I get the following error message: A coordinate in file conf.gro does not contain a '.' Additionally, I check the coordinate file of confout.gro in step_001. It showed that 'nan' symbol appeared in confout.gro. Just like: 856 1RDX

[gmx-users] Cannot write trajectory frame; maybe you are out of disk space?

dear all, i am getting following error on giving command: mdrun -deffnm nvt -v -nt 8 File input/output error: Cannot write trajectory frame; maybe you are out of disk space? i have gromacs 4.6.4 version, 12.04 ubuntu, 7.9GiB memory and 976 GB Disk space, i am simulating 414aa long protein for 10n

Re: [gmx-users] help about logfile

Hi Justin: Thanks for your reply. I checked the initial setting and the output file about simulation control (mdout.mdp and .log file) and found that it's ok. There are some strange results related to sample frequency (Statistics over *** steps using *** frames in .log file) as described below:

[gmx-users] Average number of salt bridge

Hi, I want to calculate the average number of salt bridge interactions between two residues. I used g_saltbr it gives the details for all the residues. Using g_dist I calculated the distance between the charged group of those two residues, but I want a number for salt-bridges like g_hbond gives ??

[gmx-users] Replicating triclinic unit cells

Hi GMX users I need replicate a triclinic unit cell. However, both genconf and topotools (VMD plugin) generate only orthorrombic cells. Anyone knows some free software or script to do that? eef ___ Eudes Eterno Fileti Instituto de Ciência e Tecnologia da UNIFESP

[gmx-users] how to pull both side

Dear All, Can gromacs pull both sides (end) of a body way? for example pulling two end of a cylinder unitl it breaks. I knew Gromacs can pull two bodies (A and B) objects away. Can someone inform about this functionality of pulling (both sides/end of a same body)? Thanks a lot! Thomas -- grom

[gmx-users] installing latest version of gromacs 4.6.3

hello all, I followed below mentioned instructions on how to install latest version of GROMACS latest version of Gromacs and installed it but now when I run gromacs, it is telling me gromacs is not install you can install it by typing "sudo apt-get install gromacs" which is just installing it fro

[gmx-users] membrane protein tutorial

Dear JustinI am using your tutorial (membrane protein) for my system.I inserted my peptid into lipid bilayer. Now I want to solvate withwater using genbox tool.To remove those water molecules are into lipid bilayer, I want to usekeepbyz.pl script by Chris Neale. In step 4 of this script:4. use vi t

[gmx-users] failed restart

Hi all gromacs users, My simulation crashed, and i try to restart it by using the following command: mdrun -s topol.tpr -cpi state.cpt The version of the software is 4.5.4, and i got the following error: File appending requested, but only 1 of the 4 output files are present Output files present: m

[gmx-users] restart failed

Hi all gromacs users, My simulation crashed, and i try to restart it by using the following command: mdrun -s topol.tpr -cpi state.cpt The version of the software is 4.5.4, and i got the following error: File appending requested, but only 1 of the 4 output files are present Output files pre

[gmx-users] Fwd: remd

sir, I have a basic doubt about remd simulation. In remd is it possible to run 16 replicas in 8 processors? -- gromacs.org_gmx-users mailing listgromacs.org_gmx-users@maillist.sys.kth.se https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users * Please search the archive at ht

Re: [gmx-users] RF0 and g_energy

Hello I made a rerun on a MD simulation using Reaction-Field-zero for electrostatics. When I analyze the *.edr file with g_energy, there appears Coul-SR and Coul-14. How can I get the Coulomb long range term? This is very important for making LIE calculations. I used AMBER99SB FF and rlist = 1.2 rc

[gmx-users] Windows/x64, VCVS2012 compiled, crash on checkpoint writing

Gromacs 4.6.4 compiles (and links) perfectly w/VS2012 and nvcc from CUDA 5.5 on windows/x64 (MSVC 2012 Version 11.0.60610.01 Update 3). But -- when compiled with VS2012 (because of linking against CUDA 5.5 is only possible then - in contrast to VS2010), mdrun crashes on writing the checkpoint fil

[gmx-users] about using do_dssp for a few residues

Dear all, I was playing "do_dssp" command in the last a few days. If I want to know the secondary structures of all the residues on the protein over the trajectory, everything seems good! However, the obtained picture (ss.xpm->ss.eps) is obviously too colourful, as all the residues are shown on

[gmx-users] membrane protein tutorial

Dear Justin I am using your tutorial (membrane protein) for my system. I inserted my peptid into lipid bilayer. Now I want to solvate with water using genbox tool. To remove those water molecules are into lipid bilayer, I want to use keepbyz.pl script by Chris Neale. In step 4 of this script: 4.

