Re: [gmx-users] Fwd: Probability of number of atomic contacts

Hi, Which GROMACS tools documentation did you check to see whether it can be done already? :-) I don't know the answer, but that's where to start! Mark On Thu., 28 Feb. 2019, 10:43 Mahsa, wrote: > Thank you very much for your comments! > > How would it be possible to get probability vs.

[gmx-users] How to calculate double donor and double acceptors in gromacs?

Dear gromacs users, These days, I am working on bulk water system problem. One point than I want to know is is there a way to calculate double donor and double acceptors in gromacs? Actually I tried to use "gmx hydorder" command but I could't know how to use ouput, for instance output.xmp file.

Re: [gmx-users] thread mpi

Thanks Justin, finally it worked fine with cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_BUILD_OWN_FFTW=ON -DGMX_SIMD=AVX_256. Vincenzo Il giorno gio 28 feb 2019 alle ore 14:31 Justin Lemkul ha scritto: > > > On 2/28/19 6:27 AM, Vincenzo Carravetta wrote: > > Whern I run GROMACS version 2019

[gmx-users] Pulling ion across the bilayer-choosing pull_coord1_geometry

Hi Justin, I have one general and one specific question about doing the pulling simulation. Can you let me know how I should choose pull_coord1_geometry among distance, direction, and cylinder? How can I distinguish these three geometries to use them in different systems? How can different

Re: [gmx-users] Fwd: Probability of number of atomic contacts

Thank you very much for your comments! How would it be possible to get probability vs. number of contacts or probability vs coordination number averaged across the simulations? Can it be done directly with Gromacs tools or I need some scripts for that? Best regards, Mahsa On Thu, Feb 28, 2019

Re: [gmx-users] Fwd: Probability of number of atomic contacts

On 2/28/19 8:59 AM, Mahsa wrote: Hi Justin, Could you please comment on my questions in the previous post? Best regards, Mahsa -- Forwarded message - From: Mahsa Date: Sun, Feb 17, 2019 at 2:36 PM Subject: Re: [gmx-users] Probability of number of atomic contacts To:

Re: [gmx-users] how to increase GMX_OPENMP_MAX_THREADS

Great! Feel free to revive the thread if you have further questions. -- Szilárd On Wed, Feb 27, 2019 at 7:53 PM Lalehan Ozalp wrote: > Dear Szilárd, > > They most certainly are clear! I originally thought the GPU of the terminal > would be very useful. Your suggestions are of great help. >

Re: [gmx-users] Can I align individual domains (not the whole structure) in the RMSD?

Hi, On Thu, 28 Feb 2019 at 04:00 ZHANG Cheng <272699...@qq.com> wrote: > Sorry, can someone help me with this question? I think this question is > very important, though it seems to be very basic. I can see in many > publicationis, the authors do not explicitly state how the alighment is > done

Re: [gmx-users] Residue numbering in Gromacs and VMD

Hi, Sure! Try the search box on http://manual.gromacs.org/documentation/current/index.html for "renumber residues" for some suggestions. Mark On Thu, 28 Feb 2019 at 07:54 Pandya, Akash wrote: > Hi all, > > I have run my simulations and want to carry out analysis on my > trajectories using VMD

Re: [gmx-users] can dynamic selection be used with gmx rdf?

Hi Mark, Thanks for your reply. I have tried the following run: gmx rdf -f ../../../traj_200to500.xtc -s ../../../step7_4.tpr -o -cn -rmax 0.8 -excl -ref -sf selection1.dat -sel -sf selection2.dat where the selections files are: selection1.dat: rdist = name CAL distance from name O22; name

[gmx-users] Fwd: Probability of number of atomic contacts

Hi Justin, Could you please comment on my questions in the previous post? Best regards, Mahsa -- Forwarded message - From: Mahsa Date: Sun, Feb 17, 2019 at 2:36 PM Subject: Re: [gmx-users] Probability of number of atomic contacts To: Thank you very much, Justin! I tried

Re: [gmx-users] Residue BGC not found in the database

On 2/27/19 10:17 AM, mary ko wrote: Thanks Justin. How should I check if there is a Ter between protein and glucose ? If I get you right, for my protein and Bglc system I just need the Bgc in the .pdb to be changed to Bglc. Do I need to seprate Bglc from the protein and follow the

Re: [gmx-users] thread mpi

On 2/28/19 6:27 AM, Vincenzo Carravetta wrote: Whern I run GROMACS version 2019 with the following command: gmx_mpi mdrun -nt 96 -cpi *.cpt -v -deffnm * I get this error message: *Fatal error:* *Setting the total number of threads is only supported with thread-MPI and* *GROMACS was

Re: [gmx-users] thread mpi

Just submit with proper number of threads set up in your batch script. On Feb 28, 2019 7:28 AM, Vincenzo Carravetta wrote: Whern I run GROMACS version 2019 with the following command: gmx_mpi mdrun -nt 96 -cpi *.cpt -v -deffnm * I get this error message: *Fatal error:* *Setting the total

Re: [gmx-users] thread mpi

Set up OMP_NUM_THREADS accordingly. Should be bettween 2 and 6. On Feb 28, 2019 7:28 AM, Vincenzo Carravetta wrote: Whern I run GROMACS version 2019 with the following command: gmx_mpi mdrun -nt 96 -cpi *.cpt -v -deffnm * I get this error message: *Fatal error:* *Setting the total number of

[gmx-users] thread mpi

Whern I run GROMACS version 2019 with the following command: gmx_mpi mdrun -nt 96 -cpi *.cpt -v -deffnm * I get this error message: *Fatal error:* *Setting the total number of threads is only supported with thread-MPI and* *GROMACS was compiled without thread-MPI* despite, according to the

Re: [gmx-users] Can I align individual domains (not the whole structure) in the RMSD?

Sorry, can someone help me with this question? I think this question is very important, though it seems to be very basic. I can see in many publicationis, the authors do not explicitly state how the alighment is done for the RMSD. Thank you! Cheng -- Original