[gmx-users] (no subject)

dear gromacs users I tried to add ions to my .gro file as it was showing the warning that:- System has non zero charge. But a new error occured when i run grompp command again:- Program grompp_d, VERSION 4.6.3 Source code file: /build/buildd/gromacs-4.6.3/src/kernel/toppush.c, line: 1412 Fatal er

Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using

Hi Tsierk, Hi tried your protocol without success. I have also tried different centering combination (on protein/DNA/Ligand/Protein+DNA/DNA+Ligand/Protein+ligand) and different flags combo (-pbc mol -ur compact/rect). I have added also the pbc whole before -pbc nojump but the result at the end is

Re: [gmx-users] entropy vs time plot

On 2014-05-21 06:54, tarak karmakar wrote: Hi Tsjerk, Thanks for the quick reply. I did the following g_covar -f ../../npt_prod -s ../../npt_prod -n loop_II.ndx -o eigenval -v eigenvec.trr -av average.pdb -b 0 -e 1 g_anaeig -v eigenvec -entropy -temp 300 -b 0 -e 1 What I want to plot is

[gmx-users] topology in local?

Dear GROMACS user community, I have the following problem: I would like to let a simulation run on a computer where another simulation, prepared by another user, is already running; my simulation and the simulation of the other user need different topologies (I mean, for example, the files ffbonde

Re: [gmx-users] topology in local?

Dear Nicola, Any number of users can use the top directory, with the choice of his/her force field. If anyone wants to edit the top files, then he can copy the top directory to somewhere and use the GMXLIB variable. You can use the GMXLIB environment variable, and point your top directory's path

Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using

Hey Vito, Can you paste your exact workflow? Cheers, Tsjerk On Wed, May 21, 2014 at 9:53 AM, Vito Genna wrote: > Hi Tsierk, > > Hi tried your protocol without success. > I have also tried different centering combination (on > protein/DNA/Ligand/Protein+DNA/DNA+Ligand/Protein+ligand) > and di

Re: [gmx-users] topology in local?

On 5/21/14, 5:22 AM, Nicola Staffolani wrote: Dear GROMACS user community, I have the following problem: I would like to let a simulation run on a computer where another simulation, prepared by another user, is already running; my simulation and the simulation of the other user need different

[gmx-users] grompp

Dear Gromacs users, I am new to Gromacs. I am trying to add ions to my protein system. After typing command: grompp -f grompp.mdp -c EcoLon6mer-sol.gro -p EcoLon6mer.top -o genion_input.tpr where the grompp.mdp contains: ; ions.mdp - used as input into grompp to generate ions.tpr ; Parameters d

Re: [gmx-users] topology in local?

Dear Chandan, thank you for your reply. Anyway, before making any change to my GROMACS and therefore risking to "destroy", can I ask again your advice? From what I have read about environment variables, if another simulation is already runn

Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using

Hi Tsierk, Ok. 1) trjconv_mpi -s em.tpr -f test.xtc -o test-nojump.xtc -pbc nojump (output System) 2) trjconv_mpi -s em.tpr -f test-nojump.xtc -o test-center.xtc -center -n index.ndx (centering all the frames on different targets Protein/DNA ecc ecc) (output system) 3) trjconv_mpi -s em.tpr

Re: [gmx-users] topology in local?

and grompp runs quite quickly, that's perfect, much less risky (for such a clumsy programmer like me!!) than changing the address $GMXLIB is pointing too (many won't agree on it, I guess ;) Thank you Justin!! Nicola On Wed, May 21, 2014 at 12:00 PM, Justin Lemkul wrote: > > > On 5/21/14, 5:22

Re: [gmx-users] topology in local?

On Wed, May 21, 2014 at 3:57 PM, Nicola Staffolani wrote: > Dear Chandan, > > thank you for your reply. Anyway, before making any change to my GROMACS > and therefore risking to "destroy", can I ask again your advice? > Sure. > > From what I have read about environment > variables

Re: [gmx-users] topology in local?

By the way, if I echo $GMXLIB, I can't see it, but GROMACS is working: is it OK? On Wed, May 21, 2014 at 12:27 PM, Nicola Staffolani wrote: > Dear Chandan, > > thank you for your reply. Anyway, before making any change to my GROMACS > and therefore risking to "destroy", can I ask again your adv

Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using

Hey Vito, After the first step, does the trajectory (say the last frame) look fine? If it does (everything nicely assembled), then after the second step, does it still look fine, and is it placed properly in the center of the box? Cheers, Tsjerk On Wed, May 21, 2014 at 12:50 PM, Vito Genna wr

Re: [gmx-users] High density after genbox

Thank you Mark, My Bad. Now fixed. Hope the simulations I did before were not affected, I had defined atomtypes with the correct mass in the .itp file used. Sujith On Wed, May 21, 2014 at 12:59 AM, Mark Abraham wrote: > Probably "garbage in, garbage out." However you're measuring the dens

[gmx-users] Query regarding dssp plot

Dear Gromacs users, When I am using the DSSP program to generate the secondary structure changes of my protein (23 amino acids) and its mainchain, I am getting the results in the form of .eps file and using Ghostview, I visualized and saved in .jpeg format. But the figure looks blurred and

Re: [gmx-users] topology in local?

On 5/21/14, 7:34 AM, Nicola Staffolani wrote: By the way, if I echo $GMXLIB, I can't see it, but GROMACS is working: is it OK? Yes, that just suggests you've manually configured your path and library setup rather than sourcing GMXRC (which magically sorts everything out for you and sets en

Re: [gmx-users] grompp

On 5/21/14, 5:34 AM, Urszula Uciechowska wrote: Dear Gromacs users, I am new to Gromacs. I am trying to add ions to my protein system. After typing command: grompp -f grompp.mdp -c EcoLon6mer-sol.gro -p EcoLon6mer.top -o genion_input.tpr where the grompp.mdp contains: ; ions.mdp - used as i

Re: [gmx-users] Query regarding dssp plot

On 5/21/14, 7:56 AM, Aditya Padhi wrote: Dear Gromacs users, When I am using the DSSP program to generate the secondary structure changes of my protein (23 amino acids) and its mainchain, I am getting the results in the form of .eps file and using Ghostview, I visualized and saved in .

Re: [gmx-users] Query regarding dssp plot

Dear Justin, Thank you for the reply. I was using my 50 ns trajectory for generating the .xpm and .eps files. But when I tried the first 200 ps trajectory, I can see a clear image with helical content. I was wondering how to solve this because I have to use the whole 50 ns .tpr and .trr fil

Re: [gmx-users] Query regarding dssp plot

On 5/21/14, 8:13 AM, Aditya Padhi wrote: Dear Justin, Thank you for the reply. I was using my 50 ns trajectory for generating the .xpm and .eps files. But when I tried the first 200 ps trajectory, I can see a clear image with helical content. I was wondering how to solve this because I

Re: [gmx-users] topology in local?

and so how do I make GMXLIB point to somewhere else than /usr/share/gromacs/top? On Wed, May 21, 2014 at 12:58 PM, Chandan Choudhury wrote: > On Wed, May 21, 2014 at 3:57 PM, Nicola Staffolani > wrote: > > > Dear Chandan, > > > > thank you for your reply. Anyway, before making any change to my G

Re: [gmx-users] High density after genbox

The simulation uses the .itp contents, which goes into the .tpr. But in general the other tools either don't read that part of the .tpr, or you didn't give it to them in the first place (so they make do with atommass.dat). Mark On Wed, May 21, 2014 at 1:53 PM, sujithkakkat . wrote: > Thank you

Re: [gmx-users] topology in local?

On 5/21/14, 8:38 AM, Nicola Staffolani wrote: and so how do I make GMXLIB point to somewhere else than /usr/share/gromacs/top? If Gromacs is installed in /usr/share/gromacs, that's where it should point. Otherwise, just override it by setting $GMXLIB in your shell however you like. Hopeful

Re: [gmx-users] topology in local?

just to improve my knowledge in programming: and I can override it by typing: GMXLIB="address_of_the_new_topology_in_my_computer" right? But in that case, if I first open a child shell, then the change will be effective only there, and as soon as I come back to the parent shell, GMXLIB will be p

Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using

Dear Tsjerk, No, it doesn't. (http://wikisend.com/download/324888/Post-nojump.png) I think that the first step need to be changed that's why I tried (whit no success) the flag -pbc whole. I'm still looking for a solution. Thanks again. V Vito Genna, PhD-Fellow Italian Institute of Technology D

Re: [gmx-users] topology in local?

On 5/21/14, 9:06 AM, Nicola Staffolani wrote: just to improve my knowledge in programming: and I can override it by typing: GMXLIB="address_of_the_new_topology_in_my_computer" right? The details depend on your shell. For csh you need setenv, for bash you need export, etc. Quotes shouldn

Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using

On Wed, May 21, 2014 at 6:37 PM, Vito Genna wrote: > Dear Tsjerk, > > No, it doesn't. (http://wikisend.com/download/324888/Post-nojump.png) > I think that the first step need to be changed that's why I tried (whit > no success) > the flag -pbc whole. I'm still looking for a solution. > > It seems

Re: [gmx-users] Cannot Generate CHARMM36 Topology for POPC with Virtual Sites

Dear Justin, I am facing the same problem and only difference is that I am using POPE lipids. I am using GROMACS 4.6.5 and error exists for in built CHARMM27 and CHARMM36 march release. Parameters are missing for following atomtypes. MNH3 CTL2 MCH3 CTL2 I have gone through the ff files and I

Re: [gmx-users] topology in local?

