RE: [gmx-users] About the binary identical continuation by restarting from the checkpoint file

Hi, Mark, I reduce the length of test runs to only 6 steps now. The binary identical continuation still cannot be obtained. I use gmxcheck to compare the results according to your suggestions and I find two reasons to cause different trajectories. One is a water molecule happening to

[gmx-users] Placing a peptide above aqueous phase of bilayer

Dear users, I want to place the peptide above aqueous phase of the bilayer.I have gone throught the mailing list and read the manual also, but since am a beginner to gromacs it will be very helpful if someone could mail me the commands to insert peptide above bilayer.I understood that it can be

RE: [gmx-users] Turning off electrostatic or Van der Waals interactions

Hi, Setting epsilon_r = 0 in your mdp file will turn off all electrostatics. If you are concerned about efficiency, you should set all charges in your topology to zero. Berk Date: Tue, 24 Feb 2009 09:49:25 +0200 Subject: Re: [gmx-users] Turning off electrostatic or Van der Waals

RE: [gmx-users] pull_pbcatom appears global and could benifit from a sanity check during grompp

Hi, pull_pbcatom is indeed a global atom index. I will add this information to the mdp description. I don't see how any atom number would not be affected by reordering your topology, except if you are thinking of group that consist of exactly one molecule. But pull_pbcatom does not have to be

[gmx-users] SO3- force field

Dear all, I want torun SO3- form that is oxidation of cys in protein (SH -- SO3-). When I used pdb2gmx, SO3-'s atom type didn't define. Please, does anyone have experince with SO3- and can point me to reasonable parameter. thanks for any comment Jin Hee

Re: [gmx-users] SO3- force field

Jin Hee wrote: Dear all, I want to run SO3- form that is oxidation of cys in protein (SH -- SO3-). It probably is SO3 2- or HSO3- (note that crystallography does not detect hydrogens). You will have to search the literature for this one... When I used pdb2gmx, SO3-'s atom type

Re: [gmx-users] Turning off electrostatic or Van der Waals interactions

Thanks! 2009/2/24 Berk Hess g...@hotmail.com Hi, Setting epsilon_r = 0 in your mdp file will turn off all electrostatics. If you are concerned about efficiency, you should set all charges in your topology to zero. Berk -- Date: Tue, 24 Feb 2009 09:49:25

RE: [gmx-users] About the binary identical continuation by restarting from the checkpoint file

Hi, Are you running NPT, single processor with 4.0.3? Then you are experiencing the bug that the box is not updated in the checkpoint file. Please change to 4.0.4. Berk From: gu...@hotmail.com To: gmx-users@gromacs.org Subject: RE: [gmx-users] About the binary identical continuation by

[gmx-users] Interpretation of g_hbond results

Hi, I have a quick question about interpreting the output from g_hbond. I am using the -ac option to calculate H-bond lifetimes between my protein and a series of different, bound ligands. I read the associated paper, but I would like to confirm the interpretation of the results before I

[gmx-users] Conversion of trajectories to netcdf format

Hi, I would like to use nMolDyn for the analysis of the GROMACS trajectories. I tried VMD and catdcd to convert trr/tpr files to dcd/pdb files. But the conversion of the dcd/pdb files to nc (netcdf) files using the dcd_to_nc program of the nMolDyn package does not work. Obviously the header of

[gmx-users] density_SW_model

Dear all, I ran a 1ns simulation in SW water (polarizable model) under NPT (P=1 bar , T=300 K) conditions. I checked the density and had a constant plateau value around 640 g/L , which is obviously too low. I used the flexible and rigid version (520 solvent molecules), with isotropic

[gmx-users] pull_pbcatom appears global and could benifit from a sanity check during grompp

Thank you Berk, I did not realize that one might want to use a pull_pbcatom that is not part of the pull_group. In that case it makes sense that it should remain a global atom index. My comment regarding being affected by reordering the topology was indeed poorly constructed. What I meant

Re: [gmx-users] density_SW_model

Sang-Min Park wrote: Dear all, I ran a 1ns simulation in SW water (polarizable model) under NPT (P=1 bar , T=300 K) conditions. I checked the density and had a constant plateau value around 640 g/L , which is obviously too low. I used the flexible and rigid version (520 solvent

Re: [gmx-users] Interpretation of g_hbond results

On Tue, Feb 24, 2009 at 9:44 PM, Justin A. Lemkul jalem...@vt.edu wrote: Hi, I have a quick question about interpreting the output from g_hbond. I am using the -ac option to calculate H-bond lifetimes between my protein and a series of different, bound ligands. I read the associated

Re: [gmx-users] density_SW_model

Hello David, thank you for your response. Yes, this is the right mdp file. The total system contains also a small NMA molecule (6 atoms), which should not affect significantly the density (520 solvent molecules). Sang Min On Tue, 24 Feb 2009, David van der Spoel wrote: Sang-Min Park

Re: [gmx-users] Interpretation of g_hbond results

Justin A. Lemkul wrote: Hi, I have a quick question about interpreting the output from g_hbond. I am using the -ac option to calculate H-bond lifetimes between my protein and a series of different, bound ligands. I read the associated paper, but I would like to confirm the interpretation

