[gmx-users] gromacs with v-rescale thermostat

Dear users, recently I have observed a strange behavior of my simulations. The total potential energy of presumably independent simulations showed undesired correlation (R=0.6) even when started with different velocities (gen-seed=-1) and solute coordinates. I found out that the reason is the

Re: [gmx-users] Simulations of inorganic polymers

On 12/18/15 8:47 AM, Ganesh Shahane wrote: Dear Gromacs Users, I need to simulate a specific polymer which consists of carbon, hydrogen and fluorine atoms. Could anyone please suggest some force fields for simulating inorganic polymer molecules that have been ported to gromacs? Your

Re: [gmx-users] POVPC MARTINI ff

Try again =) On 17 December 2015 at 16:17, shivangi nangia wrote: > Hello, > > Thanks for your reply. > > That weblink, however, is not working. > > Is there somewhere else I can look. > > CHARMM GUI MARTINI membrane builder also does not have POVPC MARTINI ff. > >

[gmx-users] Simulations of inorganic polymers

Dear Gromacs Users, I need to simulate a specific polymer which consists of carbon, hydrogen and fluorine atoms. Could anyone please suggest some force fields for simulating inorganic polymer molecules that have been ported to gromacs? Thank you. -- Best Regards, Ganesh Shahane -- Gromacs

Re: [gmx-users] regarding the use of g_hbond

On 12/18/15 5:42 AM, soumadwip ghosh wrote: Hi all, I am trying to plot the no.of hydrogen bonds between two parallel chains of a double stranded DNA as a function of time. What I am observing is a decrease (which is expected) for two types of nucleic acids but the problem is the

[gmx-users] Help calculation on cluster

Hi, I am doing some simulations in a cluster. I want to know if there is an option to run the simulation in order that I can close the terminal?. I tried to make sbatch but the problem is that when I entered the command there is a step to choose the system and with sbatch I could not choose

Re: [gmx-users] Help calculation on cluster

On 12/18/15 2:40 PM, Mishelle Oña wrote: Hi, I am doing some simulations in a cluster. I want to know if there is an option to run the simulation in order that I can close the terminal?. I tried to make sbatch but the problem is that when I entered the command there is a step to choose the

Re: [gmx-users] PCA analysis results

Hi Nithyanan, It's guessing a bit, as the actual answer can only be obtained by tracking some parameters during the simulation, but I would suggest to aim for at least 200 ns. It think the relaxation will take more time than you have, so say until (at least) 100 ns, and then you need to have

[gmx-users] PCA analysis results

Dear GROMACS users, I have performed 50ns MD for 567 aa monomer protein using gromos53a6 ff in explicit water in the cubic box with 2fs time step. I have used g_covar and g_anaeig to perform Principal Component Analysis/ Essential Dynamics analysis. But when I view the animation of the

Re: [gmx-users] PCA analysis results

Hi Nithyanan, How did you preprocess the trajectory? Did you cluster and/or make everything whole? By the way, 50 ns is probably too short for a protein of that size. It will probably still be relaxing and the eigenvectors will be those of the relaxation. Cheers, Tsjerk On Fri, Dec 18, 2015

Re: [gmx-users] PCA analysis results

Hi Dr Tsjerk, I didn't do any clustering or make it whole. I just use the .xtc that I ontained after the simulation since I found out there is no pbc effect of the protein. On Sat, Dec 19, 2015 at 3:42 AM, Tsjerk Wassenaar wrote: > Hi Nithyanan, > > How did you preprocess

Re: [gmx-users] Help calculation on cluster

Thanks for your reply Micholas, I ask my system admins but he told me that for queuing the job I need to enter the selected group in the command line. My command is g_mmpbsa -f traj.xtc -s topol.tpr -i mmpbsa.mdp -n index.ndx -nomme -pbsa -nodecomp -apol apolar.xvg -nodiff My question was if I

Re: [gmx-users] PCA analysis results

Dr Tsjerk, Thank you for your explanation. The PDB model I used in this simulation was obtained from I-TASSER. There is no ligand involved. Dr, may I know what would be the optimal/ suggested simulation time for this protein with 567 aa? On Sat, Dec 19, 2015 at 4:06 AM, Tsjerk Wassenaar

Re: [gmx-users] Help calculation on cluster

Not really the best place to ask this question (check with your system admins), but You could run your command from a "screen session". Just run screen when you first log into the machine, go about your business setting up your simulation and then start it. Once it is running, type

Re: [gmx-users] PCA analysis results

Hi Nithyanan, Right. So now we have that clear, I've had a look at the PDB file :p What you see is the result of filtering over a single eigenvector. You protein is kind of curling up through rotations of domains. You can't describe these rotations with a single eigenvector. They will be

Re: [gmx-users] gromacs with v-rescale thermostat

Hi, Indeed, we changed this behaviour for 5.0 (and noted it at http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_5.0.x) Mark On Sat, Dec 19, 2015 at 1:00 AM wrote: > Dear users, > recently I have observed a strange behavior of my simulations. The

Re: [gmx-users] Calculating shear viscosity of a liquid - different results from different verions of Gromacs

Hi, There are some known issues fixed in 4.6 ( http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x) but since the authors of this code haven't added any test cases, AFAIK it could have gotten broken at any time. I can't see any obvious .mdp issues. I would encourage you to attempt