Re: [gmx-users] Adding external magnetic filed to GROMACS

Thank you Alex, I need to know how to edit the source code to generate the magnetic force. the question is how I can edit it? Thanks On Fri, Mar 24, 2017 at 1:54 PM, Alex wrote: > There are no magnetic fields in Gromacs, unless you are willing to edit > the source code and

Re: [gmx-users] Adding external magnetic filed to GROMACS

There are no magnetic fields in Gromacs, unless you are willing to edit the source code and generate forces arising from it. Alex On 3/24/2017 12:47 PM, Sam Dav wrote: Hello all, I'm new user and I have done some simulations. Now, I'm trying to use an external magnetic field and I found its

[gmx-users] Adding external magnetic filed to GROMACS

Hello all, I'm new user and I have done some simulations. Now, I'm trying to use an external magnetic field and I found its not implemented such as electric field. Does anyone know how to add it and which filed I should modify?. Thank you in advance Sam -- Gromacs Users mailing list * Please

[gmx-users] Clarification for the meaning of ncoords in GROMACS 5.0.4 pull code

Hi, I have two molecules which are not moving in the z axis due to being continuous across the periodic boxes. I want to keep the distance between them fixed by pulling along x and y axes. So as I am pulling along x and y axes does my ncoords = 2 ? By going along with this logic as long as my

[gmx-users] membed software inconsistency error

Dear Gromacs Users, I'm trying to embed a protein into a lipid bilayer using the -membed option of gmx mdrun. After executing the command: gmx mdrun -s topol.tpr -deffnm out -membed embed.dat -mp topol.top -mn index.ndx I select the groups for the Protein and Lipid_Bilayer when prompted for them,

Re: [gmx-users] Pull code grompp error

Hi Kausar, I tried it with an index file. It seemed to run fine but did not produce any "pull" i.e. shifting away of the DNA molecule from the protein. I used a harmonic potential. And also, why do I need to specify the index file when, according to the error itself, it can be run without making

Re: [gmx-users] COMMAND IN HBOND

Hi, Thank you for the reply. Actually, we get the number of hydrogen bonds in .xvg file using gmx hbond -s prd.tpr -f prd.xtc -n index.ndx -num hbnum.xvg . Can we generate an output file similar to that, which prints the bonding residues of protein and ligand? Thanks, Neha On Fri, Mar

Re: [gmx-users] COMMAND IN HBOND

Dear Neha, Gromacs doesn’t offer that much in terms of viewing. This sounds more like a PyMol/VMD/Other question. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18

[gmx-users] COMMAND IN HBOND

Hi gromacs users, What is the command to view the residues of protein and atoms of ligand involved in hydrogen bond? Thanks, Neha -- 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] FSync error

Hi Mark, I understand it's prehistoric. But, I would be happier if somebody makes understand the system admins at the CDAC-BRAF that their version is prehistoric. The problem has not been solved yet. I'm running the simulation in parts reading from the checkpoint files. Will that be too risky

Re: [gmx-users] Getting charges of the system out of the simulation in human-readable form

Hi, On Fri, 24 Mar 2017 11:25 Marko Sever wrote: So my question is, what is the most simple way to get a file with residue and atom types in addition to charges out of the files created at the end of the simulation? There isn't one apart from what is written by eg gmx

Re: [gmx-users] FSync error

Hi, Mdrun can't access that file properly, but there's no real way for it to understand why. A network file system could disappear and mdrun can't know that. By the way, 4.5.6 is prehistoric - please update for faster simulations, more chance of people being able to help you, and fewer bugs!

[gmx-users] Getting charges of the system out of the simulation in human-readable form

So my question is, what is the most simple way to get a file with residue and atom types in addition to charges out of the files created at the end of the simulation? I tried dumping the .tpr file but its file structure is a bit too complicated, I'd preffer something easier. Also since I

Re: [gmx-users] Regarding structure

I am sorry.. Sent with Mailtrack On Fri, Mar 24, 2017 at 9:44 AM, Jonathan Saboury wrote: > Please be considerate to others and only post a topic once. Not only

Re: [gmx-users] Analysis pull code simulation data to obtain Strain Stress curve

Hi there, Everyone is confused about how to get stress-strain curves from Justin's tutorial. Because it has nothing to do with nanomechanics. Obtaining Young's modulus from a particle-based simulation is quite elementary, if a clear physical picture is present. Please describe your system

[gmx-users] FSync error

I'm getting the following error in a 500ps pull code simulation. I checked out the forum for probable solve and it says it might be due to disk space usage or permission. In my case, I have enough disk quota left and I have permission to write in the directory. Can you please help? Usual MD

[gmx-users] Analysis pull code simulation data to obtain Strain Stress curve

Dear all My target is to calculate nanomechanical properties (i.e. young's modulus/elastic modulus) from a strain-stress curve. For this purpose, I study Beven lab umbrella sampling pull code simulation. After that, I also run the same procedure simulation on my desire system. But I am now

Re: [gmx-users] Pull code grompp error

Define you pull group in index file as the error message says. On Fri, Mar 24, 2017 at 12:18 PM, Souparno Adhikary wrote: > Hi, > > Below is my .mdp code for pulling as found in the tutorial by Justin > Lemkul. I made the required changes to match my version syntax. > >

Re: [gmx-users] Regarding structure

If you interested in just one glycine one possible solution is to prepare it with acpype instead. It respects your hydrogens and you can set charge as command line option. On Friday, March 24, 2017 6:14 AM, Jonathan Saboury wrote: Please be considerate to others

[gmx-users] Pull code grompp error

Hi, Below is my .mdp code for pulling as found in the tutorial by Justin Lemkul. I made the required changes to match my version syntax. pull= umbrella pull_ngroups= 2 pull_group0= Protein_chain_A pull_group1= DNA_chain_B pull_group2=