Re: [gmx-users] combine two gro into one

Sikandar Mashayak wrote: yeah I know its simple, but only concern I have is that, the index of atom/residue in two files may not be in agreement, so I have to change/shift index of atoms in one of the file. but anyway I guess I will have to do it manually That part can be done with ge

Re: [gmx-users] combine two gro into one

yeah I know its simple, but only concern I have is that, the index of atom/residue in two files may not be in agreement, so I have to change/shift index of atoms in one of the file. but anyway I guess I will have to do it manually thanks sikandar On Thu, May 13, 2010 at 10:02 PM, Justin A. L

[gmx-users] fep: continuation of run after lambda = 1

Hi I am simulating a system consisting of a protein embedded in membrane, solvated with water using the Martini forcefield. I have set up a free energy perturbation simulation where a subset of the protein particles are being converted from their original particle type (state A, lambda =0) to a ne

Re: [gmx-users] combine two gro into one

Sikandar Mashayak wrote: I need to do water channel simulations... I have two gro files with me...one for wall atoms and one for water atoms...assuming the co-ordinates of atoms are appropriate, I just need to rename the indices of each atom appropriately and append one file to anotherI p

[gmx-users] combine two gro into one

I need to do water channel simulations... I have two gro files with me...one for wall atoms and one for water atoms...assuming the co-ordinates of atoms are appropriate, I just need to rename the indices of each atom appropriately and append one file to anotherI plan to do it by hand...but it w

Re: [gmx-users] luck works but demo fails

- Original Message - From: Emily Curtis Date: Friday, May 14, 2010 5:12 Subject: [gmx-users] luck works but demo fails To: gmx-users@gromacs.org > I think that I finally managed to get gromacs installed correctly.  When I > type luck in the command line I get a random phrase.  When I t

Re: [gmx-users] luck works but demo fails

Emily Curtis wrote: I think that I finally managed to get gromacs installed correctly. When I type luck in the command line I get a random phrase. When I try to run "demo" I get the following error messages: dyld: Library not loaded: libmkl_intel_lp64.dylib Referenced from: /Users/emily/

[gmx-users] Free energy and and-to-end distances

Hi, I am trying to calculate the relative free energy differences of conformations of a peptide as a function of end-to-end distance (linear distance between N-terminal nitrogen atom to C-terminal carbon atom). According to the manual pull code should not be used because the two

Re: [gmx-users] Simulation explodes (protein-ligand-protein)

Giovana Bergamini wrote: Hi! We have a problem with a protein-ligand-protein simulation. It is a somewhat large system (approx. 360 amino acid residues with approx. 70 monosaccharides), that requires a larger box for proper simulation. We used exclusions (especifically for the problematic atoms

Re: [gmx-users] genconf and density of system

Moeed wrote: Hello, I intend to generate a stack of molecules with the command line: genconf -f Hexane.gro -nbox 8 6 4 -o Hexane-STACK.gro Hexane.gro has box size of 3*3*3 nm3 and I need to have about 7 molecules per nm^3. So I multiplied 7 by 27 (box size) to get (7*27=)189 molecuels. Wh

Re: [gmx-users] adding h2po4 to system

On 5/13/10 8:31 PM, Tiago Barros wrote: Dear all, There was a similar thread in the archives, but I could not find the solution to my problem from the only reply (nor in the manual). I've been trying to add 3 h2po4 ions to my system, as these appear to be tightly bound to the protein I want

[gmx-users] adding h2po4 to system

Dear all, There was a similar thread in the archives, but I could not find the solution to my problem from the only reply (nor in the manual). I've been trying to add 3 h2po4 ions to my system, as these appear to be tightly bound to the protein I want to use in my calculations. I got hold

[gmx-users] genconf and density of system

Hello, I intend to generate a stack of molecules with the command line: genconf -f Hexane.gro -nbox 8 6 4 -o Hexane-STACK.gro Hexane.gro has box size of 3*3*3 nm3 and I need to have about 7 molecules per nm^3. So I multiplied 7 by 27 (box size) to get (7*27=)189 molecuels. What I get from the ab

[gmx-users] luck works but demo fails

I think that I finally managed to get gromacs installed correctly. When I type luck in the command line I get a random phrase. When I try to run "demo" I get the following error messages: dyld: Library not loaded: libmkl_intel_lp64.dylib Referenced from: /Users/emily/gromacsfolder/bin/pdb2gmx

[gmx-users] Simulation explodes (protein-ligand-protein)

Hi! We have a problem with a protein-ligand-protein simulation. It is a somewhat large system (approx. 360 amino acid residues with approx. 70 monosaccharides), that requires a larger box for proper simulation. We used exclusions (especifically for the problematic atoms) and restrictions (tested v

Re: [gmx-users] g_spatial

Nilesh Dhumal wrote: Hello, I am trying to calculate spatial distribution function (SDF) for my system. I have defined the residue name of solute (its glucose, one glucose molecule) and solvent (its cations of ionic liquids, 128 cations) by group numbers. During the g_spatial calculation can I

[gmx-users] g_spatial

Hello, I am trying to calculate spatial distribution function (SDF) for my system. I have defined the residue name of solute (its glucose, one glucose molecule) and solvent (its cations of ionic liquids, 128 cations) by group numbers. During the g_spatial calculation can I select this group numbers

