[gmx-users] Fwd:

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. The number of H-bond formation is very low I have a question about is there any influence of the drug in my protein? With Regards, *Saranya

Re: [gmx-users] ligand

Hi Justin Thank you so much with best Farial From: Justin Lemkul To: gmx-us...@gromacs.org Sent: Monday, 14 August 2017, 16:35:58 Subject: Re: [gmx-users] ligand On 8/14/17 2:03 AM, ‪farial tavakoli‬ ‪ wrote: > Dear Justin > Thanks for your advice.Now I am

[gmx-users] Scaling in gromacs

Dear GMX users In order to benchmark my simulation system I would like to know in gromacs which code scales linearly till 10K cores? Thanks Best Regards Praveen -- Thanks & Regards Dr. Praveen Kumar Sappidi, DST-National Postdoctoral Fellow Computational Nanoscience Lab Chemical Engineering

[gmx-users] Kudos to trjconv -pbc cluster coder

Whoever it was that did the coding for the cluster option, you did a great job :-) Been using it on some rather initially messy looking coordinate and trajectory files in the last couple of weeks. Transforms them into things of beauty. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and

[gmx-users] Question on gmx_wham with two reaction coordinates.

Hi all I have a question on dealing with two reaction coordinates by gmx_wham. I did umbrella sampling on glucose 6-phosphate molecule on a poly-Lys peptide surface. Because the peptide is neither cylindrical nor spherical symmetric, I have to restraint each window around a specific point, using

Re: [gmx-users] How to use the index.ndx when running rms?

Dear All, After a few tests, I finally got it. Actually, the command line below does NOT generate a new set of group. echo r 1-442 q|gmx make_ndx -f md_0_1.tpr -o index.ndx Instead, it outputs ALL the 18 groups, each group contains its relevant atom numbers. After reading

Re: [gmx-users] Recent successful compile on Mac Pro with OpenCL? Failing Test #20: MdrunTests

Hi Mark, Thank-you for the suggestion. Not sure if I’ve hit a bit of a circular problem. Using Xcode clang and also a brew installed llvm I get this error during cmake: -- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES) (found version "1.0") -- Could NOT find OpenMP_CXX

Re: [gmx-users] non zero free energy values in mass transformation

Hi Deepak, I'd like to share a reference with you. http://www.tandfonline. com/doi/abs/10.1080/00268970600893060 If you could take a look at results (14) versus (15), and results (28) versus (29)... You see that when only the potential energy is considered, the mass doesn't contribute to the

Re: [gmx-users] How to use the index.ndx when running rms?

On 8/14/17 11:09 AM, ZHANG Cheng wrote: Dear Gromacs, After running echo r 1-442 q|gmx make_ndx -f md_0_1.tpr -o index.ndx I got a index.ndx file. Then I run echo 19 19|gmx rms -s md_0_1.tpr -f md_0_1.xtc -o rmsd.xvg -tu ns But still only 18 options could be recognised. The index.ndx file is

[gmx-users] How to use the index.ndx when running rms?

Dear Gromacs, After running echo r 1-442 q|gmx make_ndx -f md_0_1.tpr -o index.ndx I got a index.ndx file. Then I run echo 19 19|gmx rms -s md_0_1.tpr -f md_0_1.xtc -o rmsd.xvg -tu ns But still only 18 options could be recognised. The index.ndx file is already in the same folder. So how to

Re: [gmx-users] Recent successful compile on Mac Pro with OpenCL? Failing Test #20: MdrunTests

Hi, OK. That might be hard to work out how to fix, because I'm not sure we have a Mac+AMD machine around. My guess is that somehow the compilation in the driver assumes the use of xcode compilers, so that might be a thing for you to try. The file it can't find is one that is installed as part of

Re: [gmx-users] NVT error

Please don't reply to the entire digest, and be sure to change the subject line. On 8/14/17 9:51 AM, Faez Iqbal Khan wrote: Dear Justin, I talk to administrator They said: "Dear Faez, I picked this up in your error file: There is no domain decomposition for 105 ranks that is compatible

Re: [gmx-users] Donors and Acceptors - gmx hbond - gromacs.org_gmx-users Digest, Vol 160, Issue 67

Hi Mark, I've tried your suggestion. I've made an index file with my oxygen (O) and my hydroxyl group (OH). Here my results: H-bond average (calculated using num.xvg): O = 1.10 +/- 0.62 OH = 2.06 +/- 0.66 (The first line from .log for each group) # DonorHydrogen

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 160, Issue 63

Dear Justin, I talk to administrator They said: "Dear Faez, I picked this up in your error file: There is no domain decomposition for 105 ranks that is compatible with the given box and a minimum cell size of 1.025 nm Change the number of ranks or mdrun option -rcon or -dds or your LINCS

Re: [gmx-users] ligand

blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; } Dear justin Thank you so much  Yours sincerelyFarial Sent from Yahoo Mail for iPhone On Monday, August 14, 2017, 4:35 PM,

Re: [gmx-users] Problem with Ryzen, threads and core dumps?

