Re: [gmx-users] Fwd: monitor the size of the computational box

gmx energy or g_energy has (should have) an option to output the box size as volume or x/y/z lengths as a function of time. Peter On 13/07/15 10:41, Giannis Gl wrote: Dear all, I would like to ask what is the best way to monitor the size of the computational box (i.e. the volume) during a

Re: [gmx-users] Radius of Gyration

On 13/07/15 10:40, Daskalakis Vangelis wrote: Dear users, I am employing gromacs 5.05 to simulate a water cluster (spherical shape) forming on some salt in PBC (NVT). I want to calculate the Radius of Gyration (Rg, through g_gyrate) throughout the simulation time. I have a I assume you mean

Re: [gmx-users] (no subject)

On 7/13/15 3:27 AM, Andrew Bostick wrote: Dear Mark and Justin I read Atila question in mailing list. If I use ATB (http://compbio.biosci.uq.edu.au/atb/) for ligand topology preparation, should I modify and correct the charges like the PRODRG server? Never blindly trust a black box.

[gmx-users] Radius of Gyration

Dear users, I am employing gromacs 5.05 to simulate a water cluster (spherical shape) forming on some salt in PBC (NVT). I want to calculate the Radius of Gyration (Rg, through g_gyrate) throughout the simulation time. I have a forming water (spherical) cluster, but due to PBC this spherically

[gmx-users] Fwd: monitor the size of the computational box

Dear all, I would like to ask what is the best way to monitor the size of the computational box (i.e. the volume) during a simulation. I know that it must stay constant during the simulation but, in my case, it seems that it doesn't. There is an error poping up when I try to use the gmx hbond

Re: [gmx-users] Radius of Gyration

Thank you Peter for your reply. I have tried 'trjconv -pbc cluster -center' before, but despite being so slow (for around 6000 waters), I actually get again some spikes on the Rg due to PBC. I will give it a try again, thank you. On 13/07/15 12:02, Peter Kroon wrote: * Dear users, ** I am

Re: [gmx-users] Regression test for mdrun only installation

Hi, No. The full gmx binary is needed for that test suite, for running preparatory and analysis tools in the suite. Probably the mdrun and the gmx must share a common suffix w.r.t. _mpi or _d (or no suffix at all), but otherwise if an mdrun-only build is installed on top of a full build, then

Re: [gmx-users] How does x2top recognize between alkane C and alkene C

On 7/13/15 1:38 AM, sridhar dwadasi wrote: Dear gromac users, I'm using g_x2top (4.6.7 version), to generate a topology. The compound contains double bonds. I have a problem in setting correct topology. The C1 in both the cases -C1H=C2H2 and -C1H2- is being assigned the same type, though I'm

Re: [gmx-users] Error in lipid_protein simulation ( Energy minimization)

On 7/13/15 12:42 AM, shabana yasmeen wrote: Dear Users! I am doing simulation of protein and lipids but facing problem in energy minimization as I run: grompp -f minim.mdp -c system_solv_ions.gro -p topol.top -o em.tpr i received Warnings as: WARNING 1 [file ffnonbonded.itp, line 3098]:

[gmx-users] Regression test for mdrun only installation

Dear GMX-Users, just one quick question: is there a simple way to do the regression test with a mdrun-only build of gromacs 5.05? cheers, Daniel

Re: [gmx-users] Grompp checkpoint bug?

Hi, Thanks, I've proposed a docs fix for the next 5.0.x. In the long term, I think we will stop supporting grompp -t -e, so I recommend people use a workflow that calls grompp without those flags, and mdrun -cpi state.cpt to achieve what continuity is possible. Mark On Mon, Jul 13, 2015 at 8:42

Re: [gmx-users] Radius of Gyration

Depending on exactly what you want to measure, gmx clustsize might be useful for you. Erik Erik Marklund, PhD Postdoctoral Research Fellow Fulford JRF, Somerville College Department of Chemistry Physical Theoretical Chemistry Laboratory University of Oxford South Parks Road Oxford OX1 3QZ

[gmx-users] Extending Simnulation - how analyze?

Hi, I’m new user of Gromacs and I need extend a simulation of 1000ps. On Gromacs 5.0.5 I use this command line as tutorial said. gmx convert-tpr -s md_0_1.tpr -extend 1000 -o md_0_2.tpr gmx mdrun -v -s md_0_2.tpr -cpi md_0_1.cpt -append It produced the md_0_2.tpr , but when I run rms command to

Re: [gmx-users] Extending Simnulation - how analyze?

Hi, What did the .log file report about your attempt to append? Mark On Mon, Jul 13, 2015 at 11:18 PM Andrea Spinelli spinell...@gmail.com wrote: Hi, I’m new user of Gromacs and I need extend a simulation of 1000ps. On Gromacs 5.0.5 I use this command line as tutorial said. gmx

Re: [gmx-users] Grompp checkpoint bug?

Dear Mark, Thanks for the reply. I filed a redmine bug report at http://redmine.gromacs.org/issues/1775. Let me know if there’s any other data you guys need to get this issue fixed. Kind regards Dries -- Gromacs Users mailing list * Please search the archive at

[gmx-users] (no subject)

Dear Mark and Justin I read Atila question in mailing list. If I use ATB (http://compbio.biosci.uq.edu.au/atb/) for ligand topology preparation, should I modify and correct the charges like the PRODRG server? Best, Andrew -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Installing gmx 5.0.5 in mpi

Hi, On Mon, Jul 13, 2015 at 4:31 AM Raju ra...@kaist.ac.kr wrote: Dear gmx users, I have a 24 HPC with gtx 980ti of PC and wants to install gmx 5.0.5. I was able to install by configuring cuda and openmpi but when i use the following the commands the installation wents sucfess but they