[gmx-users] RE: simulation of a metal binding sites

Hi, I have incorporated some metal binding sites(zinc ion) in my protein. Now I want to see whether that region binds to zinc ions or not and what is the effect of ion binding to the topology of the protein .. Can this be done using gromacs and how ?? Regards -- Bharat Ph.D. Candidate Room No.

Re: [gmx-users] Protein-membrane system

Hi, "3000 water molecule per lipids per second" corresponds to 0.000384 water molecules transferred across the membrane per nano second (assume the system contains 128 lipids). It seems water translocation should not be observed in a simulation of 10 ns, but I am not sure. And I only find one r

Re: [gmx-users] zero atoms for FE P

Moeed wrote: Hello, I tried to follow the FE tutorials and get my own system working but it seems I am missing something coz I get a blank dgdl file. log file is saying: There are 0 atoms and 0 charges for free energy perturbation Removing pbc first time What I do is runnin

[gmx-users] zero atoms for FE P

Hello, I tried to follow the FE tutorials and get my own system working but it seems I am missing something coz I get a blank dgdl file. log file is saying: There are 0 atoms and 0 charges for free energy perturbation Removing pbc first time What I do is running EM (lambda 0) on a solvated syst

Re: [gmx-users] Protein-membrane system

Dear Aldo, It is totally OK to see water molecules within the bilayer, both in simulations and real life. If I am not totally wrong, 3000 water molecule per lipids per second are being transferred across the bilayer without any protein involvement. If your system is stable, the lipids densit

Re: [gmx-users] mpirun error?

Justin Kat wrote: Dear Gromacs, My colleague has attempted to issue this command: mpirun -np 8 (or 7) mdrun_mpi .. (etc) According to him, he gets the following error message: MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode -1. NOTE: invoking

[gmx-users] mpirun error?

Dear Gromacs, My colleague has attempted to issue this command: mpirun -np 8 (or 7) mdrun_mpi .. (etc) According to him, he gets the following error message: MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode -1. NOTE: invoking MPI_ABORT causes Open MPI to kil

Re: [gmx-users] g_hbond and 4.5.2 version

Hi, That suggets it's related to the new merge-on-the-fly-code and not the pbc handling. And it's me, not Justin, who's fixing and probably creating the bugs. :-) Cheers, Erik Zuzana Benkova skrev 2011-02-16 19.58: Dear Justin, maybe following information helps you. When I evaluated the n

[gmx-users] Re: angle constrain, constrained PF6 anion

Hello, I got your files. However, the error is completely another than you mention and it occurs directly at the first time-step of the simulation. Inner product between old and new vector <= 0.0! constraint #1 atoms 1377 and 1381 Wrote pdb files with

Re: [gmx-users] g_hbond and 4.5.2 version

Dear Justin, maybe following information helps you. When I evaluated the number of hydrogen bonds between two different groups, particularly, water and frozen atoms of the siloxane surface I got the same results with both version of GROMACS, 4.0.3 and 4.5.2.GreetingsZuzanaOn 02/15/11, Zuzana Benkov

Re: [gmx-users] Protein-membrane system

Aldo Segura wrote: Dear gmx-users, I completed a MD (10 ns) of my protein-membrane system. When I perform a visual inspection (VMD) of md_0_1.gro file I observed a few water molecules within the bilayer. In previous steps (e.g. equilibration) this was not observed. Could be expected such beh

[gmx-users] Protein-membrane system

Dear gmx-users, I completed a MD (10 ns) of my protein-membrane system. When I perform a visual inspection (VMD) of md_0_1.gro file I observed a few water molecules within the bilayer. In previous steps (e.g. equilibration) this was not observed. Could be expected such behavior? Best regards

[gmx-users] Re: Re: g_rmsf reference structure? (Tsjerk Wassenaar)

Thank you very much for the clarification! Message: 1 Date: Wed, 16 Feb 2011 10:46:18 +0100 From: Tsjerk Wassenaar Subject: Re: [gmx-users] g_rmsf reference structure? To: Discussion list for GROMACS users Message-ID: Content-Type: text/plain; charset=ISO-8859-1 Hi, The reference i

[gmx-users] Re: gromacs QM/MM compilation with gaussian (Txema Mercero)

http://lists.gromacs.org/pipermail/gmx-users/attachments/20110216/8495d798/attachment-0001.html -- Message: 5 Date: Wed, 16 Feb 2011 10:43:56 +0100 From: Tsjerk Wassenaar Subject: Re: [gmx-users] Periodic Boundary Conditions g_mindist -pi To: Discussion list for GROMACS

Re: [gmx-users] Re: gromacs QM/MM compilation with gaussian (Txema Mercero)

>>>> >>>> Thanks, >>>> >>>> Ifat >>>> >>>> >>>> >>>> The output: >>>> >>>> 343.7 10.813 5.924 16.445 16.445 16.445 >>>> >>>> 343.8 10.809 5.949

Re: [gmx-users] Re: gromacs QM/MM compilation with gaussian (Txema Mercero)

;> >>> 345      0.173   21.981 16.445 16.445 16.445 >>> >>> 345.1   0.191   21.954 16.445 16.445 16.445 >>> >>> 345.2   0.183   21.958 16.445 16.445 16.445 >>> >>> 345.3   0.181   22.012 16.445 16.445 16.445 >>> >>&g

[gmx-users] Re: gromacs QM/MM compilation with gaussian (Txema Mercero)

.445 16.445 >> >> 345.4 0.17 22.054 16.445 16.445 16.445 >> >> 345.5 0.168 22.054 16.445 16.445 16.445 >> >> 345.6 0.189 22.039 16.445 16.445 16.445 >> >> 345.7 0.171 22.007 16.445 16.445 16.445 >> >> 345.8 0.186

Re: [gmx-users] initial structures for md simulations

On 16/02/2011 11:24 PM, oguz gurbulak wrote: /Dear All/, I want to generate some initial crystalline structures of my targetmolecules for md simulations. /Are there any free softwares/ to do this? Some sources for obtaining initial coordinates can be found here http://www.gromacs.org/Doc

Re: [gmx-users] Re: Periodic Boundary Conditions g_mindist -pi

45 16.445 16.445 >> >> 345.6   0.189   22.039 16.445 16.445 16.445 >> >> 345.7   0.171   22.007 16.445 16.445 16.445 >> >> 345.8   0.186   22.031 16.445 16.445 16.445 >> >> 345.9   0.171   22.077 16.445 16.445 16.445 >> >> 346  

[gmx-users] initial structures for md simulations

Dear All,   I want to generate some initial crystalline structures of my target molecules for md simulations. Are there any free softwares to do this?   And are there any complete sources that give the theoretical structures of organic molecules ( like hydrocarbons ) determined by the exper

Re: [gmx-users] Re: Periodic Boundary Conditions g_mindist -pi

6.445 16.445 16.445 347 10.762 5.999 16.445 16.445 16.445 347.1 10.781 5.984 16.445 16.445 16.445 347.2 10.784 6.002 16.445 16.445 16.445 -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gm

[gmx-users] Re: Periodic Boundary Conditions g_mindist -pi

45 > > 346.6 10.813 5.996 16.445 16.445 16.445 > > 346.7 10.781 6.006 16.445 16.445 16.445 > > 346.8 10.793 6.026 16.445 16.445 16.445 > > 346.9 10.745 5.985 16.445 16.445 16.445 > > 347 10.762 5.999 16.445 16.445 16.445 > > 347.1 10.781

[gmx-users] Re: gromacs QM/MM compilation with gaussian

Hi there! We are trying to compile gromacs with Gaussian 03 rev D.02 (we also have g09). We followed the instructions in http://wwwuser.gwdg.de/~ggroenh/roadmap.pdf despite that they do no fit exactly with the g03 rev d03 version,for instance, FrcNCN is no in l710 but in utilam.F Despite of that

Re: [gmx-users] g_rmsf reference structure?

Hi, The reference is used for fitting. The RMSF is calculated with respect to the average (fitted) structure, unless you explicitly specify that deviations from the reference should be used. Cheers, Tsjerk On Wed, Feb 16, 2011 at 7:08 AM, Mark Abraham wrote: > On 16/02/2011 3:44 PM, kulleperum

Re: [gmx-users] Periodic Boundary Conditions g_mindist -pi

Hi Ifat, I guess this is a jump over the periodic boundaries. You should remove jumps from the trajectory (-pbc nojump) before running g_mindist -pi. Cheers, Tsjerk On Wed, Feb 16, 2011 at 10:19 AM, ifat shub wrote: > Hi, > > > > I am running a simulation on the complex 1aik.pdb in 310K. I wan

[gmx-users] Periodic Boundary Conditions g_mindist -pi

Hi, I am running a simulation on the complex 1aik.pdb in 310K. I wanted to see if the complex is seeing its next periodic image, so I used the g_mindist command with the -pi option. My command line was: g_mindist -f run.xtc -s run.gro -n index.ndx -od tmp.xvg -pi The output (see below) was sta