Hi everyone, I had some time on the weekend to try to troubleshoot this. Updating the BIOS and trying different compilers didn’t help, but updating the kernel to 4.11.12 has made for a much more stable system. I ran a 1 ns five times and it only crashed once. Regards, Steffen > On Aug 8,

Re: [gmx-users] Recent successful compile on Mac Pro with OpenCL? Failing Test #20: MdrunTests

Hi Mark, Here are the results for a few different runs: (1) gmx mdrun -v -deffnm md_0_1 -nb cpu Runs fine and completes (2) gmx mdrun -v -deffnm md_0_1 Gives a similar error message: --- Program: gmx mdrun, version 2016.2 Source file:

Re: [gmx-users] Can I specify the residue numbers for RMSD?

On 8/14/17 8:15 AM, ZHANG Cheng wrote: Dear Gromacs, My MD contains a protein (442 residues) and 203 free glycines. The numbering of the residues is: 1-442: the protein residues 443-645: the 203 free glycines When I use the "rms" command, all the 645 residues are considered as the

Re: [gmx-users] Potential Shift Verlet

Hi, I don't think so, because it's trivial - it's defined as the value of the potential at the distance of the cutoff. Mark On Thu, 10 Aug 2017 19:44 Natalie Paige Schieber < natalie.schie...@colorado.edu> wrote: > Hi all, > > I am using the potential-shift-verlet keyword for the

Re: [gmx-users] Donors and Acceptors - gmx hbond

Hi, I would use the selection groups judiciously, for example have one of them with only donor atoms in it. Mark On Fri, 11 Aug 2017 00:05 Marcelo Depólo wrote: > Hi all! > > > I've been wondering how donors and acceptors are defined in gmx hbond. In > the help

Re: [gmx-users] Recent successful compile on Mac Pro with OpenCL? Failing Test #20: MdrunTests

Hi, That's a bit mysterious, because we check that that works in our automated testing. If running a simulation works then everything is fine, but it's possible the same error arises. Can you try that, please, and report back? Mark On Fri, 11 Aug 2017 23:48 Steffen Graether

Re: [gmx-users] PBC ISSUES IN GROMACS

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions had useful information Mark On Mon, 14 Aug 2017 09:17 Neha Gupta wrote: > Hi gromacs users, > > After simulation for 5 ns, I generated a movie.pdb file using .gro and .xtc > > However, in the

Re: [gmx-users] ligand

On 8/14/17 2:03 AM, ‪farial tavakoli‬ ‪ wrote: Dear Justin Thanks for your advice.Now I am trying to create a .gro file from the united atom pdb structure file obtained from ATB by using :editconf -f xxx.pdb -o xxx.gro but faced to this warning: WARNING: all CONECT records are ignored would

[gmx-users] Drift with groups+tabulated potential.

Dear GROMACS Community, I am trying to do a simulation using a tabulated potential which forces me to use the group cut-off. I get a drift in the conserved quantity of -600KJ/mol/ns. My system consists of 1000 rigid TIP4P water molecules and a Na+ ion. It seems that the problem is in the group

Re: [gmx-users] PBC ISSUES IN GROMACS

On 14/08/17 09:17, Neha Gupta wrote: Hi gromacs users, After simulation for 5 ns, I generated a movie.pdb file using .gro and .xtc However, in the movie file, I witnessed bizarre long bonds... How to fix it? Any suggestions please? trjconv -pbc whole Thanks, Neha -- David van der

[gmx-users] PBC ISSUES IN GROMACS

Hi gromacs users, After simulation for 5 ns, I generated a movie.pdb file using .gro and .xtc However, in the movie file, I witnessed bizarre long bonds... How to fix it? Any suggestions please? Thanks, Neha -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] ligand

Dear Justin Thanks for your advice.Now I am trying to create a .gro file from the united atom pdb structure file obtained from ATB  by using :editconf -f xxx.pdb -o xxx.gro but faced to this warning: WARNING: all CONECT records are ignored would you please advice me how can i solve this problem?