Re: [gmx-users] density_SW_model

Sang-Min Park wrote: Hello David, thank you for your response. Yes, this is the right mdp file. The total system contains also a small NMA molecule (6 atoms), which should not affect significantly the density (520 solvent molecules). Sang Min OK, I suggest that if you can reproduce the

Re: [gmx-users] density_SW_model

Hi David, I ran also a system with NMA+SPC,NMA+SPCE and other models, but the density was always reasonable (around 1 Kg/L). I used hereby the version 3.3.1. and all simulations were done in double precision including the simulations with SW water. I will also install the newer version 4.x

Re: [gmx-users] Interpretation of g_hbond results

Manik Mayur wrote: On Tue, Feb 24, 2009 at 9:44 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Hi, I have a quick question about interpreting the output from g_hbond. I am using the -ac option to calculate H-bond lifetimes between my protein and a

Re: [gmx-users] Interpretation of g_hbond results

David van der Spoel wrote: Justin A. Lemkul wrote: Hi, I have a quick question about interpreting the output from g_hbond. I am using the -ac option to calculate H-bond lifetimes between my protein and a series of different, bound ligands. I read the associated paper, but I would like

[gmx-users] how to compute bending modulus of the membrane with NPs

Dear all I'm trying to measure the bending modulus (Kc) of lipid bilayer. I've found some papers, showing that spectral intensity needs to be calculated using the wave vector q. This method has been applied directly for pure membrane, or for bilayers with cholesterol. In my simulations, there is

[gmx-users] g_sorient -ro output

Hi, all! I have a question about interpreting the output from a GROMACS tool, g_sorient. I'm analising the solvent orientation around some specific atoms of my molecules, using GROMACS 3.3.3. I have read the mailing lists, but I could not find anything specific about it (although the

RE: [gmx-users] About the binary identical continuation by restarting from the checkpoint file

Hi, I change to Gromacs 4.0.4 now, and perform NPT with four CPU cores. The results of continuation runs are still different from the undivided run. Neither phenomenon described previously disappears. Guang-Jun From: g...@hotmail.com To: gmx-users@gromacs.org Subject: RE:

Re: [gmx-users] About the binary identical continuation by restarting from the checkpoint file

GuoGuangjun wrote: Hi, I change to Gromacs 4.0.4 now, and perform NPT with four CPU cores. The results of continuation runs are still different from the undivided run. Neither phenomenon described previously disappears. The first phenomenon is a non-problem. The files are identical

[gmx-users] OPLS-AA topologies for ATP/ADP.

Does anybody have the topology files for ATP and/or ADP for the OPLS-AA forcefield?. If not, how can I parameterize this molecules?. Best regards. Lucio Montero. Lucio Ricardo Montero Valenzuela Instituto de Biotecnologia, UNAM Departamento de Biologia Molecular de Plantas Av. Universidad

RE: [gmx-users] About the binary identical continuation by restarting from the checkpoint file

Hi, Did you redo the run you continued from as well with 4.0.4? Also there are two other issues that can prevent binary identical contiuation: dynamic load balancing and FFT optimization (when using PME with fftw). Dynamic load balancing can be turned off with mdrun -dlb no You can turn off

Re: [gmx-users] Interpretation of g_hbond results

Justin A. Lemkul wrote: David van der Spoel wrote: Justin A. Lemkul wrote: Hi, I have a quick question about interpreting the output from g_hbond. I am using the -ac option to calculate H-bond lifetimes between my protein and a series of different, bound ligands. I read the associated

[gmx-users] g_density for a centain slice

Dear all,   I have a surface in xy plane. I want to use g_density to calcuate the density profile of solvent along z axis. As my surface groups is not homogeneuously distributed on the surface, some parts are hydrophilic and some parts are hydrophobic. therefore I need to divide the surface

[gmx-users] IBUPROFEN

Dear GMX-users and developers, I am interested in doing simulation of ibuprofen (NSAIDs Drug). But I am facing some difficulties in getting the right topologies ( OPLS-AA force field). I get my pdb field from PRODRG server. Does anyone can help me in getting the correct file? Any comments

[gmx-users] mdrun error

Dear all, I am doing a protein simulation for 20ns in single processor machine. after 11.1ns when I am trying to rerun mdrun its coming out with the following error. -- Inner product between old and new vector = 0.0! constraint #0 atoms 1 and 2 Warning: 1-4

[gmx-users] how to convert the *.cube file to a (x, y, z) format file

hi gmx-users, I have run g_spatial and got a *.cube output file. But I don't know how to convert the *.cube file to a (x,y,z) format file in order to load it into other plot software. Any suggetion is appreciated Jinyao Wang wan...@ciac.jl.cn 　　2009-02-25

[gmx-users] ffG43a1bon.itp: how to add new bond type in ffG43a1bon.itp

Dear Gromacs users, I am using Gromacs vs 3.3.3 on Open Suse LInux with ffG43a1 force field. My molecule contain aromatic carbon-chlorine bond, and i want to assign bond type for this but there is no entry in ffG43a1bon.itp correspond to aromatic carbon-chlorine bond. I got Force constant