Re: [gmx-users] Re: still can not run md for creatine

Justin, Regarding the charges you mention, what do you think about RESP charges for this kind of compounds (drugs) parameterization? Best wishes Esteban -- On Mon, Nov 15, 2010 at 11:12 PM, Justin A. Lemkul wrote: > > Just the $0.02 that I always seem to contribute in these types of > discuss

[gmx-users] Protein in Electric Field

Dear All I want to simulate a protein in Electric Field how can I do that? where should I start from! It's very Important for me! Please help me! Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http:

Re: [gmx-users] Installing mdrun-gpu Using Gromacs-4.5.3

Hi Solomon, > [100%] Building C object src/kernel/CMakeFiles/mdrun.dir/md_openmm.c.o > Linking CXX executable mdrun-gpu > ld: warning: in /usr/local/openmm/lib/libOpenMM.dylib, file was built for > i386 which is not the architecture being linked (x86_64) The above linker message clearly states wh

Re: [gmx-users] compressing two selections or just the reverse of pulling simulation

Samrat Pal wrote: Hi All, In general what we do in pulling simulations that we pull one selection keeping the other fixed. In that case the distance between the two selections increases with time. Now, I want to push the selections i.e. one selection will be kept fixed and the oth

Re: [gmx-users] electrostatic interaction

Mark Abraham wrote: On 16/11/2010 7:14 AM, nishap.pa...@utoronto.ca wrote: Hello, I want to turn off electrostatic interactions between CH4 and SOL in my system. I am using ffG53a6 forcefield for CH4 and spc for my water model. CH4 is an united atom and so I can't make the charges zero

Re: [gmx-users] Re: still can not run md for creatine

Just the $0.02 that I always seem to contribute in these types of discussions - the topology you have shown below contains some likely problems. The charges (and massive charge group size) can lead to artifacts. We've got a paper due out soon about the implications of incorrect charges, but

[gmx-users] compressing two selections or just the reverse of pulling simulation

Hi All,    In general what we do in pulling simulations that we pull one selection keeping the other fixed. In that case the distance between the two selections increases with time. Now, I want to push the selections i.e. one selection will be kept fixed and the other will be pushed towa

Re: [gmx-users] Installing mdrun-gpu Using Gromacs-4.5.3

Thank you very much for writing! I have tried what was suggested, and the following errors were produced follow the use of the make mdrun command: [100%] Building C object src/kernel/CMakeFiles/mdrun.dir/md_openmm.c.o Linking CXX executable mdrun-gpu ld: warning: in /usr/local/openmm/lib/libOpen

Re: [gmx-users] Extracting protein plus a shell of water from a .xtc file

On 16/11/2010 2:30 AM, Paolo Conflitti wrote: Dear gmx-users, I'm trying to extract a protein plus a shell of water of a given radius from the .xtc and .gro files obtained from a simulation step. My purpose is to make a second box, smaller then the first, with the protein and the shell of so

Re: [gmx-users] Re: still can not run md for creatine

On 16/11/2010 6:22 AM, Vitaly Chaban wrote: Olga - What is gromos43a1.ff? I do not remember the files with ff-extension in gromacs. I am sure you should include the topology files in the There's a new force field organization in 4.5.x. PRODRG still presumes the previous organization, which le

Re: [gmx-users] electrostatic interaction

On 16/11/2010 7:14 AM, nishap.pa...@utoronto.ca wrote: Hello, I want to turn off electrostatic interactions between CH4 and SOL in my system. I am using ffG53a6 forcefield for CH4 and spc for my water model. CH4 is an united atom and so I can't make the charges zero in the topology. Is the

Re: [gmx-users] Parameterization

Dear Yuvraj: There is a protocol to find the charges and force field parameters for new molecules for the AMBER force field. The best way is to try to find the parameters from a publication. If you dont find anything then use RED to find the charges (http://q4md-forcefieldtools.org/RED/). Then use

Re: [gmx-users] Installing mdrun-gpu Using Gromacs-4.5.3

Hi, Did you run CMake in a fresh directory? If not try $ rm CMakeCache.txt $ cmake -DGMX_OPENMM=ON $ make mdrun Cheers, Rossen On 11/14/10 5:58 PM, Solomon Berman wrote: Good day friends, I am trying to install mdrun-gpu on my MacBook Pro, using Mac OS X Snow Leopard v. 10.6.5. I typed the

[gmx-users] Tinker FF parameters vs. GROMACS

Hi, All. I have a non-standard force-field defined in TINKER, but I'd like to use it in GROMACS. The TINKER documentation doesn't do a good job of describing how they define their torsion functions. Does anybody on this list know how TINKER's torsion potentials are defined and possibly how to c

[gmx-users] electrostatic interaction

Hello, I want to turn off electrostatic interactions between CH4 and SOL in my system. I am using ffG53a6 forcefield for CH4 and spc for my water model. CH4 is an united atom and so I can't make the charges zero in the topology. Is there any other way I can turn off electrostatic inter

[gmx-users] Parameterization

How to parametrize N-acetyl Glucosamine present in my PDB file with AMBER force field to use in GROMACS. Please suggest some solutions. Thanks -- Yuvraj -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://ww

Re: [gmx-users] PGI link error: unknown switch --rpath & attempted static link of dynamic object fftw/lib/libfftw3.so

Hi, this is a bug in the autoconf version GROMACS is using. Since we are moving to cmake we are not updating it thus this is an issue which won't be fixed. There are two options: - Create a folder. Copy (or symlink) the static library into that folder. Point the linker (-L) to that folder. Becaus

[gmx-users] Re: still can not run md for creatine

Olga - What is gromos43a1.ff? I do not remember the files with ff-extension in gromacs. I am sure you should include the topology files in the inverse order as compared to what is below: 1) general FF with atoms, bonds, angles, etc (~ include "gromos43a1.ff"); 2) molecule definition, its own atoms

[gmx-users] Re: Freeze Groups in Gromacs 4.5.x (bug?)!!!

Hey, Miguel - Hmm... I think, frozen particles will give unnatural pressure of your system, that's why barostats do not do their jobs as expected. Maybe it could be interesting to rescale the coordinates of the frozen atoms with the box vectors (with certain corrections in pressure calculation)...

[gmx-users] Re: still can not run md for creatine

Hey Vitaly, Thank you for your reply. Here is the files: *itp:* ; ; ; This file was generated by PRODRG version AA081006.0504 ; PRODRG written/copyrighted by Daan van Aalten ; and Alexander Schuettelkopf ; ; Questions/comments to d...@davapc1.bioch.dundee.ac.uk ; ; W

[gmx-users] Re: still can not run md for creatine

Hey, Olga - > Also please can you tell me where can I get "ffgmx.itp" file? /$gromacs_folder/share/gromacs/top/ffgmx.itp as well as all other standard topology files are there. By trying to run md I am getting an error: Fatal error: > moleculetype UNK is redefined Please post you top and itp fi

[gmx-users] Extracting protein plus a shell of water from a .xtc file

Dear gmx-users, I'm trying to extract a protein plus a shell of water of a given radius from the .xtc and .gro files obtained from a simulation step. My purpose is to make a second box, smaller then the first, with the protein and the shell of solvent in order to optimize the performance of

[gmx-users] g_sas and g_rdf

Hi everyone, I'm trying to look at the radial distribution function of water around the surface of my protein. For that, I calculated the surface area per residue (g_sas -or). Since I didn't find in the litterature any criteria to choose a minimum area value to count a residue as a a surface resid

Re: [gmx-users] Freeze Groups in Gromacs 4.5.x (bug?)!!!

Dear Mark, users and developers... Indeed, the source of the problems comes from both the constraints and the pressure bath. The temperature bath did not seem to interfere. Now, the problem is clear, to remove constraints is not only compulsory but also recommendable for such simulations.

Re: [gmx-users] bitinilated peptide

Gloria Saracino wrote: Hi everybody, I would like to submit a biotinilated peptide to MD with 53a6 force field. Do you know where I can look for the topology and parameters file? I would start with a literature search, then the Users' Contribution section of the Gromacs site, then perhaps

[gmx-users] bitinilated peptide

Hi everybody, I would like to submit a biotinilated peptide to MD with 53a6 force field. Do you know where I can look for the topology and parameters file? thank you in advance -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search

Re: [gmx-users] PGI link error: unknown switch --rpath & attempted static link of dynamic object fftw/lib/libfftw3.so

Hi, I want to build an all static library because a job running on background nodes may not be able to find the dynamic libraries installed on the front node in my system. My configure line for GCC is: ./configure --prefix=/path-to/gromacs_4.5.3 --enable-mpi --enable-double CC=cc CFLAGS=-O3

Re: [gmx-users] still can not run md for creatine

On 15/11/2010 8:45 PM, Olga Ivchenko wrote: Dear All, I still have troubles of starting running md for creatine. For which I created topology using PRODRG programm. The only difference between creatine.top and creating.itp is that creatine top has additional lines: #include "ffgmx.itp" #incl

[gmx-users] still can not run md for creatine

Dear All, I still have troubles of starting running md for creatine. For which I created topology using PRODRG programm. The only difference between creatine.top and creating.itp is that creatine top has additional lines: #include "ffgmx.itp" #include "creatine.itp" Also please can you tell me w