Re: [gmx-users] wanted to fix cpn in lipid layer MD, -position/distance restrains

Hi, i have included the restrain file,the whole MD system is obtained from charmm-gui ,and i have included restrain too -- 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] gmx convert-tpr, gmx check Q ?

On 4/12/16 9:24 AM, badamkhatan togoldor wrote: Thank you for reply of Justin. So as I understood from there no need to convert-tpr and just do it like, gmx mdrun -deffnm pro$ -cpi pro1.cpt -append That's it ? Yes. -Justin From: Justin Lemkul To:

Re: [gmx-users] Question for Gromacs Users

On 4/12/16 2:22 PM, Brier, Troy wrote: To whom it may concern, I am attempting to run a single protein in water Martini coarse grain simulation. I used martinize.py (version 2.4) to coarse grain the protein and add a dilsulfide bond. When attempting to run the minimization phase (I am using

[gmx-users] Question for Gromacs Users

To whom it may concern, I am attempting to run a single protein in water Martini coarse grain simulation. I used martinize.py (version 2.4) to coarse grain the protein and add a dilsulfide bond. When attempting to run the minimization phase (I am using Gromacs version 5.1) I receive the following

Re: [gmx-users] Preparing dual topology for free energy calculation

Hi, You should contact the tool's authors for that issue. I don't have any experience with it. Good luck Dries Hi Rompaey, Thanks for your valuable advice. As per your advice I went through the paper (

Re: [gmx-users] wanted to fix cpn in lipid layer MD, -position/distance restrains

This is not enough detail for us to know what the problem is. Did you set things up correctly so that posre_cpn.itp is actually used? You can check by gmx energy and see if you have restraint energies there. To use these restraints your .top file needs to #include "posre_cpn.itp" , which you

Re: [gmx-users] Details of 5.0 benchmark report?

Adam, The job scripts used in those benchmarks are all specific to the machines, and while admittedly the launch configuration information could be useful to have next to each data point, I'm afraid we don't have such data readily extracted from the run logs, I believe. I did not compile the

[gmx-users] Run mdrun in parallel

Hi all, Currently, I'm trying to run mdrun command in parallel. the following is my batch script using Slurm as a resource manager: =Batch Script== #!/bin/bash #SBATCH -J Eq1 #SBATCH -o eq1-%j.out #SBATCH -A pro #SBATCH -N 2 #SBATCH -n 16 gmx mdrun -deffnm

Re: [gmx-users] gmx convert-tpr, gmx check Q ?

Thank you for reply of Justin. So as I understood from there no need to convert-tpr and just do it like,  gmx mdrun -deffnm pro$ -cpi pro1.cpt  -append That's it ? From: Justin Lemkul To: gmx-us...@gromacs.org Sent: Tuesday, 12 April 2016, 15:23 Subject: Re:

[gmx-users] wanted to fix cpn in lipid layer MD, -position/distance restrains

Dear all, i am doing MD of cyclic peptide nanotube in lipids,i wanted to keep the tube fixed thoughout simulation but with below restrains after 40ns two to three rings moves away from the positions . gmx genrestr -f cpn.gro -o posre_cpn.itp -fc 1000 1000 1000 i wanted to keep the position

Re: [gmx-users] Preparing dual topology for free energy calculation

Hi Rompaey, Thanks for your valuable advice. As per your advice I went through the paper ( https://www.google.be/url?sa=t=web=j=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2872215/=0ahUKEwjq3I7M-YbMAhXI_w4KHQeeCX8QFggoMAU=AFQjCNHnkqQys4V7UYCURTPZyKQEYrGdWQ=rpmfKD8E07TCQ_XfeUyE3Q). They also used

Re: [gmx-users] SETTLE vs. LINCS -- different final energies of energy minimized structures

On 4/11/16 4:08 PM, Rakesh Sharan wrote: Hi all, I am getting significantly different final energy during energy How large is the difference? If it is dramatic, then your coordinates should also be quite different and visualization should provide some clues. But given that the water

Re: [gmx-users] gmx convert-tpr, gmx check Q ?

On 4/12/16 8:16 AM, badamkhatan togoldor wrote: Dear GMX-Users,I have a technical question regarding to the gmx convert-tpr and gmx check. I have a little bit doubt in that. Simulation was calculating 5.000.000 steps, 10ns and it has stopped due to the some cluster time limit. So I want to

[gmx-users] gmx convert-tpr, gmx check Q ?

Dear GMX-Users,I have a technical question regarding to the gmx convert-tpr and gmx check.  I have a little bit doubt in that.  Simulation was calculating 5.000.000 steps, 10ns and it has stopped due to the some cluster time limit. So I want to continue it from that stopped step. So, gmx

Re: [gmx-users] Gromacs Installation

Thanks. - Original Message - From: "Justin Lemkul" To: gmx-us...@gromacs.org Sent: Tuesday, April 12, 2016 4:54:19 PM Subject: Re: [gmx-users] Gromacs Installation On 4/12/16 7:08 AM, ABANTIKA PAL wrote: > Hi, > > I have installed GROMACS 5.1.2 by performing the steps

Re: [gmx-users] CHARMM36 ff with NBFIX in grimaces

Thanks Justin. In order to validate the results from Luo and Roux 2010 study, I need to run the simulations with and without NBFIX. But thank you very much for your respond, I appreciate it. > On 12 Apr 2016, at 13:25, Justin Lemkul wrote: > > > > On 4/12/16 5:35 AM, gozde

Re: [gmx-users] CHARMM36 ff with NBFIX in grimaces

On 4/12/16 5:35 AM, gozde ergin wrote: Dear all, I try to simulate the salt solution by using charmm36 ff in gromacs. I downloaded charmm36.ff from MacKerell web page. forcefield.to file ; ; This force field generated by charmm2gmx.py from ; multiple charmm parameter files ; and multiple

Re: [gmx-users] Gromacs Installation

On 4/12/16 7:08 AM, ABANTIKA PAL wrote: Hi, I have installed GROMACS 5.1.2 by performing the steps described in the installation guide. All the steps have been executed successfully. But, no executable of mdrun is created in the build folder. Moreover, upon executing "which gromacs", its

[gmx-users] Gromacs Installation

Hi, I have installed GROMACS 5.1.2 by performing the steps described in the installation guide. All the steps have been executed successfully. But, no executable of mdrun is created in the build folder. Moreover, upon executing "which gromacs", its showing no gromacs in

[gmx-users] CHARMM36 ff with NBFIX in grimaces

Dear all, I try to simulate the salt solution by using charmm36 ff in gromacs. I downloaded charmm36.ff from MacKerell web page. forcefield.to file ; ; This force field generated by charmm2gmx.py from ; multiple charmm parameter files ; and multiple charmm topology files #define _FF_CHARMM

[gmx-users] Vizualization of the multi chain protein in MARTINI

Dear Gromacs users! I will be thankfull for any suggestions regarding possibilities of the discrimination between different chains (normally defined as separate itp files in topology.top) of the protein in case of its modeling using MARTINI system. I have not found how to discriminate ( by