Re: [gmx-users] which source file is handling for writing distance restraint potential energy to edr file?

Hi, There isn't a single place that handles this, and you don't want to get involved ;-) What you can do is get the forces via a http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy using .tpr files that do and do not have the restraints, read the two sets of forces into some program

[gmx-users] which source file is handling for writing distance restraint potential energy to edr file?

Dear Gromacs users, Is there someone that can help me to find out which source file handles writing distance restraint potential energy to edr file? I want to extract the restrained force instead of potential energy through changing the source code. Any help would be appreciated. -- Thanks &

[gmx-users] genebox and solvate command

when I have run the genbox command, it has shown that "This tool has been removed from Gromacs 5.0. Please see http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0 for ideas how to perform the same tasks with the new tools." In gromacs site, it is written that genbox This tool

Re: [gmx-users] DSSP secondary structure

I changed and reduced the ratio but the xpm file was not changed at all. On Sunday, February 14, 2016 5:05 PM, Justin Lemkul wrote: On 2/14/16 1:54 AM, mohammad r wrote: > Thank you Justin, > > I used xpm2ps command with below m2p file but the resolution was not

[gmx-users] How I merge all .tpr files

Dear Gromacs users, I have run 50 ns simulation job in five steps. Now I am going to analyze  energy, rmsd, rmsf etc of these simulations. I have merged all files like .gro, .xtc, .edr etc. But I want to merge all extend tpr files in one file for analyzing purpose. Is there any command to merge

Re: [gmx-users] fatal error trying to simulate glycosylated proteins

On 2/14/16 8:19 PM, David Newman wrote: Hi, I'm trying to simulate the dynamics of glycosylated proteins using gromacs 4.6.5 and have acquired forcefield parameters from PTM-Vienna (ffG45a3(v1.6) and ffG54a7(v1.7)) and CHARMM-GUI (36-jun2015) that supposedly allow for analysis of PTMs but

[gmx-users] fatal error trying to simulate glycosylated proteins

Hi, I'm trying to simulate the dynamics of glycosylated proteins using gromacs 4.6.5 and have acquired forcefield parameters from PTM-Vienna (ffG45a3(v1.6) and ffG54a7(v1.7)) and CHARMM-GUI (36-jun2015) that supposedly allow for analysis of PTMs but both result in a fatal error when trying to

Re: [gmx-users] Simulation Terminated on Clusters Due to "cannot rename checkpoint file"

Hi, GROMACS works correctly if you have permissions to read and write and enough space to do so. But I expect that you can't try to run from $WORK using mdrun -cpi $HOME/old.cpt if $HOME is full. I suggest you consult the docs for the cluster, and consult your sysadmins for any help with your

Re: [gmx-users] Simulation Terminated on Clusters Due to "cannot rename checkpoint file"

Hi, Mark, Thank you for your response. I am not sure if this is the right way to reply, because I cannot see the content of gmx maillist emails. I am running in my own space. Here is the story. Everybody has a $HOME and $WORK directory on the cluster. The $HOME is for permanent storage with

[gmx-users] gmx cluster

Hi Everyone I performed a 10ns MD using Gromos 43a1 ff and obtained frames at 10ps interval. However, When i gave gmx cluster command, I obatined 661 clusters. Does this indicate my proteini is not stable? However When i viewed trajectory in VMD, it seems good with least fluctuations in

Re: [gmx-users] DSSP secondary structure

On 2/14/16 1:54 AM, mohammad r wrote: Thank you Justin, I used xpm2ps command with below m2p file but the resolution was not changed. I've attached the xpm file, even the legend can't be seen. is there anyway to get the result file in pdf format? m2p file (I found it in the gromacs website):

Re: [gmx-users] Installation problem

Hi, As you have read in the install guide (hint, hint) CUDA and OpenCL support are mutually exclusive. Your second attempt was clearly run in the same build directory, so you have not changed your previous choice where OpenCL was on. Either turn it off, change build directory, or clear the

[gmx-users] Porting to Gromacs of Parmbsc1

I wish to use Parmbsc1 for DNA simulations. Are there any timelines to port Parmbsc1 into Gromacs along with amber14sb? Regards, Sarath -- 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

Re: [gmx-users] Installation problem

Thanks. I thought it would be better to have ocl as well just in case. However, I tried you suggestion: cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON ; make and it still have the same error [100%] Building C object src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion-gen.c.o

Re: [gmx-users] Porting to Gromacs of Parmbsc1

Hi, Nobody's working on it to my knowledge, but if a forcefield has been published, seems likely to be of use to multiple people, and a validation script can show it works correctly with respect to the reference implementation, then we'll consider it for inclusion in GROMACS. Mark On Sun, 14

Re: [gmx-users] Simulation Terminated on Clusters Due to "cannot rename checkpoint file"

Hi, You need write permission for the folder as well. Thus, run in your own file space. Mark On Sun, 14 Feb 2016 01:16 Ray Chao wrote: > D​ear gmx users, > > Just a little revision for my last question. > > I am running my cases on the cluster. The simulation was always

[gmx-users] pulling simulation

I see. Thank you dear Justin. Best regards, Mehrnoosh On Sat, Feb 13, 2016 at 6:54 PM, Mehrnoosh Hazrati < mehrnoosh.hazr...@modares.ac.ir> wrote: > Dear all, > > I'm trying to do umbrella sampling. But after running "perl distances.pl", > I get a "summary_distances.dat file which has NO