[gmx-users] output force - 2

Hello dear gmx-users! So, I run md and got all files md.cpt, .trr, .gro, mdf.xvg,... etc. then I did: grompp_d -f sp.mdp -c md.gro -n index.ndx -p topol.top -o sp.tpr where sp.mdp differ from md.mdp in one line: energygrps = Protein SOL (in md.mdp: energygrps = System) after that I did: mdrun_d

[gmx-users] select waters in CNT

Hi all, I want to select waters in CNT using g_select. g_select -f md.xtc -s md.tpr -sf selection.dat -os -oc -oi -om -selrpos whole_mol_com -seltype whole_mol_com selection.dat contains:resname SOL and ((x-1)^2+(y-1)^2= 1) and (z =-0.7037 and z = 0.6833 ). and an error occure,Reading

[gmx-users] g_gyrate

Dear all I have the following system. Substrate with 3696 particles and 4 polymer chains with 45 beads/chain.  After typing g_gyrate, I have the following option: Group 0 (  System) has  680 elements Group 1 ( ZZZ) has   500 elements Group 2 ( AAA) has    45

Re: [gmx-users] g_gyrate

I'm not sure what the problem is. If you want to merge groups to get the radius of gyration over the union of those groups, then you need to use make_ndx on your previous .ndx file to generate such a group. Mark - Original Message - From: C. Batistakis cbat...@yahoo.gr Date: Tuesday,

Re: [gmx-users] output force - 2

Петр Попов wrote: Hello dear gmx-users! So, I run md and got all files md.cpt, .trr, .gro, mdf.xvg,... etc. then I did: grompp_d -f sp.mdp -c md.gro -n index.ndx -p topol.top -o sp.tpr where sp.mdp differ from md.mdp in one line: energygrps = Protein SOL (in md.mdp: energygrps = System)

[gmx-users] g_density options

I'm a GROMACS user and I want to authomatize solvent parametrization in GROMOS force-field. The parametrization of a solvent converg also on the density. The problem is that g_density always ask on which element of the system compute the density and it is waiting for a replay that I can't

Re: [gmx-users] g_density options

vferra...@units.it wrote: I'm a GROMACS user and I want to authomatize solvent parametrization in GROMOS force-field. The parametrization of a solvent converg also on the density. The problem is that g_density always ask on which element of the system compute the density and it is waiting for

Re: [gmx-users] g_density options

Justin A. Lemkul wrote: vferra...@units.it wrote: I'm a GROMACS user and I want to authomatize solvent parametrization in GROMOS force-field. The parametrization of a solvent converg also on the density. The problem is that g_density always ask on which element of the system compute the

Re: [gmx-users] g_density options

vferra...@units.it wrote: Thanks a lot, but... How can I exctract density information by using g_energy? Have you tried it? You're given a list from which to choose. Type the number of the property you want (i.e., Density), then either a blank line or the number zero to terminate

Re: [gmx-users] output force - 2

Is the way to decompose pull force? 2010/10/12 Justin A. Lemkul jalem...@vt.edu Петр Попов wrote: Hello dear gmx-users! So, I run md and got all files md.cpt, .trr, .gro, mdf.xvg,... etc. then I did: grompp_d -f sp.mdp -c md.gro -n index.ndx -p topol.top -o sp.tpr where sp.mdp differ

Re: [gmx-users] output force - 2

Is it possible to slightly change the source code to adjust output of pullf in appropriate form? And if it is, how? Petr. 12 октября 2010 г. 17:49 пользователь Justin A. Lemkul jalem...@vt.edu написал: Петр Попов wrote: Is the way to decompose pull force? None that I'm aware of.  The

[gmx-users] Equilibration of POPC - Lipid molecules jump out of box

Dear gmxusers, I have obtained a box of POPC with a starting dimension of 12.48, 12.36, and 6.92 (nm) using genconf -nbox 2 2 1. The original lipid was downloaded from Prof. Tieleman's site (popc128a.pdb). My intention is to equilibrate the new bilayer such that the lipids,

[gmx-users] swiss param query,

Dear Gromacs Users, I have generated the topology and parameters files for my ligand through swiss param site. Now i am trying to run a simulation of protein ligand complex in POPC bilayer using OPLS force field in Gromacs, but when I am using the grompp command in gromacs for tpr generation I am

Re: [gmx-users] g_gyrate

Dear Mark I will try to be more specific. In the case I have 4 chains in a simulation box, by typing g_gyrate -f traj.xtc -s topol.tpr -nmol 4 I take the following:  Group 0 (  System) has  180elements  Group 1 ( AAA) has    45 elements  Group 2 ( BAA) has    45

Re: [gmx-users] output force - 2

- Original Message - From: Justin A. Lemkul jalem...@vt.edu Date: Wednesday, October 13, 2010 0:50 Subject: Re: [gmx-users] output force - 2 To: Gromacs Users' List gmx-users@gromacs.org Петр Попов wrote: Is the way to decompose pull force? None that I'm aware of. The only

Re: [gmx-users] Compiling with ICC: advantages and -if yes- a suitable protocol? (it seems I can't)

On 12/10/10 00:33, Mark Abraham wrote: I have heard (read: read on random blogs here and there) that on Intel compiling GROMACS with icc instead of gcc can bring up to 50% performance improvement. If you are referring to this post

Re: [gmx-users] swiss param query,

ram bio wrote: Dear Gromacs Users, I have generated the topology and parameters files for my ligand through swiss param site. Now i am trying to run a simulation of protein ligand complex in POPC bilayer using OPLS force field in Gromacs, but when I am using the grompp command in gromacs for

