[gmx-users] Re: Pull code with pull_geometry = cylinder generates error: Distance of pull group 1 (4.030185 nm) is larger than 0.49 times the box size (3.012310)

Thank you David for your response. Please see my reply below. On 2012-10-04 11:50, Emma Eriksson wrote: > Dear all, > > I am using the pull code in Gromacs 4.5.5 to constrain the distance in one > direction (z) between a small molecule and a lipid bilayer. I run separate > simulations with dist

Re: [gmx-users] residue-residue interaction energies

Hi Justin, thank you for your quick reply. When you say: "..Probably by analyzing them individually with mdrun -rerun to recalculate each frame. Tedious, but can be easily scripted..." do you mean I have to run g_enemat module using -b and -e options in order to set the first and the last frame

[gmx-users] Re: DNA orientation restrain

Thanks, Erik. Actually, I tried to use periodic molecules in my previous simulations. But I think that can be only applied to DNA molecules of certain length, say 10bps, 20bps. But my DNA molecule here doesn't meet that criteria. Dudu -- View this message in context: http://gromacs.5086.n6.na

[gmx-users] Re: gmx-users Digest, Vol 102, Issue 45

Dear Vitaly, I had to struggle with the equilibration of an ionic liquid at charged electrodes - it means a spatial inhomogeneous system and high forces due to the electrostatics). I found the following tricks working for me: * Pre-equilibration with a reduction of the step size (e.g. from 2

[gmx-users] Re: Segmentation fault, mdrun_mpi

Justin Lemkul wrote > My first guess would be a buggy MPI implementation. I can't comment on > hardware > specs, but usually the random failures seen in mdrun_mpi are a result of > some > generic MPI failure. What MPI are you using? I am using the OpenMPI package, version 1.4.3. It's one of t

Re: [gmx-users] Re: DNA orientation restrain

Hi, Yes. Although not applicable to all systems, as you correctly state, a slightly extended periodic DNA helix could still yield a smaller box since the non-periodic molecule would need a minimum distance to its periodic copy, the length of which depending on the non-bonded interactions. Hence

[gmx-users] how to center the protein?

Dear: I am using the command: trjconv -f md.trr -s md.tpr -dump 54000 -o md.pdb -pbc mol trjconv -f md.pdb -s md.tpr -o fit.pdb -fit rot+rans to extract a frame of my md simulation and I found my protein is not in the centre of simulation box. here is a figure for it: https://dl.dropbox.

Re: [gmx-users] Interaction energy..

Hi justin, As per your advice, g_enemat -f ener.edr -groups groups.dat -nocoul -nolj Opened ener.edr as single precision energy file Will read groupnames from inputfile Read 2 groups group 0WARNING! could not find group (null):energy-energy (0,0)in energy file WARNING! could not find group (nul

Re: [gmx-users] how to center the protein?

HI you can put the protein in center by adding flag -center to trjconv ( see trjconv -h) use the proper index file ( if you made ) -n .. You can also use the -pbc cluster and extract the specific time frame by flag -dump see trjconv very carefully ,It has the way to do it. With best wishes

Re: [gmx-users] Interaction energy..

On 10/8/12 5:40 AM, rama david wrote: Hi justin, As per your advice, g_enemat -f ener.edr -groups groups.dat -nocoul -nolj Opened ener.edr as single precision energy file Will read groupnames from inputfile Read 2 groups group 0WARNING! could not find group (null):energy-energy (0,0)in ene

Re: [gmx-users] Interaction energy..

Hi justin, I correct command as follow and g_enemat -f ener.edr -groups groups.dat -coul -lj out-put is like Opened ener.edr as single precision energy file Will read groupnames from inputfile Read 2 groups group 0WARNING! could not find group (null):energy-energy (0,0)in energy file WARNING! c

Re: [gmx-users] Interaction energy..

On 10/8/12 6:00 AM, rama david wrote: Hi justin, I correct command as follow and g_enemat -f ener.edr -groups groups.dat -coul -lj out-put is like Opened ener.edr as single precision energy file Will read groupnames from inputfile Read 2 groups group 0WARNING! could not find group (null):e

Re: [gmx-users] Re: Segmentation fault, mdrun_mpi

On 10/8/12 4:39 AM, Ladasky wrote: Justin Lemkul wrote My first guess would be a buggy MPI implementation. I can't comment on hardware specs, but usually the random failures seen in mdrun_mpi are a result of some generic MPI failure. What MPI are you using? I am using the OpenMPI package,

Re: [gmx-users] residue-residue interaction energies

On 10/8/12 3:14 AM, federico vaglio wrote: Hi Justin, thank you for your quick reply. When you say: "..Probably by analyzing them individually with mdrun -rerun to recalculate each frame. Tedious, but can be easily scripted..." do you mean I have to run g_enemat module using -b and -e optio

Re: [gmx-users] Re: Fwd: How to can i replace a molecule

On 10/8/12 12:48 AM, shika wrote: it is because when i put genbox -cp protein_box.gro -ci solvent.gro -nmol 1381 -p control.top -o prot_solv.gro the error turn out like this : System total charge: 0.000 Grid: 17 x 16 x 14 cells nri = 12718, nrj = 100152 Try 9119box_margin = 0.45overlap: Kill

Re: [gmx-users] Interaction energy..

Hi justin, g_enemat -f ener.edr -groups groups.dat -coul -nolj Out-put is like Opened ener.edr as single precision energy file Will read groupnames from inputfile Read 2 groups group 0WARNING! could not find group (null):energy-energy (0,0)in energy file WARNING! could not find group (null):en

Re: [gmx-users] Interaction energy..

