[gmx-users] Is there any way to count the number of water molecules around a ligand during simulation of its binding pathway?
Dear Gromacs Users I would like to calculate the presence of water molecules number as a function of time, around a ligand during binding to its pocket from a trj.xtc file. How can I do it by Gromacs or any other program? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Fatal error: Rerun .trr trajectory
Dear Gromacs Users When I rerun .trr trajectory files for re-calculating energies and forces, the following error was received. Any suggestion to solve it please? Command line: gmx mdrun -v -s md.tpr -rerun md.trr ... --- Program: gmx mdrun, version 2018 Source file: src/programs/mdrun/md.cpp (line 884) Fatal error: Rerun trajectory frame step 1 time 20.00 does not contain a box, while pbc is used. Thanks Hassan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] ZNO-HSA (Human Serum albumin) Interaction
Dear Gromacs Users; I am studying the toxicity effect of ZnO nanoparticle (with a partial charges of +1.026 and -1.026 for Zinc and Oxygen atoms, respectively) on the Albumin structure by Gromacs. For MD simulation the nanoparticle was placed at a distance of 1nm of protein, after running pdb2gmx, the simulation box was solvated by TIP3P waters. The net charge of protein in physiological condition is -14 that was neutralized by adding sodium and chloride ions to box. Then, energy minimization, NVT and NPT were done. >From the beginning of md simulation, the protein structure began to be unfolded slowly before binding nanoparticle to it and after binding, the protein structure changed dramatically. I cannot consider the charge of ZnO as zero like silver or gold nanoparticles. So, I am confused that whether the study method is correct or wrong for this interaction? Do the results seem logical? Thanks Hassan Aryapour -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] pulling simulation
Dear Justin A. Lemkul, Thank you for answer. In US simulation the initial configurations were generated by translating ligand along the z-axis up to desired distance. Is it necessary to rotate my protein complex in correct orientation until protein exit side align with the z-axis and ligand could leave its binding site? How can I find exit site in protein? The binding pocket is deeply buried inside the protein and not solvent accessible. Best Wishes Hassan On Tue, Jul 5, 2016 at 5:23 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/5/16 3:30 AM, Hassan Aaryapour wrote: > >> Dear Justin A. Lemkul, >> >> >> >> How do you calculated the coordinates for center (3.280, 2.181, 2.4775) >> and >> box dimensions 6.560 x 4.362 x 12 in Umbrella Sampling by the following >> program: >> >> gmx editconf -f complex.gro -o newbox.gro -center 3.280 2.181 2.4775 -box >> 6.560 4.362 12. >> >> > I defined an original box that was 1 nm larger than any protein atom in > all 3 dimensions, and then took x/2, y/2, and sufficient space along z to > pull as far as I needed to. > > When I calculate the geometrical center by chimera or accelrys discover >> studio for my protein complex, it was emerged from box edges. How to >> resolve it by softwares (not manually)? >> >> > I don't know what magic capabilities each program has, though there's no > reason to do any of it outside of GROMACS. The solution is > system-specific, so I don't know that you can really get away from having > to do something manually. The initial box definition is done with editconf > -d (automatic) but then the actual box vectors needed depend on the size of > the proteins and the length of the reaction coordinate (something that > needs to be set by the user). > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to define coordinates of protein and simulation box in the pulling simulation automatically?
Dear Justin A. Lemkul, How do you calculated the coordinates for center (3.280, 2.181, 2.4775) and box dimensions 6.560 x 4.362 x 12 in Umbrella Sampling by the following program: gmx editconf -f complex.gro -o newbox.gro -center 3.280 2.181 2.4775 -box 6.560 4.362 12. When I calculate the geometrical center by chimera or accelrys discover studio for my protein complex, it was emerged from box edges. How to resolve it by softwares (not manually)? Best Regards Hassan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Count the number of water molecules around a macromolecule
Dear Gromacs Users How can I count the number of water molecules in the first hydration shell of a macromolecule in the trajectory file? Thanks Hassan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to delete Zinc atom from .xtc and .gro files
Dear Gromacs Users, How can I remove Zinc atoms from .xtc and .gro files after MD simulation. Thanks Hassan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How can I split .xtc file to two part?
Dear Gromacs Users How can I make a movie from gromacs trajectory file (200 ns)? VMD was failed because of low memory of computer (16GB). for resolving this problem, can I split .xtc file to two part? how? Thanks Hassan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Topology file for serotonin (5-HT)
use swissparam server, http://swissparam.ch/ On Mon, Jul 27, 2015 at 3:13 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/27/15 1:03 AM, Ganesh Shahane wrote: Hi Justin, Yes. I tried the same, but during the preparation of the .tpr file using grompp it gives an error saying No default proper dihedral types for 3 dihedral angles which are not present in the ffbonded.itp of the charmm36 force-field. These 3 dihedrals consist of atoms that encompass the alkyl amine and the indole groups of serotonin. Now, if I remove these dihedrals in question from the serotonin's .itp file which I have prepared, the simulation runs just fine. I am trying to calculate the free energy of solvation for serotonin. Considering this, is it okay to ignore some of these dihedrals? Absolutely not. You can't just delete inconvenient interactions. If there are missing parameters, you need to derive suitable dihedral terms. Or just throw the molecule at ParamChem and see how it does. CGenFF should work fine for this molecule. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Repulsive potential
Dear Atsutoshi, Very thanks for your reply. I run repulsive/nonrepulsive potential simulations for a system contains (Di-peptide + 2Ligand) for 5ns as suggestions and, compared final results by VMD. I don't think that there is really difference between two simulation, ligands are aggregated in both simulation. All necessary results is uploaded as follow: http://d01.megashares.com/?d01=HrNDcu4 http://d01.megashares.com/?d01=kdLuTf7 I would greatly appreciate if you could kindly tell your comments and, if possible share your required file. Sincerely Hassan On Tue, Jul 21, 2015 at 11:42 AM, atsutoshi.ok...@takeda.com wrote: Dear Hassan, I’m sorry for my late reply. I missed your e-mail. I think the easiest way to introduce repulsive potential is to use draft code for inter-molecular bonded interaction at https://gerrit.gromacs.org/#/c/2566/. But nobody has yet tried that it works as Mark said. Another way, as Justin told us, is to define a dummy atom within the structure using a virtual site, then specifying a nonbonded interaction only between these virtual sites using [nonbond_params]. However, I am getting some errors using this methods and trying it if it works well. Atsutoshi *From:* Hassan Aaryapour [mailto:hassan.grom...@gmail.com] *Sent:* Friday, June 26, 2015 7:41 PM *To:* Okabe, Atsutoshi *Subject:* Repulsive potential Dear Atsutoshi Okabe, I read your email to “mark abraham” about introducing weak repulsive potential. I have this problem and, don't know how to do it. I would greatly appreciate if you could share your experience and, help me do that for a simulation system contains Protein + 6Ligands + Ions and waters molecule. Best Wishes Hassan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to calculate magnesium (MG) parameters for gbsa.itp
Dear Gromacs Users, I have taken error below after runnig: gmx grompp -f md-implicit-gpu.mdp -c conf.gro -p topol.top -n index.ndx -o md-implicit.tpr GB parameter(s) missing or negative for atom type 'MG' ... Fatal error: Can't do GB electrostatics; the implicit_genborn_params section of the forcefield is missing parameters for 1 atomtypes or they might be negative. How can I calculate Magnesium (MG) parameters for gbsa.itp in implicit simulation? I would greatly appreciate if anyone could kindly help me. Best Wishes Hassan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] (no subject)
Dear Justin, Where can I find the primary literature for setting up proper parameters in mdp files? I downloaded all literatures in General Information section in link below (http://ffamber.cnsm.csulb.edu/ffamber.php), but I did not find anything related to the Cutoffs. Regards Hassan On Sun, Jun 28, 2015 at 10:54 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/28/15 3:22 PM, Vidyalakshmi CM wrote: Hi, You may use the mdp files from the tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/ (It has topologies for energy minimzation, nvt and npt simulations and md simulations run). The tutorial .mdp settings are for OPLS-AA and may not be generally applicable to any other force field. This is a non-trivial consideration in running simulations properly. AMBER force field is a bit generic; different parameter sets use subtly different parameters. The primary literature for the parameter set of interest will contain the proper run settings. Use whatever those settings are. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Install gromacs with intermolecular bonded interaction support
Dear Gromacs-Users, I want to do a gromacs installation with intermolecular bonded interaction support to apply a weak repulsive potential between ligands to avoid aggregation. All of the patches in this URL ( https://gerrit.gromacs.org/#/c/2566/) were added or replaced with original files in source of gromacs-5.0.5. for installing I obtained below error in make step. $ cmake .. -DGMX_BUILD_OWN_FFTW=ON $ make -j 8 [ 5%] Building C object src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topio.c.o /home/qmmm/Documents/Softs/gromacs-5.0.5/src/gromacs/gmxpreprocess/topio.c:37:20: fatal error: gmxpre.h: No such file or directory #include gmxpre.h ^ compilation terminated. src/gromacs/CMakeFiles/libgromacs.dir/build.make:537: recipe for target 'src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topio.c.o' failed make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topio.c.o] Error 1 make[2]: *** Waiting for unfinished jobs CMakeFiles/Makefile2:1653: recipe for target 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2 Makefile:146: recipe for target 'all' failed make: *** [all] Error 2 I would greatly appreciate if someone could help me to resolve this error. Best Wishes Hassan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to do parallel simulation by OpenMP?
Dear Gromacs Users How can I connect multiple stand-alone computers together in a network to make parallel simulation by OpenMP? Thanks Hassan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to introduce Mg2+ ions to system that are necessary for nucleotide co-enzymes?