[gmx-users] Re: gmx-users Digest, Vol 73, Issue 79

Thanks for that. It would have taken me ages to spot the quotation marks error... Everything working fine now, of course... On 13 May 2010, at 14:58, gmx-users-requ...@gromacs.org wrote: Re: Use of restraints gives segmentation fault -- gmx-users mailing listgmx-users@gromacs.org http:

[gmx-users] about SHAKE, SETTLE, LINCS and double x single precision

Hi there, >From what I've read and known, here in the list as well, one of the main reasons why Gromacs run in single precision is because it has LINCS, besides SHAKE, which I believe requires double precision for accuracy. I am drawing such conclusion (that can be wrong) partially based on Lipp

Re: [gmx-users] Use of restraints gives segmentation fault

On May 13, 2010, at 3:58 PM, XAvier Periole wrote: Why don't you simply define a extra bond between your two CYS side chains beads? Sorry, I red to quick ... On May 13, 2010, at 3:31 PM, Anna Duncan wrote: I'm trying to energy minimise a protein structure. In one area of the struct

Re: [gmx-users] Use of restraints gives segmentation fault

Why don't you simply define a extra bond between your two CYS side chains beads? On May 13, 2010, at 3:31 PM, Anna Duncan wrote: I'm trying to energy minimise a protein structure. In one area of the structure there are some salt bridges and when I do an energy minimisation without any

Re: [gmx-users] Use of restraints gives segmentation fault

Anna Duncan wrote: I'm trying to energy minimise a protein structure. In one area of the structure there are some salt bridges and when I do an energy minimisation without any restraints these are disrupted, which is something I want to avoid. To that end, I've tried restraining the resi

[gmx-users] Use of restraints gives segmentation fault

I'm trying to energy minimise a protein structure. In one area of the structure there are some salt bridges and when I do an energy minimisation without any restraints these are disrupted, which is something I want to avoid. To that end, I've tried restraining the residues that are invo

Re: [gmx-users] rerun trajectory does not match input file

John Shultz wrote: Thank you Justin, is there a way I can choose both Protein LIG? It has the following options for me You need to make a custom group that merges these two. -Justin Reading toplogy and shit from md.tpr Reading file md.tpr, VERSION 4.0.5 (single precision) 5 steps (100

Re: [gmx-users] rerun trajectory does not match input file

Thank you Justin, is there a way I can choose both Protein LIG? It has the following options for me Reading toplogy and shit from md.tpr Reading file md.tpr, VERSION 4.0.5 (single precision) 5 steps (100 ps) remaining from first run. Opening library file /usr/local/gromacs/share/gromacs/top/am

Re: [gmx-users] rerun trajectory does not match input file

John Shultz wrote: I am trying to rerun a simulation using this command mdrun -rerun -v -deffnm md I think I must have made a mistake when I prepared the original mdp file because I get this message Number of atoms in trajectory (3883) does not match the run input file (37770) I have these fi

[gmx-users] rerun trajectory does not match input file

I am trying to rerun a simulation using this command mdrun -rerun -v -deffnm md I think I must have made a mistake when I prepared the original mdp file because I get this message Number of atoms in trajectory (3883) does not match the run input file (37770) I have these files in my directory Com

Re: [gmx-users] gromacs doubt

manjula kasinathan wrote: hi all i have done protein protein interaction and the complex structure was taken for MD simulation using Gromacs.while performing mdrun step for position restrain i got error. i have carried out mdrun for 1ps and the command given for mdrun and positi

Re: [gmx-users] xmgrace

Command is xmgrace and it needs to be in your $PATH. On 13 May 2010 12:19, shahid nayeem wrote: > Dear all > I downloaded xmgr-4.1.2.tar.gz and tried to install by following commands. > tar -xvzf xmgr-4.1.2.tar.gz > cd xmgr-4.1.2 > ./configure > make > make install > But it gives error command x

[gmx-users] xmgrace

Dear all I downloaded xmgr-4.1.2.tar.gz and tried to install by following commands. tar -xvzf xmgr-4.1.2.tar.gz cd xmgr-4.1.2 ./configure make make install But it gives error command xmgr not found. Please help. shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.

Re: [gmx-users] RE: .rtp libraries

Hi Stephen, > I am particularly interested in lipid .rtp libraries hopefully for something > that has all-atom force fields, as I personally believe simulations should be > as real as possible, and also believe non-polar hydrogens still illicite some > force in the overall scheme of the molecul

Re: [gmx-users] RE: .rtp libraries

Hi Stephen, Is it possible for you to post the link to the articles you read about mitochondrial simulations and the 200 membrane lipids? Thanks in advance Esteban On Thu, May 13, 2010 at 12:00 PM, lloyd riggs wrote: > > Dear All, > > I recentlly started using Gromacs again. I was just wounde

[gmx-users] RE: .rtp libraries

Dear All, I recentlly started using Gromacs again. I was just woundering if anyone had some .rtp libraries available to add on to the software, or for VMD. I am particularly interested in lipid .rtp libraries hopefully for something that has all-atom force fields, as I personally believe simu

[gmx-users] gromacs doubt

hi all i have done protein protein interaction and the complex structure was taken for MD simulation using Gromacs.while performing mdrun step for position restrain i got error. i have carried out mdrun for 1ps and the command given for mdrun and position restrain are grompp -f