On 10/8/12 7:09 AM, rama david wrote: Hi justin, g_enemat -f ener.edr -groups groups.dat -coul -nolj Out-put is like Opened ener.edr as single precision energy file Will read groupnames from inputfile Read 2 groups group 0WARNING! could not find group (null):energy-energy (0,0)in energy fi

[gmx-users] Re: domain decomposition trick for highly parallel, non-equilibrium runs

Sorry for double post, first message had the wrong subject. Dear Vitaly, I had to struggle with the equilibration of an ionic liquid at charged electrodes - it means a spatial inhomogeneous system and high forces due to the electrostatics). I found the following tricks working for me: * Pre-equ

[gmx-users] Re: gmx-users Digest, Vol 102, Issue 52

Dear usres Thank you for your replies 1- Is it possible define a ion as a propane molecule and then I do adding propane molecules instead of methane molecules in my system? 2- Other wise, I select 300 molecules of methane and remove them from my system(randomly and by hand, for example 500 mole

Re: [gmx-users] domain decomposition trick for highly parallel non-equilibrium runs

On Sat, Oct 6, 2012 at 6:03 PM, Dr. Vitaly Chaban wrote: > Would anyone perhaps suggest some tricks to increase the stability of > the highly parallel jobs (NP > 100), which use domain decomposition > among nodes. It would be more helpful to know what you are talking about, i.e. a definition of s

[gmx-users] Re: pull=constraint gives zero forces

Following up on this post. I've tried the same runs using version 4.0.7, which gave immediate segmentation faults. Not sure if this is a clue or a trivial consequence of switching versions, but there it is. Any other ideas why the pullf output just contains zeros? Cheers, Alex alex.bjorling wro

[gmx-users] About Lincs Algorithim for Cyclic Peptide

Dear Justin Thank you For your Previous reply    I have used the EM.gro file of Cyclic Peptide  For NPT Equlibrartion Without using  Lincs Algorithim it run Suceesfully But with Lincs Algorithm It shows Errror As follows Though  I have reduce the time step     relative constraint deviation aft

Re: [gmx-users] About Lincs Algorithim for Cyclic Peptide

On 2012-10-08 17:17, vidhya sankar wrote: Dear Justin Thank you For your Previous reply I have used the EM.gro file of Cyclic Peptide For NPT Equlibrartion Without using Lincs Algorithim it run Suceesfully But with Lincs Algorithm It shows Errror As follows Though I have reduce the time

Re: [gmx-users] About Lincs Algorithim for Cyclic Peptide

On 10/8/12 11:17 AM, vidhya sankar wrote: Dear Justin Thank you For your Previous reply I have used the EM.gro file of Cyclic Peptide For NPT Equlibrartion Without using Lincs Algorithim it run Suceesfully But with Lincs Algorithm It shows Errror As follows Though I have reduce the ti

Re: [gmx-users] Unable to fire-up the parallel processes on cluster

On 10/8/12 10:08 AM, Venkat Reddy wrote: Dear Gromacs users, I am trying to invoke a parallel job on three nodes (i101,i102,i103) using the command as given in gromacs manual mpirun -p i101,i102,i103 8 mdrun_mpi -v -s npt_100.tpr -deffnm npt_100 but its giving me an error like: mpirun was unab

Re: [gmx-users] Re: gmx-users Digest, Vol 102, Issue 52

On 10/8/12 7:48 AM, Ali Alizadeh wrote: Dear usres Thank you for your replies 1- Is it possible define a ion as a propane molecule and then I do adding propane molecules instead of methane molecules in my system? Unlikely. 2- Other wise, I select 300 molecules of methane and remove them

Re: [gmx-users] I want to add 460 molecules into a box

On 10/8/12 2:49 PM, Ali Alizadeh wrote: Dear users I want to add 460 molecules into a box but i can not add more than 400 molecules, genbox -ci het.gro -nmol 460 -box ... Even, when i change VanderWaals radii( i reduce it,vdwwradii.dat ) but maximum molecules to be 440. Decrease more th

[gmx-users] Gromacs-CPMD ....versions???

Hello Fellow Users, I wanted to know about the gromacs versions compatible with interfacing ...with CPMD QM/MM...??? is that particular version provided by Dr. Biswas is the only one or the latest versions are also capable of doing so??? Any News or info..or way??? Thank you all cheers Raghav

[gmx-users] Re: domain decomposition trick for highly parallel, non-equilibrium runs

Dear Kathleen: It is important to either load velocities or generate them. If you do neither, then initial forces will rapidly be scaled up to thermally appropriate velocities, and if the initial forces are concerted, then you can get significant undesired concerted motion that can do things li

[gmx-users] Re: pull=constraint gives zero forces

Please post your entire .mdp file and a snip of the output in your pullf and pullc files. (Your initial post on this topic was also missing these, although the text reads as if you intended to include them). I'll note that there are no forces when using constraints, so the fact that you get zer

[gmx-users] (no subject)

Dear all, When I try to install gromacs-4.5.5 on my centos system, I meet trouble. I installed fftw-3.3.2 and then install gromacs-4.5.5. When I type /.configure command, I got the error information: checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-g

[gmx-users] distance between protein and ligand

Hi, I have simulated a protein-ligand complex for 5ns. I checked distance between the important residues of protein and the ligand using g_dist. My question is can the distance between the two groups decrease from the initial distance (docked complex as starting structure for simulation). I know

[gmx-users] generation of .itp file

sir, I want to generate .itp from a pdb file. Is there any option in gromacs. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please do

Re: [gmx-users] Re: pull=constraint gives zero forces

Hi Alex, constraint pulling has a bug in 4.5.5, see: http://redmine.gromacs.org/issues/825. I'm guessing that's causing your problems. Fixing it is very easy (see the link) or you can also use an earlier version like 4.5.3 that works. Best, Jaakko On 9.10.12 2:26 , Christopher Neale wrote: