Re: [gmx-users] Center of mass

Thanks Dr. Justin. Thank you for your generous support. On Wed, Oct 26, 2016 at 10:27 AM, Justin Lemkul wrote: > > > On 10/25/16 7:07 PM, Mouri Ahmed wrote: > >> Hi >> >> I have been looking at options for calculating center of mass distance >> between two proteins. >> >> >> If anyone has wo

Re: [gmx-users] Center of mass

On 10/25/16 7:07 PM, Mouri Ahmed wrote: Hi I have been looking at options for calculating center of mass distance between two proteins. If anyone has worked with the center of mass in gromacs and have notes they could share I'd very grateful. http://manual.gromacs.org/documentation/2016/o

[gmx-users] Center of mass

Hi I have been looking at options for calculating center of mass distance between two proteins. If anyone has worked with the center of mass in gromacs and have notes they could share I'd very grateful. Best Regards Mouri -- Gromacs Users mailing list * Please search the archive at http://w

Re: [gmx-users] mdrun_mpi performance

On 10/25/16 12:34 PM, Steve Seibold wrote: HelloI finally got my mpi gromacs 5.0.4 installed and running (thank you Justin!). The problem is that the mdrun_mpi is running at 0.55ns/day on my quad-core 2.8 GHz computer while on my quad-core 2.0 GHz computer it is running 6.0ns/day. On both c

[gmx-users] Fwd: Trouble compiling gromacs 5.1.2 with plumed 2.2.3

-- Forwarded message -- From: Anna Vernon Date: 25 October 2016 at 10:55 Subject: Re: [gmx-users] Trouble compiling gromacs 5.1.2 with plumed 2.2.3 To: Giovanni Bussi Cc: Carlo Camilloni Giovanni, My apologies, I have been doing this over a week and it is more than a little fr

[gmx-users] steinhardt order parameter

Hi gromacs users, Is there a code in gromacs to calculate steinhardt order parameter or the corresponding order parameter in 2D ? ( http://plumed.github.io/doc-v2.1/user-doc/html/belfast-10.html) Can one of the existing analysis codes in gromacs be used to calculate these order parameters ? If so

[gmx-users] mdrun_mpi performance

HelloI finally got my mpi gromacs 5.0.4 installed and running (thank you Justin!). The problem is that the mdrun_mpi is running at 0.55ns/day on my quad-core 2.8 GHz computer while on my quad-core 2.0 GHz computer it is running 6.0ns/day. On both computers I am using all threads. The only diff

Re: [gmx-users] Trouble compiling gromacs 5.1.2 with plumed 2.2.3

Hi, The simplest explanation would be that you're somehow actually using different MPI compilers for the two stages. You should make sure you're following the PLUMED installation instructions, and perhaps contact their forums/whatever also. Your setup seems so vanilla that things should just be wo

Re: [gmx-users] protein-protein complex gets "separated" in EM step

Dear Justin, Thank you! That fixed the problem! Cheers, Gregor Von meinem iPhone gesendet > Am 25.10.2016 um 16:19 schrieb Justin Lemkul : > > > >> On 10/25/16 10:16 AM, Gregor Hagelüken wrote: >> Dear all, >> >> I am attempting to do a MD simulation off a protein-protein complex. I have >>

[gmx-users] Free energy change

Dear gromacs user, I have calculated the free energy change of a charged molecule in box1, but now, I need to do it again but in a bigger box. Box1: (a1, b1, c1) and number of water molecules: N1 Box2: (a2, b2, c2) and number of water molecules: N2 To avoid the second simulation, I was wondering

[gmx-users] Trouble compiling gromacs 5.1.2 with plumed 2.2.3

So... I compiled and installed gmx 5.1.2 on its own and it was fine. I patched it up with plumed 2.2.3 and it could not compile anymore. The error message was this: usr/bin/ld: ../../lib/libgromacs.so.1.2.0: undefined reference to symbol 'MPI_Isend' //usr/lib/x86_64-linux-gnu/libmpich.so.12: err

