[gmx-users] Adding ions

Hi, When I start from a energy minimized protein in vacuum and solvate it using genbox, the output message says that the protein has zero charge. So I skip the genion step. I follow this with energy minimization of the solvated protein followed by restraining the protein and then doing a short mdr

[gmx-users] energygrp_excl and PME

Hi everyone; I am simulating a functionalized nanotube with (CH3) group .the nanotube atoms are uncharged and rigid but the atoms of (CH3) group are charged and flexible ,and are defined in the residue name of [atom] section of topology file with (CNT)and (FUNC) , Respectively. I have decid

Re: [gmx-users] how to determine the box size

On 9/07/2010 12:59 PM, jojo J wrote: Hello Mark, Thank you for your reply. AS for the steps you mentioned to solvate a molecule: I have a simple molecule replicated by genconf -nbox in one direction. When I try to energy minimize this single molecule grompp em gives error: rlist is longer tha

Re: [gmx-users] top file

jojo J wrote: Hello, Thank you for your answer. I mean if I need to go back and comment those lines. (if the results are trusted ..actually I forgot to comment the lines..) There's no need to comment out lines referring to solvent, ions, etc if they are not present. These statements j

Re: [gmx-users] top file

Hello, Thank you for your answer. I mean if I need to go back and comment those lines. (if the results are trusted ..actually I forgot to comment the lines..) On 8 July 2010 23:10, Justin A. Lemkul wrote: > > > jojo J wrote: > >> Helllo, >> >> I got top file using pdb2gmx but I did not commen

Re: [gmx-users] top file

jojo J wrote: Helllo, I got top file using pdb2gmx but I did not comment unnecessary lines at the end of the file ( no water in my system ). With this top file I energy minimized my system. I wanted to know if I am fine ...? Depends on your definition of "fine." Do you mean to ask if yo

Re: [gmx-users] how to determine the box size

jojo J wrote: Hello Mark, Thank you for your reply. AS for the steps you mentioned to solvate a molecule: I have a simple molecule replicated by genconf -nbox in one direction. When I try to energy minimize this single molecule grompp em gives error: rlist is longer than half box size or lo

[gmx-users] top file

Helllo, I got top file using pdb2gmx but I did not comment unnecessary lines at the end of the file ( no water in my system ). With this top file I energy minimized my system. I wanted to know if I am fine ...? Thank you, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.or

[gmx-users] how to determine the box size

Hello Mark, Thank you for your reply. AS for the steps you mentioned to solvate a molecule: I have a simple molecule replicated by genconf -nbox in one direction. When I try to energy minimize this single molecule grompp em gives error: rlist is longer than half box size or longer than shortest di

Re: [gmx-users] genbox and water model

Sai Pooja wrote: Hi, I am using CHARMM forcefield with the tip3p. What input file(-cs) should i use to solvate the protein using the genbox command? The default is spc216.gro. What would be compatible with my system? I looked up the directory which has spc216.gro file. It has tip4p.gro fi

[gmx-users] genbox and water model

Hi, I am using CHARMM forcefield with the tip3p. What input file(-cs) should i use to solvate the protein using the genbox command? The default is spc216.gro. What would be compatible with my system? I looked up the directory which has spc216.gro file. It has tip4p.gro file but for some reason do

RE: [gmx-users] Compiling problems on MacOS X 10.6.4

Yes, it did work. Thanks a lot! George From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of J. Rui Rodrigues [joaquim.rodrig...@estg.ipleiria.pt] Sent: Thursday, July 08, 2010 12:32 PM To: Discussion list for GROMACS users Subj

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

Dear all, I have post this question about a two weeks ago. During these days, I followed suggestions from Mark and weixin, but did not fix it. Here, I repeat it again to seek more help. I attempt to extend MD simulation for a coarse-grained system. CG models are in MARTINI form. Simulation was ca

RE: [gmx-users] Compiling problems on MacOS X 10.6.4

Hi, Looks like auto-detection for 64bit support on macs is not working with your machine. I had a similar problem some time ago on a Mac 10.5.8: http://lists.gromacs.org/pipermail/gmx-users/2010-April/050501.html As a workaround, you could pass the following flags to configure to see if it cure

Re: [gmx-users] Location of a molecule in a dodecahedron

Birgit Hischenhuber wrote: Hi, I simulate a molecule in a dodecahedron. I used at the step with the editconf: editconf -f name.gro -o name.dod.pdb -bt dodecahedron -d 2.0 After my simulation I looked at the first frame and saw, that at two direction the molecule is actually 2 nm

[gmx-users] Location of a molecule in a dodecahedron

Hi, I simulate a molecule in a dodecahedron. I used at the step with the editconf: editconf -f name.gro -o name.dod.pdb -bt dodecahedron -d 2.0 After my simulation I looked at the first frame and saw, that at two direction the molecule is actually 2 nm away of my edge, but the at the t

RE: [gmx-users] Compiling problems on MacOS X 10.6.4

Sorry, I forgot to post the output of file src/*/*.o | head src/gmxlib/3dview.o: Mach-O object i386 src/gmxlib/atomprop.o:Mach-O object i386 src/gmxlib/bondfree.o:Mach-O object i386 src/gmxlib/calcgrid.o:Mach-O objec

Re: [gmx-users] problems with g_wham

O.K cheers Chris. I do intend to equilibrate the system at the desired temperature before constructing the histogram. chris.ne...@utoronto.ca wrote: > Depending on your system and chosen thermostat, gen-vel=no can be a > dangerous idea (very small original velocities simply get scaled up); > beside

[gmx-users] problems with g_wham

Depending on your system and chosen thermostat, gen-vel=no can be a dangerous idea (very small original velocities simply get scaled up); besides, you should be able to equilibrate from a gen-vel=yes pretty quickly. I don't disagree with Justin's comment, but just because it works doesn't m