Re: [gmx-users] How to construct mixed lipid bilayer (Björn Sommer)

Am 13.11.2013 14:51, schrieb gmx-users-requ...@gromacs.org: Message: 4 Date: Wed, 13 Nov 2013 18:44:08 +0530 From: Nikhil Agrawal Subject: [gmx-users] How to construct mixed lipid bilayer To:gmx-us...@gromacs.org Message-ID: Content-Type: text/plain; charset=ISO-8859-1 Dear All, can an

[gmx-users] test 2, please ignore

-- gromacs.org_gmx-users mailing listgromacs.org_gmx-users@maillist.sys.kth.se https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to t

[gmx-users] Average number of salt bridge

Hi, How can I calculate the average number of salt bridges between two residues during the entire simulation ??... Thanks --- Bharat -- gromacs.org_gmx-users mailing listgromacs.org_gmx-users@maillist.sys.kth.se https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users * Ple

[gmx-users] g_select

Dear gromacs users; I have been trying to find out the waters close to certain residue. Here is my selection dat: waterO = name "OW"; close = waterO and within 0.35 of resnr 334; close ** I have been using the command of "g_select -f md_30.xtc -b 3 -e 300

[gmx-users] about using do_dssp for a few residues

Dear all, I was playing "do_dssp" command in the last a few days. If I want to know the secondary structures of all the residues on the protein over the trajectory, everything seems good! However, the obtained picture (ss.xpm->ss.eps) is obviously too colourful, as all the residues are shown on

[gmx-users] Average number of salt bridge

Hi, How can I calculate the average number of salt bridges between two residues during the entire simulation ??... Thanks --- Bharat -- gromacs.org_gmx-users mailing listgromacs.org_gmx-users@maillist.sys.kth.se https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users * Ple

[gmx-users] gmx to amber

Dear GMX Users I want to access gmxtoamber script to convert gromacs output to amber.  Could anyone give me this script? Best Regards Kiana -- gromacs.org_gmx-users mailing listgromacs.org_gmx-users@maillist.sys.kth.se https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users * Plea

[gmx-users] error with make install command

make installcommand gave following error output output: [ 0%] Building NVCC (Device) object src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o cc: error trying to exec 'cc1plus': execvp: No such file or directory CMake Error at gpu_utils_generated_gpu_utils.

Re: [gmx-users] GROMACS-4.6.3 CUDA version on multiple nodes each having 2 GPUs

Hi Jignesh, I don't get what the issue is, you need to be more specific than "fails" and "none of them worked." You should provide exact command line, stderr output and log files as we can't get what exactly is the error you are getting. Previously you seemed to hint that you had inhomogeneous ha

Re: [gmx-users] GROMACS-4.6.3 CUDA version on multiple nodes each having 2 GPUs

Hi, if you run on a single node with 2 GPUs, this command line should work: > mpirun -np 2 mdrun -v -deffnm $configfile If you run on two nodes, try this: mpirun -np 4 mdrun Choosing -np equal to the total number of GPUs should work (although it might not be the best option performance-wise).

[gmx-users] installation error : mpi compiler not found

while installing gromacs ..i gave following command: cmake .. -DGMX_GPU=ON -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/home/marydoe/programs to build with GPUs, MPI and install in a custom location. error : CMake Warning at cmake/gmxGetCompilerInfo.cmake:90 (message): The version of the C and C++

Re: [gmx-users] GROMACS 4.6.4 is released

Hi, Good question. That is our hope, from the way we have selected and implemented the changes in 4.6.x series. Except actual bug fixes, of course! The idea is that the new patch release implements the same physics, so a restart should be seamless. You can take any 4.6.x and restart it on a differ

Re: [gmx-users] remd

Yes, just tell your MPI setup to do that. Performance will degrade, and mdrun will complain that it can't set processor affinities, which is fine for your purpose. Mark On Nov 14, 2013 7:06 AM, "Shine A" wrote: > sir, > > I have a basic doubt about remd simulation. In remd is it possible to

Re: [gmx-users] Recompile Gromacs 4.6.3

Hello, all Could any one help me on this problem? I intend to make some modification on minimize.c in mdlib. Do I need to do "cmake make make install" all over again? Or is there a quick way for recompiling? Thanks for any tips. JhengWei Li Institute of Atomic and Molecular Sciences, Academia Sin

Re: [gmx-users] Recompile Gromacs 4.6.3

Sorry , somehow I didn't receive the reply message on mailbox And thanks for Mark's help!! JhengWei Li Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan On Thu, Nov 14, 2013 at 6:02 PM, Jheng Wei Li wrote: > Hello, all > Could any one help me on this problem? > I i

Re: [gmx-users] remd

On 11/14/13 1:05 AM, Shine A wrote: sir, I have a basic doubt about remd simulation. In remd is it possible to run 16 replicas in 8 processors? No. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutica