[gmx-users] How can i save all run processes ...

Dear Mark/Leila thanks for your reply i knowing that for seeing all processes have done in my terminal page, i must to use *history* tool but *history* just give us main commands in my terminal page...i want to see all processes with details (e.g. which group is choosed or the volume of my box or..

Re: [gmx-users] During minimization "A charge group moved too far between two domain decomposition steps"

Not likely Xavier. It isn't a single water acting unusual. It is many waters (probably all) and all biotins making odd angles/lengths. Nevertheless I tried the suggestion and I am getting different results, but not sure if they are good results. "vmd rebuilt_system.gro em.xtc" shows the system bu

Re: [gmx-users] During minimization "A charge group moved too far between two domain decomposition steps"

Could be a water molecule broken at the box limits. Try to rebuild the water molecules before minimizing. Trjconv -pbc mol -f in.gro -o out.gro would do it. > On Jan 11, 2015, at 00:17, Jonathan Saboury wrote: > > My system is blowing up during minimization. I'm getting the error: > ---

[gmx-users] During minimization "A charge group moved too far between two domain decomposition steps"

My system is blowing up during minimization. I'm getting the error: - Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated - I looked at "http://www.gromacs.org/Documentation/Terminolog

Re: [gmx-users] "invalid order for directive atomtypes", but only one ligand

Sorry about the archive Justin, won't happen again. That fixed it! Thank you! For future reference here is the new "system.top": http://pastebin.com/raw.php?i=F46xVUdr -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List befor

Re: [gmx-users] potential energy

On 1/10/15 4:39 PM, mah maz wrote: some solvent in nanotube actually! What do you mean by various energy components? In the results, I just have terms for potential, kinetic, total energy and conserved energy which are all positive in all steps. That's not possible. There are a large number

Re: [gmx-users] potential energy

some solvent in nanotube actually! What do you mean by various energy components? In the results, I just have terms for potential, kinetic, total energy and conserved energy which are all positive in all steps. On Sun, Jan 11, 2015 at 12:52 AM, mah maz wrote: > I see! You are right. But my syste

Re: [gmx-users] potential energy

On 1/10/15 4:22 PM, mah maz wrote: I see! You are right. But my system is a nanotube not in gas phase. Is it possible in this case? Nanotube in some solvent? What do the various energy components show you? Remember, it's all additive, so you should be able to easily identify which terms ar

Re: [gmx-users] potential energy

I see! You are right. But my system is a nanotube not in gas phase. Is it possible in this case? Thanks alot! On Sun, Jan 11, 2015 at 12:40 AM, mah maz wrote: > Thank you Justin! > you mean we can have a stable system with positive potential and total > energy? > Regards, > Mah > > On Sun, Jan 1

Re: [gmx-users] potential energy

On 1/10/15 4:10 PM, mah maz wrote: Thank you Justin! you mean we can have a stable system with positive potential and total energy? Sure. For example, gas-phase systems generally have positive potential energy. -Justin -- == Justin A. Lemkul

Re: [gmx-users] potential energy

Thank you Justin! you mean we can have a stable system with positive potential and total energy? Regards, Mah On Sun, Jan 11, 2015 at 12:22 AM, mah maz wrote: > Dear all, > I wanted to know if the potential energy gained by "g_energy -f ener.edr > -o" the total potential energy of the system or

Re: [gmx-users] potential energy

On 1/10/15 3:52 PM, mah maz wrote: Dear all, I wanted to know if the potential energy gained by "g_energy -f ener.edr -o" the total potential energy of the system or partial ones like vdw energy. If it is the total energy, to my knowledge it should be negative, It's the full potential energy.

[gmx-users] potential energy

Dear all, I wanted to know if the potential energy gained by "g_energy -f ener.edr -o" the total potential energy of the system or partial ones like vdw energy. If it is the total energy, to my knowledge it should be negative, and its summation with the kinetic energy should be negative showing the

[gmx-users] PME question in GMX4.6.5

Dear GMX and PEM experts, I am using gromacs 4.6.5. My system is neutral charge (net charge=0). I used PME with the following options: - ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics ewald_geometry = 3dc pme_order

[gmx-users] The problem is fixed

Dear Gromacs users, I have fixed the problem "There is a dangling bond at at least one of the terminal ends...", So don't consider my previous message. Sorry. Best regards, Igor Shchechkin -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Question

On 1/10/15 10:21 AM, Igor Shchechkin wrote: Dear Gromacs users, I have obtained the error: "There is a dangling bond at at least one of the terminal ends...", running pdb2gmx (4.6.5 version) with the command: pdb2gmx -f J.pdb -o J.gro -p J.top J.itp. PDB file 1BJ5 from RCSB was used; 'A' ch

[gmx-users] Question

Dear Gromacs users, I have obtained the error: "There is a dangling bond at at least one of the terminal ends...", running pdb2gmx (4.6.5 version) with the command: pdb2gmx -f J.pdb -o J.gro -p J.top J.itp. PDB file 1BJ5 from RCSB was used; 'A' chain and five ligand molecules attached to it wer

Re: [gmx-users] compiling issue

Actually I can't figure where my setting is wrong. Here is my cmake command: CC=$IMPI_PATH/mpiicc CXX=$IMPI_PATH/mpiicpc CMAKE_PREFIX_PATH=$FFTW3DIR:$CUDAPATH/include:$CUDAPATH/lib64:$CUDAPATH/bin\ $CMAKE \ -DFFTW_INCLUDE_DIR=$FFTW3DIR/include \ -DFFTW_LIBRARY=$FFTW3DIR/

[gmx-users] Problem in energy minimization of Protein-ligand complex in Lipid membrane

Hello everyone, I am trying to energy minimize protein-ligand complex in lipid membrane. I am using "LAMBADA" script, after extracting Ligand. LAMBADA script do not recognise ligand molecule, after insertion when I am trying to reinsert ligand in to Prot_memb system, it does not bind to protein

Re: [gmx-users] Gromacs Installation problem

Thanks Mark. Your guess is right. It works. Regards, Shankar On Fri, Jan 9, 2015 at 7:41 PM, Mark Abraham wrote: > Hi, > > Last time I saw something like that, the person was trying to build in and > install to the same place. Sharing your cmake command line would have been > a good idea. > > M