Re: [gmx-users] protein-protein complex gets "separated" in EM step

On 10/25/16 10:16 AM, Gregor Hagelüken wrote: Dear all, I am attempting to do a MD simulation off a protein-protein complex. I have successfully performed MD runs on the individual proteins. Now, I have taken the complex structure (X-ray structure) and ran it through pdb2gmx to get a topolog

[gmx-users] protein-protein complex gets "separated" in EM step

Dear all, I am attempting to do a MD simulation off a protein-protein complex. I have successfully performed MD runs on the individual proteins. Now, I have taken the complex structure (X-ray structure) and ran it through pdb2gmx to get a topology. This also worked. The program does not complain

Re: [gmx-users] Structure Breaking during minimization

On 10/25/16 10:02 AM, Apramita Chand wrote: Dear All, I'm trying to incorporate charges and topology obtained from ATB server for taurine into GROMOS53a6 ff by copying into my local working directory and adding information in the .rtp file. All other commands work smoothly but after energy mini

[gmx-users] Structure Breaking during minimization

Dear All, I'm trying to incorporate charges and topology obtained from ATB server for taurine into GROMOS53a6 ff by copying into my local working directory and adding information in the .rtp file. All other commands work smoothly but after energy minimzation, except for the NH3+ group, all the othe

Re: [gmx-users] mpi.h fatal error.

Hi, On Tue, Oct 25, 2016 at 1:57 AM Anna Vernon wrote: > To clarify: > Here is my cmake command > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=on -DCMAKE_C_COMPILER=mpicc > -DMPIEXEC=mpirun -DMPIEXEC_NUMPROC_FLAG=-np -DNUMPROC=2 > -DREGRESSIONTEST_DOWNLOAD=ON > > > On 24 October 2016 at 17:52, Ann

Re: [gmx-users] gmx_mpi insert-molecules

On 10/25/16 8:01 AM, shahab shariati wrote: Dear gromacs users, I want to do md similation of 10 small molecules in water. To this aim, I used following commands: gmx_mpi editconf -f a.pdb -center 0 0 0 -o b.pdb There is no reason to do this; GROMACS centers all boxes at the middle of the

[gmx-users] gmx_mpi insert-molecules

Dear gromacs users, I want to do md similation of 10 small molecules in water. To this aim, I used following commands: gmx_mpi editconf -f a.pdb -center 0 0 0 -o b.pdb gmx_mpi insert-molecules -ci b.pdb -o c.gro -nmol 10 -box 10 10 10 I have 3 questions: 1) Is my manner true? 2) For 10 molecu

Re: [gmx-users] restraint

Dear Sir, Thanks for the quick response. Best Regards Mouri On Tue, Oct 25, 2016 at 9:12 PM, Justin Lemkul wrote: > > > On 10/25/16 6:11 AM, Mouri Ahmed wrote: > >> Dear Dr. Justin, >> >> Thank you very much for the help. >> >> In the gromacs tutorial, protein and ligand are being pulled away

Re: [gmx-users] restraint

On 10/25/16 6:11 AM, Mouri Ahmed wrote: Dear Dr. Justin, Thank you very much for the help. In the gromacs tutorial, protein and ligand are being pulled away from each other. In the pull_md.mdp file, which option I need to change to make them close? A negative pull rate pulls the two speci

Re: [gmx-users] restraint

Dear Dr. Justin, Thank you very much for the help. In the gromacs tutorial, protein and ligand are being pulled away from each other. In the pull_md.mdp file, which option I need to change to make them close? Best Regards Mouri On Tue, Oct 25, 2016 at 8:54 PM, Justin Lemkul wrote: > > > On

Re: [gmx-users] restraint

On 10/25/16 5:24 AM, Mouri Ahmed wrote: Hi I want to use distance restraint between protein and ligand in gromacs. I am confused with the problem. Anyone have any ideas? Use the pull code. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kir

[gmx-users] restraint

Hi I want to use distance restraint between protein and ligand in gromacs. I am confused with the problem. Anyone have any ideas? Best Regards Mouri -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * C

[gmx-users] Restraint

Hi I want to use distance restraint between protein and ligand in gromacs. I am confused with the problem. Anyone have any ideas? Best Regards Mouri -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Ca