Re: [gmx-users] mpi- gromacs

g_energy needs input to supply which energy item you would like to output. To automate this, use echo -e "1\n2\n" | g_energy_mpi -f minim_ener.edr -o minim_ener.xvg However, I don't see any point to run g_energy with mpi. If you have (mis-)compiled it with MPI, build a non-MPI version for all a

Re: [gmx-users] Fatal error, spc.itp", line 41

Chih-Ying Lin wrote: Hi I still have no idea about this. Some useful information from Archive is the application on using GROMACS' spc topology with ffamber. But, I am using Gromacs straight without ffamber. How should I solve the problem? We don't necessarily remember the context of your pro

Re: [gmx-users] mpi- gromacs

Chih-Ying Lin wrote: Hi Here is my pdb file. #!/bin/bash #PBS -l nodes=2 cat $PBS_NODEFILE echo Working directory is $PBS_O_WORKDIR cd $PBS_O_WORKDIR mpirun -np 2 g_energy_mpi -f minim_ener.edr -o minim_ener.xvg 11 0 Then, it showed Fatal error: No energy terms selected g_energy is not

[gmx-users] mpi- gromacs

Hi Here is my pdb file. #!/bin/bash #PBS -l nodes=2 cat $PBS_NODEFILE echo Working directory is $PBS_O_WORKDIR cd $PBS_O_WORKDIR mpirun -np 2 g_energy_mpi -f minim_ener.edr -o minim_ener.xvg 11 0 Then, it showed Fatal error: No energy terms selected How to fix the problem Thank you Lin __

[gmx-users] Fatal error, spc.itp", line 41

Hi I still have no idea about this. Some useful information from Archive is the application on using GROMACS' spc topology with ffamber. But, I am using Gromacs straight without ffamber. How should I solve the problem? Thank you Lin ___ gmx-users maili

[gmx-users] 4fs timestep in gromacs 4.0

Hello, I am interested in trying the 4 fs timestep options for an opls-protein/tip4p-water system. I will of course do some quick NVE tests to ensure that the energy does not drift massively, and also do some other tests that look at some properties that should equilibrate rather quickly.

Re: [gmx-users] oplsaa in Gromacs 4.0

friendli wrote: Dear all, Are the topology components of OPLSAA force field explicitly displayed in Gromacs 4.0? I mean the bond, angle, dihedral types(or parameters) following the composed atoms. They are not showed in .top file when oplsaa FF is used, not like other force field, e.g. Gromos

[gmx-users] oplsaa in Gromacs 4.0

Dear all, Are the topology components of OPLSAA force field explicitly displayed in Gromacs 4.0? I mean the bond, angle, dihedral types(or parameters) following the composed atoms. They are not showed in .top file when oplsaa FF is used, not like other force field, e.g. Gromos96. thanks Qia

[gmx-users] g_rdf: "not in list" error

Hi, When attempting to use g_rdf to calculate the structure factor for a simple Argon liquid, I get the following error: --- Program g_rdf_d, VERSION 3.3.3 Source code file: gmx_rdf.c, line: 622 Fatal error: Error: atom (Ar) not in list (5 typ

Re: [gmx-users] Gromacs 4.0 installation problem

Chavatte Philippe wrote: Hi, We are trying to install gromacs 4.0 on our new SGI cluster running under RHEL5. The configure script run fine (./configure –prefix =/install-dir). But an error occurs during the building (make) : cc -DHAVE_CONFIG_H -I. -I../../src -I../../include -DGMXLIBDIR=\

Re: [gmx-users] Gromacs 4.0 installation problem

Chavatte Philippe wrote: /usr/bin/ld: cannot find -lX11 You don't have X11 installed, probably because you don't need it on a cluster. You can configure --without-x to remove the X11 dependency. -Justin collect2: ld returned 1 exit status make[3]: *** [grompp] Erreur 1 make[3]: qui

[gmx-users] Gromacs 4.0 installation problem

Hi, We are trying to install gromacs 4.0 on our new SGI cluster running under RHEL5. The configure script run fine (./configure –prefix =/install-dir). But an error occurs during the building (make) : cc -DHAVE_CONFIG_H -I. -I../../src -I../../include -DGMXLIBDIR=\"/data1/soft/linux/gromacs

Re: [gmx-users] Fatal error, spc.itp", line 41

Chih-Ying Lin wrote: Hi I have the following error and I could not solve it after checking all the possible solutions on line. Thank you Lin --- Program grompp, VERSION 3.3.3 Source code file: toppush.c, line: 1193 Fatal error: [ file "/us

Re: [gmx-users] tip3p.gro

Chih-Ying Lin wrote: Hi In the file , /usr/local/gromacs/share/gromacs/top/ there is a document named tip3p.itp but there is no tip3p.gro how to create the tip3p.gro Search the archive; this is a frequently asked question. -Justin Thank you Lin ___

[gmx-users] tip3p.gro

Hi In the file , /usr/local/gromacs/share/gromacs/top/ there is a document named tip3p.itp but there is no tip3p.gro how to create the tip3p.gro Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gm

[gmx-users] Fatal error, spc.itp", line 41

Hi I have the following error and I could not solve it after checking all the possible solutions on line. Thank you Lin --- Program grompp, VERSION 3.3.3 Source code file: toppush.c, line: 1193 Fatal error: [ file "/usr/local/gromacs/share/gro

Re: [gmx-users] (no subject)

Hi, In bash, the correct syntax is: export PATH=$PATH:/usr/local/gromacs/bin Hope this helps, Rui Rodrigues On Wed, 29 Oct 2008 18:52:25 0100 (CET), cecilia.rosso wrote > Hi! I installed GROMACS on my computer. I try to set up my environment > adding the line > > export PATH "/usr/local/grom

Re: [gmx-users] (no subject)

Hi Cecilia, Please give your posts a descriptive title. Then, this is actually a bash-related issue, which has not much to do with Gromacs. But then again, we're nice people :) The thing is that bash wants to have: export PATH="/usr/local/gromacs/bin:${PATH}" By the way, you can also use: sourc

[gmx-users] (no subject)

Hi! I installed GROMACS on my computer. I try to set up my environment adding the line export PATH "/usr/local/gromacs/bin:${PATH}" in the .bashrc file, but when I open my terminal, the next message appeared: bash: export: `/usr/local/gromacs/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin

Re: [gmx-users] Re: H2O water density = 6.4617 g/l << 1000 g/l

Chih-Ying Lin wrote: HI As Mark described , "So when you tile these cubes of side length 1.86nm in a 3x3x3 grid, you over-fill a cube of side length 5nm and get 27 water molecules. Use the standard water .gro files in the distribution and then minimize and equilibrate. " And, how could I f

[gmx-users] Re: H2O water density = 6.4617 g/l << 1000 g/l

HI As Mark described , > "So when you tile these cubes of side length 1.86nm in a 3x3x3 grid, you > over-fill a cube of side length 5nm and get 27 water molecules. Use the > standard water .gro files in the distribution and then minimize and > equilibrate. " And, how could I find the standard wa

Re: [gmx-users] override dispalying of options

On Wed, Oct 29, 2008 at 01:33:19PM +0200, Inon Sharony wrote: > Hello GROMACS users & team > > I would like to run grompp and mdrun from the command line without > having to see all the possible flags and options. I'm running a few > commands in series, so I can't use "grompp &" and then "mdru

Re: [gmx-users] 1-4 interaction problem with a Thr

Aline Rossi wrote: ;TEMPERATURE COUPLING Tcoupl = berendsen tc-grps = Protein ISZ SOL NA+ tau_t = 0.1 0.1 0.1 0.1 ref_t = 310 310 310 310 This is asking for trouble. See here: http://wiki.gromacs.or

[gmx-users] 1-4 interaction problem with a Thr

Hi group, I'm simulating a protein+drug and always getting the "1-4 interaction between 3013 and 3016 at distance 1.825 which is larger than the 1-4 table size 1.000 nm". These atoms are a CA and a HG1 from a Thr residue. My mdp file is enclosed. What should I encrease or decrease to be able to co

[gmx-users] 1-4 interaction problem with a Thr

Sorry, I forgot to enclose the .mdp file: ; ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; title = PEP MD cpp = /lib/cpp constraints = none integrator = md tinit = 0 dt = 0.002; p

Re: [gmx-users] override dispalying of options

And, you can even (like for anything that generates output), redirect output to nowhere: (csh) grompp >& /dev/null (bash) grompp &> /dev/null By the way, bringing it to the background (&) doesn't change the binding to the terminal. Oh, and Mark is absolutely right that it is better to save to a

Re: [gmx-users] override dispalying of options

Inon Sharony wrote: Hello GROMACS users & team I would like to run grompp and mdrun from the command line without having to see all the possible flags and options. I'm running a few commands in series, so I can't use "grompp &" and then "mdrun &" Is there some way to call these functions wit

Re: [gmx-users] override dispalying of options

Inon Sharony wrote: Hello GROMACS users & team I would like to run grompp and mdrun from the command line without having to see all the possible flags and options. I'm running a few commands in series, so I can't use "grompp &" and then "mdrun &" Is there some way to call these functions witho

[gmx-users] override dispalying of options

Hello GROMACS users & team I would like to run grompp and mdrun from the command line without having to see all the possible flags and options. I'm running a few commands in series, so I can't use "grompp &" and then "mdrun &" Is there some way to call these functions without having to displa

Re: [gmx-users] n terminal

shahrbanoo karbalaee wrote: thank you justin in papers net charge of peptide is calculated +1,with amidated in terminal. that I defined with flag -ter in pdbf2gmx .and when I add tfein system I see in pdb files lys is changed LYSH. OK, so your peptide has a +1 charge

[gmx-users] Re: density graph ( density vs time)

huan wrote: Dear Justin and all gmx users, I double checked the density graph (obtained by using g_energy, option 18) which is a energy at y-axis and time at the x-axis. but how can i get a density vs time graph? g_energy defaults to kJ/mol as its unit, but in the case of density it

Re: [gmx-users] do_dssp

Morteza Khabiri wrote: Dear florian thanks for your help. I installed the DSSP in the root. It is working well when I run ./dssp in DSSP directory. It seems that the program don't have any problem. As you said I already set an environment also but any of them did not working. It made me crazy tha

[gmx-users] do_dssp

Dear florian thanks for your help. I installed the DSSP in the root. It is working well when I run ./dssp in DSSP directory. It seems that the program don't have any problem. As you said I already set an environment also but any of them did not working. It made me crazy that everything is ok, Insta

RE: [gmx-users] table use

Hi, Your apparently have pair interactions in your system. So you have to give the pair interaction table with option -tablep. If the functional shape is the same as the non-bonded interactions, you can just supply the same file name as for the non-bonded tables. Berk > From: [EMAIL PROTECTED]

Re: [gmx-users] do_dssp

Hi, On Wednesday, 29. October 2008, Morteza Khabiri wrote: > Dear gmx users, > > I run the program do_dssp for my system which is too small. Unfortunately, > I run it for a long time but I am in a doubt that it is working correctly > or not > because it is run for one day and i don't have any idea

Re: [gmx-users] Is it the correct label on Y axis ( density graph)

Mark Abraham wrote: > Jochen Hub wrote: >> huan wrote: >>> Dear all, >>> >>> I am wondering that is it the correct label of y axis in the density >>> graph which i obtained using g_energy? because it is not a density >>> unit but is labeled as kJ/mol >> >> Dear huan, >> >> 1) >> I would encour

[gmx-users] do_dssp

Dear gmx users, I run the program do_dssp for my system which is too small. Unfortunately, I run it for a long time but I am in a doubt that it is working correctly or not because it is run for one day and i don't have any idea when it will be finished and also after running I have a message which

Re: [gmx-users] Is it the correct label on Y axis ( density graph)

Jochen Hub wrote: huan wrote: Dear all, I am wondering that is it the correct label of y axis in the density graph which i obtained using g_energy? because it is not a density unit but is labeled as kJ/mol Dear huan, 1) I would encourage you to read a few reviews on MD and the gromacs

Re: [gmx-users] Is it the correct label on Y axis ( density graph)

huan wrote: > Dear all, > > I am wondering that is it the correct label of y axis in the density graph > which i obtained using g_energy? because it is not a density unit but is > labeled as kJ/mol Dear huan, 1) I would encourage you to read a few reviews on MD and the gromacs manual carf

Re: [gmx-users] Is it the correct label on Y axis ( density graph)

huan wrote: Dear all, I am wondering that is it the correct label of y axis in the density graph which i obtained using g_energy? because it is not a density unit but is labeled as kJ/mol It's just an incorrect label. The code writes kJ/mol as the units for all ordinate (i.e. Y-axis) q

[gmx-users] Is it the correct label on Y axis ( density graph)

Dear all, I am wondering that is it the correct label of y axis in the density graph which i obtained using g_energy? because it is not a density unit but is labeled as kJ/mol Thanks guys. ___ gmx-users mailing listgmx-users@gromacs.org

[gmx-users] n terminal

thank you justin in papers net charge of peptide is calculated +1,with amidated in terminal. that I defined with flag -ter in pdbf2gmx .and when I add tfein system I see in pdb files lys is changed LYSH. best -- sh-karbalaee ___