[gmx-users] Problem on forming bonds

Hi. I'm trying to subject a metalloprotein bound to cadmium to a molecular dynamics. I've defined the cadmium ion in the atom type parameter file (ffGa56a6.atp) and residue database (ffG53a6.rtp). And the bond length and bond angle between the cadmium and sulphur of the metalloprotein had been def

Re: [gmx-users] Re: gmx-users Digest, Vol 74, Issue 134

Amin, maybe your MPI-enabled executable is called mdrun_mpi. Check the directory where mdrun is and make shure (with ldd for example) the mdrun* you are using is linked to the MPI library you are using. Carsten On Jun 24, 2010, at 6:51 AM, Amin Arabbagheri wrote: > Carsten, > > Thanks for yo

Re: [gmx-users] Problem on forming bonds

Ni hao Kwee Hong, These special links should be defined in the file specbond.dat. That file you can find in the gromacs topology data directory. Have a look at the linkage of iron, e.g.. Also check the manual/wiki/mailinglist on 'specbond.dat' for more information. Hope it helps, Tsjerk On Thu,

[gmx-users] vdwtype=shift

Dear users, I have a question about vdwtype. My question is if I use vdwtype=shift in nvt.mdp file: ; Neighborsearchingns_type = grid ; search neighboring grid celsnstlist = 5 ; 10 fsrlist= 1.0 ; short-range neighborlist cutoff (

Re: [gmx-users] vdwtype=shift

you zou skrev: Dear users, I have a question about vdwtype. My question is if I use vdwtype=shift in nvt.mdp file: ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.0 ; short-range electro

[gmx-users] General Question

Dear GROMACS team members, I have a general question about the GROMACS, actually I have used GROMACS for the simulation of 59 amino acids domain part of the protein containing within it. This domain lies in the position from 34-92 out of 239 residues, this loop having only 12 residues similarity w

Re: [gmx-users] Help in parametrisation

onetwo wrote: Thanks Justin for the help, I have Manganese in my protein with other two ligands at the active site. I am using GROMOS96 43a1 force field. Mangnese may have topology similar to Magnesium 2+, What I found is that Assuming a transition metal "may" be similar to another species

Re: [gmx-users] General Question

pawan raghav wrote: Dear GROMACS team members, I have a general question about the GROMACS, actually I have used GROMACS for the simulation of 59 amino acids domain part of the protein containing within it. This domain lies in the position from 34-92 out of 239 residues, this loop having on

[gmx-users] P4_error for extending coarse grained MD simulations

Dear GMX-users, This is Justin. I am performing coarse-grained simulation on a protein-lipid bilayer system. This is a MARTINI CG model. I have successfully completed a 360ns simulation, during which the time step is 30 fs. I would like to extend the simulation to 1micro-second. The commands I us

[gmx-users] Problems with installing mpi-version of Gromacs on Cluster with Debian-Lenny

Dear All, I've been trying to compile and get Gromacs (version 4.0.7) working on a cluster that runs with Debian Lenny. I set the following variables: export SOFT=$HOME/GROMACS export PATH="$PATH":$SOFT/bin export LDFLAGS="-L$SOFT/lib" export CPPFLAGS="-I$SOFT/include" export LD_LIBRARY_PATH=$

[gmx-users] Making a .rtp file

I am trying to create a .gro file of a single detergent which I am going to then multiply and put it in water and have it form micelles. In order to create a .gro file, I know I need to create a .rtp file of my residue or add it to the desired force field .rtp file I want to run my detergent in.

[gmx-users] g_anaeig -proj

Hi everyone, please I'm doing for the first time a covariance analysis. I followed this tutorial: http://nmr.chem.uu.nl/~tsjerk/course/molmod/analysis1.html But I don't understand. -proj gives the projection of the trajectory on the fi

Re: [gmx-users] Making a .rtp file

Amanda Watkins wrote: I am trying to create a .gro file of a single detergent which I am going to then multiply and put it in water and have it form micelles. In order to create a .gro file, I know I need to create a .rtp file of my residue You do not *need* a .gro file, nor do you necessar

[gmx-users] Weird error with g_sorient

Hi All, I'm trying to use g_sorient to calculate some solvent properties in a few systems I'm simulating. It's the first time I've used the tool, so if I've missed something obvious, please let me know. I'm getting a very weird error when I execute the command: echo 1 13 | g_sorient_4.0.7

[gmx-users] Help with g_vanhove

Dear gmx users, I am trying to calculate the Van Hove correlation function (G(r,t)) using the utility g_vanhove. However, I don't seem to be able to make it work. The program outputs files, but the points are all 0 except at r=0. My simulation is a hydrated lipid bilayer with 128 molecules. I

[gmx-users] standard state correction of delta G from a PMF

Hi Chris. Thanks for getting back to me. My problem is with the conversion to standard state concentration (1M) from umbrella sampling simulations. I can't understand how to do this from my umbrella sampling simulations. Even after reading several papers that perform the correction unclear on wh

Re: [gmx-users] vdwtype=shift

section 7.3.11 of gromacs manual (v4.0)/ -Gaurav On Thu, Jun 24, 2010 at 4:40 AM, Erik Marklund wrote: > you zou skrev: >> >> Dear users, >> >> I have a question about vdwtype. My question is if I use vdwtype=shift in >> nvt.mdp file: >> >> ; Neighborsearching >> ns_type = grid ; search neighbor

Re: [gmx-users] Problems with installing mpi-version of Gromacs on Cluster with Debian-Lenny

- Original Message - From: Christian Mücksch Date: Friday, June 25, 2010 0:21 Subject: [gmx-users] Problems with installing mpi-version of Gromacs on Cluster with Debian-Lenny To: MAILINGLIST GROMACS > Dear All, > > I've been trying to compile and get Gromacs (version 4.0.7) > worki

[gmx-users] standard state correction of delta G from a PMF

Dear Elio: I think I was pretty clear in my last email: If you still have trouble, then your next post should include things like "I tried this... but I didn't understand this specific part" to make it clear that you have put in the effort here. Otherwise, hopefully somebody else has the ti

Re: [gmx-users] P4_error for extending coarse grained MD simulations

How about using the last .gro file to continue your simulation? 2010/6/24 张春雷 > Dear GMX-users, > > This is Justin. > I am performing coarse-grained simulation on a protein-lipid bilayer > system. This is a MARTINI CG model. > I have successfully completed a 360ns simulation, during which the

[gmx-users] Re: vdwtype=shift

Thank you for your help friends, But I have no any idea about amount of rvdw-switch. I would like to use vdwtype=shift(shift LJ to 0), but I don't know which number for rvdw-switch and rvdw should be choice? In manual I saw rvdw-switch=0 and rvdw=1.0, but it had this error. section 7.3.11 of gr

[gmx-users] .RTP files

Dear gromacs users, I have been trying to use a polymer in the system and for its topology generation I have created its .rtp file. I am having trouble using the .rtp file in pdb2gmx command as it shows "file input/output error". Can anyone please help me as to how i should use the .rtp file in

Re: [gmx-users] P4_error for extending coarse grained MD simulations

The last .gro file only provides coordinates of the system. No velocity is recorded. Actually, what I attempt to achieve is a binary identical trajectory. So I think the velocity from the last step is critical. I have tried another approach in which the checkpoint file is neglected. $mdrun_mpi_d