[gmx-users] spatial distribution function for ionic liquid

Dear all... I want to get spatial distribution function for ionic liquid. So, I used g_sdf command as below g_sdf -f mixture_mdpr.trr -n index.ndx -s mixture_mdpr.tpr -o sdf_plt.dat -r sdf.gro -mode 1 -grid 3.8 3.8 3.8 I rename the output file from .dat file to .plt file and I used VMD to

[gmx-users] Finding H-Bond donor-acceptor pairs

Hi ALL, I was just wondering if GROMACS has any tool to list out the hydrogen bond donor-acceptor pairs (in terms of residue names/numbers) throughout a MD simulation, say 10 ns. Can g_hbond be used to do this or is there any other command/method? Any suggestion is welcome. Regards, Anirban --

Re: [gmx-users] Finding H-Bond donor-acceptor pairs

On 1/14/10 9:24 AM, Anirban Ghosh wrote: Hi ALL, I was just wondering if GROMACS has any tool to list out the hydrogen bond donor-acceptor pairs (in terms of residue names/numbers) throughout a MD simulation, say 10 ns. Can g_hbond be used to do this or is there any other command/method? Any

RE: [gmx-users] Finding H-Bond donor-acceptor pairs

Hi Anirban, Use g_hbond with -g option. -) Osmair Date: Thu, 14 Jan 2010 13:54:09 +0530 From: reach.anirban.gh...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] Finding H-Bond donor-acceptor pairs Hi ALL, I was just wondering if GROMACS has any tool to list out the hydrogen bond

Re: [gmx-users] Simulation with Implicit solvents

Lum Nforbi wrote: Hello all, Has anyone done simulation with implicit solvents? If so, please, could you let me know how implicit solvents are set up, in general? Is there some documentation where I could find this information in? GROMACS will not support implicit solvent models before

[gmx-users] Error while pulling a settled tip4p water molecule

Hi, I am doing umbrella simulations of a water molecule, using complete tip4p molecules as pull groups (or alternatively using only the three masses of the tip4p as pull group). When doing so, mdrun exits with the error: --- Program mdrun,

RE: [gmx-users] Error while pulling a settled tip4p water molecule

Hi, I don't understand why you got this error message. Do you have two different types of water molecules with different geometries? In that case Gromacs would give this error message, because currently only one geometry is supported for settle, so you'll have to replace the others by 3 normal

Re: [gmx-users] Error while pulling a settled tip4p water molecule

Berk Hess wrote: Hi, I don't understand why you got this error message. Do you have two different types of water molecules with different geometries? In that case Gromacs would give this error message, because currently only one geometry is supported for settle, so you'll have to replace the

RE: [gmx-users] Error while pulling a settled tip4p water molecule

Date: Thu, 14 Jan 2010 14:20:48 +0100 From: joc...@xray.bmc.uu.se To: gmx-users@gromacs.org Subject: Re: [gmx-users] Error while pulling a settled tip4p water molecule Berk Hess wrote: Hi, I don't understand why you got this error message. Do you have two different types of water

Re: [gmx-users] Error while pulling a settled tip4p water molecule

Berk Hess wrote: Date: Thu, 14 Jan 2010 14:20:48 +0100 From: joc...@xray.bmc.uu.se To: gmx-users@gromacs.org Subject: Re: [gmx-users] Error while pulling a settled tip4p water molecule Berk Hess wrote: Hi, I don't understand why you got this error message. Do you have two

[gmx-users] Density

Hello, I'm experiencing some difficulties with gromacs. In order to control my system's density, I have to use g_energy or g_density. However, when I use g_energy, in my list, Density doesn't appear. Else, if I use g_density, it needs a file traj.xtc which I don't have. So please can anyone tell

Re: [gmx-users] Density

Carla Jamous skrev: Hello, I'm experiencing some difficulties with gromacs. In order to control my system's density, I have to use g_energy or g_density. However, when I use g_energy, in my list, Density doesn't appear. Else, if I use g_density, it needs a file traj.xtc which I don't have. So

RE: [gmx-users] about the traj modification

Dear Justin, Thanks for your instant reply about my problem. I've already finished the make_ndx part, choosing the protein option. But for trjconv, how can I write the command line to have the prompt Select group for output? Sorry, I'm really a beginner. Thank you! Best, Zhenwei

Re: [gmx-users] Unstable Minimizations

Problem Solved. I replaced HETATM with ATOM, I fixed BOTH N-terminal and C-terminal. I kept TER and END. Removed all CONECT. Renamed the CYS to CYS2. No other non-AminoAcid residues were present. Most of this is described by the FFAmber site http://chemistry.csulb.edu/ffamber/ 2) *(!) Residue

Re: [gmx-users] Unstable Minimizations

Hi Jack, On Thu, Jan 14, 2010 at 5:41 PM, Jack Shultz j...@drugdiscoveryathome.comwrote: Problem Solved. I replaced HETATM with ATOM, I fixed BOTH N-terminal and C-terminal. I kept TER and END. Removed all CONECT. Renamed the CYS to CYS2. No other non-AminoAcid residues were present. Most

[gmx-users] Error while pulling a settled tip4p water molecule

I have done a similar thing in the past (without using the pull code), renaming the crystal waters around the protein so that they were easier to track. I eventually figured out that it was necessary for me to place the waters sequentially in the .top file. e.g: ; This is OK Protein 1

Re: [gmx-users] about the traj modification

zh.li wrote: Dear Justin, Thanks for your instant reply about my problem. I've already finished the make_ndx part, choosing the protein option. But for trjconv, how can I write the command line to have the prompt Select group for output? Sorry, I'm really a beginner. Thank you! If you

[gmx-users] Columns in log file of g_cluster

Hello everyone, What do columns 3 and 5 (the rmsd numbers next to the number of structures in the cluster and the frame number of the central cluster, respectively) indicate in the log file of g_cluster? Thanks, Bob -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] SImulation error grompp

Hi All, I am running simulation of a system containing Coarse Grained 1SU4 (Minimized structure) and Coarse Grained DPPC lipid. I used the INFLATEGRO script to inflate the lipid and removed the overlapping lipids with proteins and then running the energy minimization. grommp says there are

[gmx-users] SImulation error grompp

-users/attachments/20100114/4df04b2e/attachment.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www

Re: [gmx-users] SImulation error grompp

how to fix this. Reply will be appreciable. Thanks, Sunny -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100114/4df04b2e/attachment.html -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] Gromacs 4.1

Hi Mark, When will Gromacs 4.1 be available? Thank you, Lum -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list.

Re: [gmx-users] Unstable Minimizations

Tsjerk Wassenaar skrev: Hi Jack, On Thu, Jan 14, 2010 at 5:41 PM, Jack Shultz j...@drugdiscoveryathome.com mailto:j...@drugdiscoveryathome.com wrote: Problem Solved. I replaced HETATM with ATOM, I fixed BOTH N-terminal and C-terminal. I kept TER and END. Removed all

Re: [gmx-users] Density

Carla Jamous wrote: Hello, I'm experiencing some difficulties with gromacs. In order to control my system's density, I have to use g_energy or g_density. Those tools report density-related quantities, they do not control it. However, when I use g_energy, in my list, Density doesn't appear.

Re: [gmx-users] Gromacs 4.1

Lum Nforbi wrote: Hi Mark, When will Gromacs 4.1 be available? There's no planned date of which I am aware. Even if there was, GROMACS 4.0 was released six or more months after its paper was published, and then underwent six or more months of noteworthy bug-fixing. Caveat simulator.

Re: [gmx-users] Gromacs 4.1

On 1/14/10 10:43 PM, Mark Abraham wrote: Lum Nforbi wrote: Hi Mark, When will Gromacs 4.1 be available? There's no planned date of which I am aware. Even if there was, GROMACS 4.0 was released six or more months after its paper was published, and then underwent six or more months of

Re: [gmx-users] Columns in log file of g_cluster

On 1/14/10 6:34 PM, Bob Johnson wrote: Hello everyone, What do columns 3 and 5 (the rmsd numbers next to the number of structures in the cluster and the frame number of the central cluster, respectively) indicate in the log file of g_cluster? Thanks, Bob Please post a header to remind us. --

[gmx-users] Configuration of Gaussian for QM/MM

Hello. I'm trying to setup QM/MM for Gaussian03. http://wwwuser.gwdg.de/~ggroenh/qmmm.html I refer the upper links, but I still can not understand. ==roadmap.pdf (page 6) modified subroutines in l701 • oneeli added an extra argument to Oneeli() for the forces on the point

[gmx-users] MPI ERROR while installing GMX4.0.7

Hello gmx-users !! I am trying to install gromacs 4.0.7 double precision with mpi. I downloaded openmpi-1.4. and installed it. Then executed ./configure --enable-mpi --program-suffix=_mpi_d --prefix=/usr/local/gromacs407_double_mpi --enable-double It showed checking for mpicc... mpicc checking