Re: [gmx-users] (no subject)

Number of hydrogen bond depends on the nature of your drug. It can be zero, one or many. On Thu, Aug 10, 2017 at 10:33 AM, saranya wrote: > Hi, > I have done protein-drug simulations for 100ns. While calculating the > hydrogen bond between the protein-drug complex I am

[gmx-users] (no subject)

Hi, I have done protein-drug simulations for 100ns. While calculating the hydrogen bond between the protein-drug complex I am getting only 2 hydrogen bonds. I just want to clarify that 2 hydrogen bonds mean very low, is it acceptable to get this minimum number of bond formation for the protein

[gmx-users] (no subject)

Hi, I have done protein-drug simulations for 100ns. While calculating the hydrogen bond between the protein-drug complex I am getting only 2 hydrogen bonds. I just want to clarify that 2 hydrogen bonds mean very low, is it acceptable to get this minimum number of bond formation for the protein

[gmx-users] gmx sasa

Dear Sir Does anyone know how to measure the SASA energy with unit (kj/mol or kcal/mol) when i give this command: *gmx sasa -f b.trr -s b.tpr -o b.xvg* I got in Y-axix "Area (nm\S2\N)" and when I give this command *gmx sasa -f b.trr -s b.tpr -odg b.xvg* I got in Y axix "D Gsolv" but I do not

Re: [gmx-users] transmembrane protein simulation

On 8/9/17 1:31 PM, abhisek Mondal wrote: Hi, I have a predicted secondary structure of a transmembrane protein containing a really long alpha helix. If I place the secondary structure of the protein inside membrane (as done for KALP in tutorial) and following all the steps perform a

Re: [gmx-users] (no subject)

I think it is all pretty simple, at least from what you are describe. If there are sufficient reason to believe that your membrane should be flat and not jagged, and your box size (supercell size, in the terminology you probably prefer) is properly set up, simply allow it to relax in vacuum at a

Re: [gmx-users] (no subject)

Dear Alex and Mark, Thank you for your kind reply. To begin with I am a Postdoc but with expertise is in DFT. It is my first venture into force field MD calculations. Hence, I am struggling. My group and the boss has similar expertise. So we have turned to public forums to ask questions. My

[gmx-users] transmembrane protein simulation

Hi, I have a predicted secondary structure of a transmembrane protein containing a really long alpha helix. If I place the secondary structure of the protein inside membrane (as done for KALP in tutorial) and following all the steps perform a production MD, is it possible to obtain a

Re: [gmx-users] Constraining starting configuration in Coarse-Grain Simulation

Hello, Thanks for your reply. Regards, M. Chakraborty On Mon, Aug 7, 2017 at 4:56 PM, Mark Abraham wrote: > Hi, > > Ok, I didn't understand you because I didn't have enough information yet. > IIRC your topology will still have to specify the constraint bond length, >

Re: [gmx-users] remove the jumps over the boundaries

blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; } Thank you s much Sent from Yahoo Mail for iPhone On Wednesday, August 9, 2017, 5:36 PM, Milan Melichercik

Re: [gmx-users] g_cluster and g_hbond calculation on GPU

Hi, Please don't re-post the same questions from different emails. You already got the answer that no analysis tools have been ported to run on GPUs. Mark On Wed, Aug 9, 2017 at 3:04 PM Kishwar Hayat Khan wrote: > Hi Everyone, > I would like to run g_cluster and g_hbond

Re: [gmx-users] remove the jumps over the boundaries

‎Hi, The message says you have used older Gromacs for analysis than was the tpr file was created with. For 2016.x versions you have to use "gmx trjconv" instead of plain trjconv. The trjconv you have called is probably from your Linux distribution and in old version - you can find its binary

[gmx-users] g_cluster and g_hbond calculation on GPU

Hi Everyone, I would like to run g_cluster and g_hbond calculation on GPU boards. I could only find -nthreads option to fasten my calculations, Is it possible to use GPU boards for this like mdrun. reg Kish -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Atom OXT in residue was not found

Dear Justin, Thanks very much for your suggestion, it works well now. All the best, Qinghua On 08/09/2017 01:28 PM, Justin Lemkul wrote: On 8/9/17 7:21 AM, Qinghua Liao wrote: Hello, I want to simulate a protein with a ligand (small molecule, 15 atoms). But I have problem of generating

Re: [gmx-users] g_hbonds calculation on GPU

Dear Rraj, Nope. No-one has made GPU support for gmx hbond (or any other analysis tool as far as I know). Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539

[gmx-users] remove the jumps over the boundaries

Dear GROMACS users I am using GROMACS 2016.3 and ran a md simulation on my complex. Now i need to visualize my .xtc file. When i loaded the confout.gro and traj_comp.xtc in VMD , it has pbc problem, so I issued this command: trjconv -s topol.tpr -f traj.xtc -o protein.pdb -pbc nojump -dt 10 but

[gmx-users] g_hbonds calculation on GPU

Hi Everyone, I would like to run g_hbons calculation on GPU boards. I could only find --nthreads option to fasten my calculations, Is it possible to use GPU boards for this like mdrun. reg Rraj -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Atom OXT in residue was not found

On 8/9/17 7:21 AM, Qinghua Liao wrote: Hello, I want to simulate a protein with a ligand (small molecule, 15 atoms). But I have problem of generating the topology file. I added the topology of the ligand as a new residue in force field database (aminoacid.rtp), but I got the error when I

Re: [gmx-users] Position restrains during alchemical transformation

Hi, I presume the position-restraints file was written by a tool that didn't anticipate this use case (and pdb2gmx likely does not). If so, I would edit my position restraints file to express my intent, ie copy the functype and parameters so that there's an A and B state on the same line, just as

[gmx-users] Position restrains during alchemical transformation

Dear all, I have a questions concerning MD free energy calculations using alchemical tranformation. I want to restrain the backbone of my protein which I mutate during TI. However, I do not know how to correctly generate position restrains. If I use the position restrain file, which I

Re: [gmx-users] clayff forcefield

Hi, Use gmx x2top -ff clayff, not gmx x2top -ff clayff.ff Mark On Wed, Aug 9, 2017 at 8:53 AM G R wrote: > On Wed, Aug 9, 2017 at 1:04 AM, < > gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: > > > Send gromacs.org_gmx-users mailing list submissions to > >

Re: [gmx-users] convert .tpr to include energy groups

Thanks a lot Justin. On Wed, Aug 9, 2017 at 1:33 AM, Tushar Ranjan Moharana < tusharranjanmohar...@gmail.com> wrote: > Hi All, > I want to calculate interaction between 2 energy groups, which were not > defined during the run. So I want to rerun and include both the energy > groups while