Re: [gmx-users] query regarding missing residues

Hello Justin and Mark, Thanks for the reply. Reason that I didnt apply loop modelling was, for that region it is not given in literature that, this region which consist of 10 residues will form a helix of will remain in loop in an disorganized way. Therefore, I was reluctant in doing loop

[gmx-users] Re: swiss param query

Hi Ram, Please note that the SwissParam parameters have been tested only with the charmm force field. But this in principle shouldn't prevent you from TRYING to use these parameters (which come from the Merck Molecular Force Field in the first place) with OPLS. The error you mention should

Re: [gmx-users] Re: swiss param query

On 2010-10-12 19.09, Michel Cuendet wrote: Hi Ram, Please note that the SwissParam parameters have been tested only with the charmm force field. But this in principle shouldn't prevent you from TRYING to use these parameters (which come from the Merck Molecular Force Field in the first place)

[gmx-users] top file for two seperate peptides

Hi, I want to simulate two seperate peptids in one box. However, when I use pdb2gmx to build the top file of this system, I found that gromacs thought there is only one peptide because it added bond, angle and other energy terms between the termius of these two peptides. Is there any way to

Re: [gmx-users] top file for two seperate peptides

Hi, Thanks. Now I add TER after every peptide coordinates. But then when I used the command pdb2gmx -chainsep, it said invalid command line argument: -chainsep. So I am wondering the version I use is different or something. My version is gromacs 4.0.7. Sincerely, Qian - Original

Re: [gmx-users] top file for two seperate peptides

Qian Wang wrote: Hi, Thanks. Now I add TER after every peptide coordinates. But then when I used the command pdb2gmx -chainsep, it said invalid command line argument: -chainsep. So I am wondering the version I use is different or something. My version is gromacs 4.0.7. The -chainsep

[gmx-users] How to incorporate WALP and KALP peptide in a Martini bilayer

Hi, I am using MARTINI coarse-grained force-field to study interaction of a transmembrane peptide WALP or KALP in a lipid-bilayer. So,I was planning to insert a martini KALP or WALP peptide inside a martini DPPC bilayer in a transmembrane manner. For that purpose, I was going through the

Re: [gmx-users] How to incorporate WALP and KALP peptide in a Martini bilayer

Sanku M wrote: Hi, I am using MARTINI coarse-grained force-field to study interaction of a transmembrane peptide WALP or KALP in a lipid-bilayer. So,I was planning to insert a martini KALP or WALP peptide inside a martini DPPC bilayer in a transmembrane manner. For that purpose, I was

[gmx-users] g_velacc problem

Hi everybody, I'm trying to use g_velacc to calculate the diffusion coeficient for my solute. For this, I performed a simple simulation to test such tool. 1000 water molecules, NPT ensemble positions and velocities colected every 0.01ps Gromacs 4.5. However, once I run: g_velacc -f traj

Re: [gmx-users] How to incorporate WALP and KALP peptide in a Martini bilayer

Hi Tom, I hoped that I could self-assemble the bilayer around the peptide. But, the problem is how to do that. I am aware of the tutorial in the Martini website. But, in that case, they use genbox -ci option to insert certain lipid molecules in an EMPTY box. But, I guess genbox -ci option

Re: [gmx-users] How to incorporate WALP and KALP peptide in a Martini bilayer

Sanku M wrote: Hi Tom, I hoped that I could self-assemble the bilayer around the peptide. But, the problem is how to do that. I am aware of the tutorial in the Martini website. But, in that case, they use genbox -ci option to insert certain lipid molecules in an EMPTY box. But, I guess

Re: [gmx-users] Compiling with ICC: advantages and -if yes- a suitable protocol? (it seems I can't)

GROMACS performance is dependent on a) non-bonded kernels (which are coded in assembler for the large majority of platforms for which icc exists, and so compiler version is largely irrelevant) I use mostly tabulated functions for the model I'm developing... So does regular PME, and these

Re: [gmx-users] why does trjcat take so much memory?

- Original Message - From: chris.ne...@utoronto.ca Date: Wednesday, October 13, 2010 10:55 Subject: [gmx-users] why does trjcat take so much memory? To: gmx-users@gromacs.org I have 28,000 .xtc files, each having a single frame and each 150K. If I run du -hs on the directory

[gmx-users] Gromacs installation problem @ RHEL5.5 server

Dear all, I have compiled and installed gromacs 4.5.1 on RHEL5.5 server. I have also installed openmpi-1.2.8, fftw-3.2.2 and gsl-1.11. After gromacs 4.5.1 installation did make tests and make links. Finally got message GROMACS is installed under /root/software and binary executable installed

Re: [gmx-users] Gromacs installation problem @ RHEL5.5 server

- Original Message - From: Sathish sathisbioi...@gmail.com Date: Wednesday, October 13, 2010 14:31 Subject: [gmx-users] Gromacs installation problem @ RHEL5.5 server To: gmx-users@gromacs.org Dear all, I have compiled and installed gromacs 4.5.1 on RHEL5.5 server. I have also

[gmx-users] why does trjcat take so much memory?

Thank you for the insight Mark. To get it on the record, this is fairly annoying for trjcat (not trjconv). If anyone else has run into this, then please do post because a memory efficient cat mechanism will only be coded if there is sufficient interest. But again, thanks for your good

Re: [gmx-users] Gromacs installation problem @ RHEL5.5 server

Dear Mark, Thanks for your reply. In my server gromacs installed at local/gromacs. I have checked out point 8 as you mentioned. It was working with this source /local/gromacs/bin/GMXRC command. and also tried , entered local/gromacs/bin path and calling to GMXRC but it shows error