RE: [gmx-users] Compiling problems on MacOS X 10.6.4

Thanks for your reply. The output from nm -arch i386 /opt/local/lib/libxml2.a | head is nm: file: /opt/local/lib/libxml2.a does not contain architecture: i386 and from nm -arch x86_64 /opt/local/lib/libxml2.a | head /opt/local/lib/libxml2.a(SAX.o): 3050 s EH_frame1 02a0

Re: [gmx-users] problems with g_wham

Many thanks Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> Hi Justin >> >> I am not using periodic boundary conditions for the simulations. I may >> have sorted it out now. I was generating velocities in the umbrella.mdp >> file, I have since set gen_vel = no, and the histogram has the corr

Re: [gmx-users] problems with g_wham

Gavin Melaugh wrote: Hi Justin I am not using periodic boundary conditions for the simulations. I may have sorted it out now. I was generating velocities in the umbrella.mdp file, I have since set gen_vel = no, and the histogram has the correct shape (should this make a difference?) If you

Re: [gmx-users] problems with g_wham

Hi Justin I am not using periodic boundary conditions for the simulations. I may have sorted it out now. I was generating velocities in the umbrella.mdp file, I have since set gen_vel = no, and the histogram has the correct shape (should this make a difference?) Cheers Gavin Justin A. Lemkul wr

[gmx-users] question about non-bonded parameters for CHARMM in GROMACS

Dear All, I am confused about the proper choice of non-bonded parameters for simulating the CHARMM force field in GROMACS. With other packages I use VDW-switch and PME with both VDW and the direct space coulomb cut-off at 1.2 and a neighbor-list cut-off of 1.4. The requirement in GROMACS that

Re: [gmx-users] problems with g_wham

Have you watched the trajectory? That will show you what your pull group is doing. Is this a periodicity effect? It should be fairly obvious iff the sign of dX, etc flip-flops in the pullx.xvg file. -Justin Gavin Melaugh wrote: Thanks Chris and Justin I do get the output I want from gro

Re: [gmx-users] Compiling problems on MacOS X 10.6.4

Hi, Please post the output of the following commands: nm -arch i386 /opt/local/lib/libxml2.a | head nm -arch x86_64 /opt/local/lib/libxml2.a | head and in the directory where you typed make: file src/*/*.o | head Rui Rodrigues -- gmx-users mailing listgmx-users@gromacs.org http://l

Re: RE: [gmx-users] mpi run

- Original Message - From: #ZHAO LINA# Date: Thursday, July 8, 2010 18:53 Subject: RE: [gmx-users] mpi run To: Discussion list for GROMACS users P {margin-top:0;margin-bottom:0;} --- | > During your installation, if you

Re: [gmx-users] mdrun_mpi: error while loading shared libraries: libimf.so: cannot open shared object file: No such file or directory

- Original Message - From: zhongjin Date: Thursday, July 8, 2010 18:53 Subject: [gmx-users] mdrun_mpi: error while loading shared libraries: libimf.so: cannot open shared object file: No such file or directory To: gmx-users@gromacs.org --

Re: [gmx-users] mdrun_mpi: error while loading shared libraries: libimf.so: cannot open shared object file: No such file or directory

Hi, you can check with ldd mdrun_mpi whether really all needed libraries were found. Is libimf.so in /opt/intel/fc/10.1.008/lib ? The intel compilers also come with files called "iccvars.sh" or "ictvars.sh". If you do source /path/to/iccvars.sh everything should be set as needed. Check the In

RE: [gmx-users] mpi run

During your installation, if you use --program-suffix=_mpi, so the mdrun_mpi will work. I suggest you to check the nodes of the cluster, probably try pbsnodes, on a master node no job may be run. Note that I do not know much about your information, so the (guessing) suggestion maybe not fit for

[gmx-users] mdrun_mpi: error while loading shared libraries: libimf.so: cannot open shared object file: No such file or directory

Dear users,   When I am using GROMACS 4.0.7 on the Compute node ，executing command: mpiexec -n 4  mdrun_mpi -deffnm SWNT66nvt >/dev/null & and then met a problem :mdrun_mpi: error while loading shared libraries: libimf.so: cannot open shared object file: No such file or directory but I have ad

Re: [gmx-users] problems with g_wham

Thanks Chris and Justin I do get the output I want from grompp(below). The distance of 5.507 nm is the distance that I want to start with and I assume it is therefore the equilibrium distance for the harmonic potential. The COM distances from the simulations fluctuate around this value which is wh

Re: [gmx-users] Nitrile_Butadiene_Rubber simulation using Gromos96

Dear Mark Many thanks Chrysostomos --- Στις Πέμ., 08/07/10, ο/η Mark Abraham έγραψε: Από: Mark Abraham Θέμα: Re: [gmx-users] Nitrile_Butadiene_Rubber simulation using Gromos96 Προς: "Discussion list for GROMACS users" Ημερομηνία: Πέμπτη, 8 Ιούλιος 2010, 4:49 - Original Message - F

Re: [gmx-users] mpi run

Hi Mahmoud, for anyone to be able to help you, you need to provide a lot more information, at least: - which mpi library are you using? - how did you compile and/or install Gromacs? - what commands do you use to run mdrun and what was the output of it? Best, Carsten On Jul 8, 2010, at 9:41 AM

[gmx-users] mpi run

Dear GMX Users, I have a PC with 4 CPU, but the Gromacs only use one CPU. the command of mpiru works on linux; however, the command of mdrun_mpi does not work. Would you please help me how to set up the mdrun_mpi in Gromacs 4.0.4 Many thanks, Mahmoud -- gmx-users mailing listgmx