Re: [gmx-users] a question about ensemble

On Thu, 2012-05-03 at 07:32 +0200, Albert wrote: hello: I wondering are the three thermostat methods: Langevin, Berendsen and Nose-Hoover chain are all compatible with semi-isotropy coupling style? If I would like to use semi-isotropy coupling method, which one would be better? thank

Re: [gmx-users] a question about ensemble

Hello Flo: thank you so much for your kind comments. Yes, I would like to couple the pressure, it really helps a lot. best Albert On 05/03/2012 10:40 AM, Dommert Florian wrote: On Thu, 2012-05-03 at 07:32 +0200, Albert wrote: hello: I wondering are the three thermostat methods:

Re: [gmx-users] a question about ensemble

Hello, 2012/5/3 Dommert Florian domm...@icp.uni-stuttgart.de On Thu, 2012-05-03 at 07:32 +0200, Albert wrote: hello: I wondering are the three thermostat methods: Langevin, Berendsen and Nose-Hoover chain are all compatible with semi-isotropy coupling style? If I would like to use

Re: [gmx-users] a question about ensemble

On Thu, 2012-05-03 at 10:45 +0200, Albert wrote: Hello Flo: thank you so much for your kind comments. Yes, I would like to couple the pressure, it really helps a lot. best Albert You're welcome. There is just one little typo On 05/03/2012 10:40 AM, Dommert Florian wrote: On

Re: [gmx-users] a question about ensemble

On Thu, 2012-05-03 at 10:48 +0200, francesco oteri wrote: Hello, 2012/5/3 Dommert Florian domm...@icp.uni-stuttgart.de On Thu, 2012-05-03 at 07:32 +0200, Albert wrote: hello: I wondering are the three thermostat methods: Langevin, Berendsen

Re: [gmx-users] a question about ensemble

2012/5/3 Dommert Florian domm...@icp.uni-stuttgart.de On Thu, 2012-05-03 at 10:48 +0200, francesco oteri wrote: Hello, 2012/5/3 Dommert Florian domm...@icp.uni-stuttgart.de On Thu, 2012-05-03 at 07:32 +0200, Albert wrote: hello: I wondering are

Re: [gmx-users] How to remove H atom from residue in gro file?

Ho THANKS MANY THANKS I'm sorry, I'm new to Gromacs, and finally got it. Thank you very much. Hagit. 2012/5/2 Mark Abraham mark.abra...@anu.edu.au On 2/05/2012 8:55 PM, Hagit G wrote: Hi gmx users, Well, I saw this question but the answer was not understood. I'm trying to work with

[gmx-users] Incorrect number of parameters

Dear Gmx Users, I run the simulation of protein-ligand complex. Then I extracted coordinates for SMD - I want to pull away my ligand. I used to topology from pevious simulation, so I removed water, ions from topol.top as the size box will be changed etc. I placed protein-ligan in new box and

Re: [gmx-users] a question about ensemble

On Thu, 2012-05-03 at 11:31 +0200, francesco oteri wrote: 2012/5/3 Dommert Florian domm...@icp.uni-stuttgart.de On Thu, 2012-05-03 at 10:48 +0200, francesco oteri wrote: Hello, 2012/5/3 Dommert Florian domm...@icp.uni-stuttgart.de On

[gmx-users] Re: Re: Re: g_wham problem with negative COM differences

Thank you. I will use position geometry. I will actually need to rerun whole thing with slightly different peptide, so at the end I will not need those curves with recreated tpr-files. But at least I will now get pull code right from beginning and I got bit more understanding on pull code

[gmx-users] Proper 1-octanol box preparation

Hi GMX users! I prepared a box of 125 1-octanol molecules using genconf -f octanol_single_molecule.gro -nbox 5 5 5 and I tried to equilibrate this system in NPT ensemble to get proper density and nice cube box, similar to octanol configuration that one can download from

[gmx-users] membrane simulation

Hi all, I'm new in Membrane simulations with Gromacs. I have to simulate a system made up of a protein just leant on a membrane patch which has previously been extended and made it free of periodicity (with trjconv). I'm reading the KALP15 in DPPCI Tutorial and, so far, I managed to obtain my

Re: [gmx-users] membrane simulation

On Thu, May 3, 2012 at 4:38 PM, scapr...@uniroma3.it wrote: Hi all, I'm new in Membrane simulations with Gromacs. I have to simulate a system made up of a protein just leant on a membrane patch which has previously been extended and made it free of periodicity (with trjconv). I'm reading the

[gmx-users] jointly-couple lipids to theromstat - MARTINI force-field

Hello, I am a bit confused by a comment which I find in all MARTINI example md.mdp scripts concerning the tc-groups : It is stated there to couple groups separately: MARTINI -Normal temperature and pressure coupling schemes can be used. It ; is recommended to couple individual groups in your

Re: [gmx-users] jointly-couple lipids to theromstat - MARTINI force-field

On Thu, May 3, 2012 at 5:17 PM, Weingarth, M.H. m.h.weinga...@uu.nl wrote: Hello, I am a bit confused by a comment which I find in all MARTINI example md.mdp scripts concerning the tc-groups : It is stated there to couple groups separately: MARTINI -Normal temperature and pressure

AW: [gmx-users] membrane simulation

Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im Auftrag von Anirban Ghosh Gesendet: Donnerstag, 3. Mai 2012 13:39 An: Discussion list for GROMACS users Betreff: Re: [gmx-users] membrane simulation On Thu, May 3, 2012 at 4:38 PM,

[gmx-users] Re: Proper 1-octanol box preparation

Hi, relating to the picture see: http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions It's just a matter of periodic boundary conditions, you don't have two, but just one cluster of octanol. What i don't understand is, that your box doesn't collapse (becoming

Re: [gmx-users] jointly-couple lipids to theromstat - MARTINI force-field

The separation of groups for temperature control is originally necessary to avoid (or correct for) temperature gradient in the system, which occurs when systems parts have different frequencies of motions. Typically the water molecules and a protein would be separated to avoid the

[gmx-users] CHARMM36 and Dispersion correction

Hi ALL, I am simulating a membrane protein immersed in a POPC bilayer using CHARMM36 FF in GROMACS 4.5.5. In NVT and NPT (i.e. in equilibration and production runs) should I use the dispersion correction or not (as suggested in some previous posts)? And if NOT using dispersion correction, then

[gmx-users] missing gbsa parameters

hi guys, i'm trying to simulate some receptor ligand system with implicit solvent using gbsa in order to get a quick folding of some tens of N-terminal peptides. this works pretty well with the target only applying the amber99sb FF. as soon as i try to simulate it together with the ligand

Re: [gmx-users] missing gbsa parameters

On 5/3/12 9:34 AM, Vedat Durmaz wrote: hi guys, i'm trying to simulate some receptor ligand system with implicit solvent using gbsa in order to get a quick folding of some tens of N-terminal peptides. this works pretty well with the target only applying the amber99sb FF. as soon as i try to

[gmx-users] membrane simulation

Than you very much for your reply. I'm using ffnonbonded.itp etc. I still have some doubts regarding to the topology file which has to be used. Should I work and modify the topology file associated with the protein by adding the information related to the DPPC lipids as reported in the manual? I

Re: [gmx-users] membrane simulation

On 5/3/12 10:39 AM, scapr...@uniroma3.it wrote: Than you very much for your reply. I'm using ffnonbonded.itp etc. I still have some doubts regarding to the topology file which has to be used. Should I work and modify the topology file associated with the protein by adding the information

Re: [gmx-users] Lamb-Protein

On 5/3/12 10:52 AM, francesco oteri wrote: Dear gromacs users, I am using g_energy to extract energies and I noticed that, amon the different groups, there groups like Lamb-Protein,Lamb-Water_and_ions and other names I dont know. I am wondering whether exist a guide explaining the differet

Re: [gmx-users] Lamb-Protein

Hi Justin, I have free-energy = no in my .mdp file, but I still see this value in g_energy. It should be absent or always 1 while the values by g_energy are close to 1 but still fluctuating along the trajectory. So, can you explain me how the value is used by gromacs? Francesco

[gmx-users] how to extract trajectories into individual pdb file?

hello: I've finished a MD job and I am wondering how can we extract individual pdb from trajectories in Gromacs? each time I always get a single pdb contains lots of snapshots. thank you very much best Albert -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] how to extract trajectories into individual pdb file?

On 4/05/2012 1:10 AM, Albert wrote: hello: I've finished a MD job and I am wondering how can we extract individual pdb from trajectories in Gromacs? each time I always get a single pdb contains lots of snapshots. See trjconv -h Mark -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] how to extract trajectories into individual pdb file?

In particular, look at the option -sep 2012/5/3 Mark Abraham mark.abra...@anu.edu.au On 4/05/2012 1:10 AM, Albert wrote: hello: I've finished a MD job and I am wondering how can we extract individual pdb from trajectories in Gromacs? each time I always get a single pdb contains lots of

Re: [gmx-users] how to extract trajectories into individual pdb file?

On 05/03/2012 05:12 PM, francesco oteri wrote: In particular, look at the option -sep thank you for kind reply. but how to superimposed the left snapshot with the first one? thanks again for helps -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] how to extract trajectories into individual pdb file?

-fit 2012/5/3 Albert mailmd2...@gmail.com On 05/03/2012 05:12 PM, francesco oteri wrote: In particular, look at the option -sep thank you for kind reply. but how to superimposed the left snapshot with the first one? thanks again for helps -- gmx-users mailing list

Re: [gmx-users] Lamb-Protein

On 5/3/12 11:04 AM, francesco oteri wrote: Hi Justin, I have free-energy = no in my .mdp file, but I still see this value in g_energy. It should be absent or always 1 while the values by g_energy are close to 1 but still fluctuating along the trajectory. So, can you explain me how

Re: [gmx-users] how to extract trajectories into individual pdb file?

thank you very much. I found a problem : there is no option to select step. eg: I would like to export one snapshot at each 10ps, I don't find such kind of options.. THX On 05/03/2012 05:21 PM, francesco oteri wrote: -fit 2012/5/3 Albert mailmd2...@gmail.com

Re: [gmx-users] how to extract trajectories into individual pdb file?

On 5/3/12 11:58 AM, Albert wrote: thank you very much. I found a problem : there is no option to select step. eg: I would like to export one snapshot at each 10ps, I don't find such kind of options.. That's what you can use -skip or -dt for. Alternatively, dump out frames at

[gmx-users] Error: 1 atoms are not part of any of the T-Coupling groups

Dear, I am working in complex protein which contains one ligand and one Mg2+ ion. I am got an error while running grompp for NVT. grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr ---

Re: [gmx-users] Error: 1 atoms are not part of any of the T-Coupling groups

On 5/3/12 12:32 PM, kalai arasan wrote: Dear, I am working in complex protein which contains one ligand and one Mg2+ ion. I am got an error while running grompp for NVT. grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr

Re: [gmx-users] a question about ensemble

Hi Florian, I remark that Langevin method is used also for explicit water system! But there a big question arises to me. The thermostatting by Langevin is achieved due to random kicks. If I simulate all atoms explicitly, there is only vacuum between the atoms. Where do the random kicks come

Re: [gmx-users] CHARMM36 and Dispersion correction

In the .mdp file in the collection I provided yesterday, DispCorr was turned off and vdwtype set to switch with a switching distance rvdw_switch = 0.8 I copied most of my mdp values from Oak Ridge National Laboratory Center for Molecular Biophysics Roland Schulz's gromacs cheatsheet:

Re: [gmx-users] trjconv correct the pbc before analysis

Thanks Justin and Mark, I compared g_rama's results for no pbc treated trajectory and pbc treated trajectory, it seems they are the same. So gromacs' analysis tools know how to deal with the broken molecules. But if one want to extract such coordinates out for computing it myself, it is

Re: [gmx-users] NBFIX to gromacs

Dear Mr. Lai, I see. I'll look more deeply into it, thanks for your answer. Ricardo.   De: Peter C. Lai p...@uab.edu Para: Ricardo O. S. Soares ross_...@yahoo.com.br; Discussion list for GROMACS users gmx-users@gromacs.org Enviadas: Quarta-feira, 2 de

[gmx-users] Re: Proper 1-octanol box preparation

Dear Ondrej - I would start with a high pressure simulation (say, P=100 bar) for 200-500 ps. After this run, the system will be compressed to its more realistic liquid density. Then, go back to P=1 bar and re-equilibrate for 100-200 ps. I guess, if the temperature were higher, the density would

RE: [gmx-users] Proper 1-octanol box preparation

Did you plot the box volume, box dimensions or density with simulation time? Over those 500,000 steps it should be shrinking. It would also be a good idea if you made a box size and number of molecules that is at least close to the density of octanol. From the image you included, the box

Re: [gmx-users] trjconv correct the pbc before analysis

On 4/05/2012 4:03 AM, mu xiaojia wrote: Thanks Justin and Mark, I compared g_rama's results for no pbc treated trajectory and pbc treated trajectory, it seems they are the same. So gromacs' analysis tools know how to deal with the broken molecules. Caveat: some tools seem to be better than

Re: [gmx-users] Incorrect number of parameters

On 3/05/2012 8:08 PM, Steven Neumann wrote: Dear Gmx Users, I run the simulation of protein-ligand complex. Then I extracted coordinates for SMD - I want to pull away my ligand. I used to topology from pevious simulation, so I removed water, ions from topol.top as the size box will be

[gmx-users] any method to determine gaussian curvature of phase

Hi,   I wanted to numerically determine the gaussian curvature of a phase obtained by self-assembly of surfactants. I was wondering whether any one can suggest any tool or any program which can create a 3D grid and then calculate the gaussian curvature on points on the 3D grid . Thanks