On Wed, May 21, 2014 at 12:00 PM, Justin Lemkul wrote: > > > On 5/21/14, 5:22 AM, Nicola Staffolani wrote: > >> Dear GROMACS user community, >> >> I have the following problem: I would like to let a simulation run on a >> computer where another simulation, prepared by another user, is already >>

Re: [gmx-users] entropy vs time plot

Dear Sir, Thanks for the piece of script. Bit modification and it works superbly. thanks, Tarak On Wed, May 21, 2014 at 1:23 PM, David van der Spoel wrote: > On 2014-05-21 06:54, tarak karmakar wrote: > >> Hi Tsjerk, >> Thanks for the quick reply. >> I did the following >> >> g_covar -f ../../

[gmx-users] Multi-node GPU runs crashing with a fork() warning

Hey Folks, I'm attempting to run simulations on a multi-node gpu cluster and my simulations are crashing after flagging a open-mpi fork() warning: *--* *An MPI process has executed an operation involving a cal

Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using

That doesn't make sense..., sorry. Cheers, Tsjerk On May 21, 2014 6:40 PM, "Chandan Choudhury" wrote: > On Wed, May 21, 2014 at 6:37 PM, Vito Genna wrote: > > > Dear Tsjerk, > > > > No, it doesn't. (http://wikisend.com/download/324888/Post-nojump.png) > > I think that the first step need to be

Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using

Would suggest that each time you try a different workflow, do so in a new subdirectory and copy the required files into there. That way you ensure are using the files you think that you are. Will help those assisting to then post an image of the coordinate files at each step of the work flow,

Re: [gmx-users] Multi-node GPU runs crashing with a fork() warning

Hi, Sounds like an MPI or MPI+CUDA issue. Does mdrun run if you use a single GPU? How about two? Btw, unless you have some rather exotic setup, you won't be able to get much improvement from using more than three, at most four GPUs per node - you need CPU cores to match them (and a large system t

Re: [gmx-users] Cannot Generate CHARMM36 Topology for POPC with Virtual Sites

On 5/21/14, 11:27 AM, Prajapati, Jigneshkumar Dahyabhai wrote: Dear Justin, I am facing the same problem and only difference is that I am using POPE lipids. I am using GROMACS 4.6.5 and error exists for in built CHARMM27 and CHARMM36 march release. Parameters are missing for following atomt

[gmx-users] Nanoparticle topology

Dear sir, I need to simulate gold nanoparticles (*NP*) interaction with some ligands (drugs). I can get ligand topology via ATB/ Prodrug server, but I can't get nanoparticle topology. Is there any external tools for *NP* modelling and topology generation.? Any other modifications to simulate metal

[gmx-users] about exchange replica with replicas 140

Dear gromacs user: I have encounter a problem when used HPC(high performance computer) to run replica exchange. I find that when I used replica over 128, it will not work, while under 128 , it is ok, even when I used cores much more than 128(several cores for one replica). The version I used i

Re: [gmx-users] about exchange replica with replicas 140

On 5/21/14, 10:53 PM, #ZHANG HAIPING# wrote: Dear gromacs user: I have encounter a problem when used HPC(high performance computer) to run replica exchange. I find that when I used replica over 128, it will not work, while under 128 , it is ok, even when I used cores much more than 128(sever

Re: [gmx-users] lifetime of hydrogen bond of bulk water too large

I mean't to type that the expected value should be around 0.27ps but I am getting 2 to 3 ps from my simulations. The autocorrelation function decays to 0. Is there something I am missing? Any insight would be appreciated. Thanks. Emvia -- Gromacs Users mailing list * Please search the archive

Re: [gmx-users] entropy vs time plot

Yah but you'll have to smooth it, mean wise, or beter averidge several runs. qtiplot or equivalent will work (even MS Excell if you have the added mean determination formulas).   Stephan Watkins   Gesendet: Mittwoch, 21. Mai 2014 um 06:54 Uhr Von: "tarak karmakar" An: "Discussion list for GRO

[gmx-users] 答复: about exchange replica with replicas 140

Dear Justin: The scripts I used is as follow: ## Set job parameters ## Job Name #BSUB -J OpenMPI ## Queue Name #BSUB -q medium_priority ## Output and Input Errors #BSUB -o job%J.out #BSUB -e job%J.err ## Specify walltime in HH:MM #BSUB -W 60:00 ## 16 Processors per Host #BSUB -R "span[ptile=