Dear Gromacs Users I want to do an unguided molecular dynamics simulations (500ns) with GTP or GDP ligands that place at a random location within a simulation box that also contained my kinase protein. How can I add or introduce Mg2+ ions to system that are necessary for GTP or GDP ligands? How much Mg2+ is required for GTP or GDP molecules in a cubic box with -d 1.0??? Is it logical I add ions to a system with -8.9 net charge using command below? # gmx genion -s ions.tpr -o conf-ion.pdb -p topol.top -pname MG –np 4 -pname NA -np 1 -nname CL Thanks Hassan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to choose the best pose of ligand from the trajectory file?
Dear Gromacs Users How can I find and score protein-ligand binding poses and choose the best pose or frame from the trajectory file after doing a Molecular dynamics simulation of 40ns? Best Wishes Hassan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Stop protein diffusion in simulation box to make a movie
Dear Gromacs Users, I made a trajectory movie using VMD and smoothing increased for getting the residues motion slower, but the protein is translate and diffuse in box, and causes very hard of seeing and analyzing how ligand structure changes during simulation. How can I stop the protein translation and following ligand motion easier? Thank you in advance Hassan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Your solvent group size (*) is not a multiple of *
Dear Gromacs Users, I'm new in gromacs and I have been trying to add ions to the simulation box using following command in gromacs 5: gmx genion -s ions.tpr -o conf-ion.pdb -p topol.top -neutral -conc 0.15 then I selected these groups(Protein, MG, Ligand, respectively): 1 | 13 | 14 This error was appeared: Program gmx, VERSION 5.0 Source code file: /home/QMMM/ProgramFiles/gromacs-5.0/src/gromacs/gmxana/gmx_genion.c, line: 503 Fatal error: Your solvent group size (2701) is not a multiple of 9 For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I found this URL http://comments.gmane.org/gmane.science.biology.gromacs.user/64577; in related to my question but i don't understand answer to resolve my error? Indeed, I 've already successfully simulated another protein with same gromacs and commands. Thank You in Advance -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Set the environment variables of FFTW3_INCLUDE_DIR and FFTW3_LIBRARIES
Dear Justin
Thank you for your assistance, I run most of my MD simulations on the
WeNMR server, which have double precision gromacs ver 4.5.3.
Thanks again
hassan
On 3/3/14, Justin Lemkul jalem...@vt.edu wrote:
On 3/3/14, 5:26 AM, Hassan Aaryapour wrote:
Dear Gmx-user;
I want to install double precision gromacs 4.5.3 and FFTW 3.3.2 in my
home directory.
first, according to the FFTW installation instructions I installed and
introduced it to bash shell it as the following order:
$tar -xzvf fftw-3.3.2.tar.gz
$./configure --enable-threads --prefix=/home/WeNMR/ProgramFiles/fftw
$make
$make install
export CPPFLAGS=-I/home/WeNMR/ProgramFiles/fftw/include
export LDFLAGS=-L/home/WeNMR/ProgramFiles/fftw/lib
but it isn't found automatically by cmake when I want to install gromacs.
and this error was appeared:
CMake Error at
/usr/local/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:108
(message):
Could not find FFTW3. Provide the fftw3 install directory in the
FFTW3_ROOT_DIR environment variable. (missing: FFTW3_LIBRARIES
FFTW3_INCLUDE_DIR)
Call Stack (most recent call first):
/usr/local/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:315
(_FPHSA_FAILURE_MESSAGE)
cmake/FindFFTW3.cmake:31 (find_package_handle_standard_args)
CMakeLists.txt:636 (find_package)
How can I set the environment variables for FFTW3_INCLUDE_DIR and
FFTW3_LIBRARIES?
Those are CMake command-line options. See the full installation
instructions
online, specifically
http://www.gromacs.org/Documentation/Installation_Instructions#4.4._Helping_CMake_find_the_right_libraries.2fheaders.2fprograms
Is there any reason you are installing outdated versions of Gromacs and
FFTW?
-Justin
can I add my FFTW installed path to CMakeLists.txt file in the
related section in below? how?
if(${GMX_FFT_LIBRARY} STREQUAL FFTW3)
#MESSAGE(STATUS Using external FFT library - fftw3)
if(GMX_DOUBLE)
find_package(FFTW3 REQUIRED)
include_directories(${FFTW3_INCLUDE_DIR})
set(FFT_LIBRARIES ${FFTW3_LIBRARIES})
set(PKG_FFT fftw3)
else(GMX_DOUBLE)
find_package(FFTW3F REQUIRED)
include_directories(${FFTW3F_INCLUDE_DIR})
set(FFT_LIBRARIES ${FFTW3F_LIBRARIES})
set(PKG_FFT fftw3f)
endif(GMX_DOUBLE)
Thank you in advance
Hassan
--
==
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==
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[gmx-users] Combine parts
Dear Gmx-user; How can I combine parts of my simulation after final MD? The results of my MD are splitted to several parts with .tgz format. Best Regards Hassan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
