Re: [gmx-users] g_density for a micelle

Hi Chris, Have a look at Makefile.am in the directory src/tools/ You can add g(mx)_rdf_mod whereever you find g_rdf, following the logic of the format. Then run automake (make sure it's the right version) and run ./configure from the gromacs directory. Finally, in src/tools/ issuing make

[gmx-users] Retaining water in protein chain

Dear gmxions, I want to retain one of water molecule in main chain of protein while converting it into separate chains as it is usualy done after genion using pdb2gmx. How can I do it ? With thanks ! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Access all of your

Re: [gmx-users] Creation of an index file with seperate lipid leaflets

Thanks to all for your help/suggestions. I gave up on modifying make_ndx, the code is just too impenetrable for a weekend scripter like me... Have made a perl script to produce a .ndx file with 2 groups, one containing all upper leaflet atoms, the other lower. --- Patrick Fuchs [EMAIL

[gmx-users] Re: query TFE gro and itp file

Dear Chiradip, May be try using PRODRG. Type PRODRG in google, and then draw your molecule, it will generate a topology and gro file for you. Mohan On 12/11/06, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Send gmx-users mailing list submissions togmx-users@gromacs.orgTo subscribe or unsubscribe

[gmx-users] Re: Re: How to generate GRO and TOP file for

Thanks Mark, I tried atleast PRODRG, but it has the limitation on total number of atoms. Anyway, I will probably try to find a source of other packages for molecue building. Mohan On 12/11/06, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Send gmx-users mailing list submissions to

[gmx-users] calculating dielectric constant

Hi all,I have some question about calculating dielectric constant:1. From the manual, it seems that there are two methods to calculate the dielectric constant: a. use g_dipoles -temp 400 -f -s directly, b) use g_dipoles -nonormalize -corr total -c dipcorr.xvg, then g_dielectric -f dipcorr.xvg -o

Re: [gmx-users] REMD restart: writing 2nd traj part on same local disk

[EMAIL PROTECTED] wrote: Dear community, I am running gmx3.3 REMD on a 32 node cluster, writing data to the local node disks, with the following command: mpiexec -np 64 $MDRUN -multi -np 64 -s $INPUT/md.tpr -o $OUT/traj.trr -x $OUT/traj.xtc -c $OUT/conf.g96 -e $OUT/ener.edr -g $OUT/md.log

Re: [gmx-users] calculating dielectric constant

Qiao Baofu wrote: Hi all, I have some question about calculating dielectric constant: 1. From the manual, it seems that there are two methods to calculate the dielectric constant: a. use g_dipoles -temp 400 -f -s directly, b) use g_dipoles -nonormalize -corr total -c dipcorr.xvg, then

Re: [gmx-users] Re: Re: How to generate GRO and TOP file for

Thanks Mohan and others thanks a lot..this things help me a lot... chiradip --- Mohan Boggara [EMAIL PROTECTED] wrote: Thanks Mark, I tried atleast PRODRG, but it has the limitation on total number of atoms. Anyway, I will probably try to find a source of other packages for molecue

[gmx-users] Re: query

HI friends Thanks for your instant help. I got TFE (trifluoroethanol) itp, pdb and gro files. Now I want to disturb you again for a command. I have one TFE molecule. I want to make a solvent box with 100 TFE and 600 Water molecules. What are the commands to translate this one TFE to 100TFE in a

Re: [gmx-users] Re: query

chiradip chatterjee wrote: HI friends Thanks for your instant help. I got TFE (trifluoroethanol) itp, pdb and gro files. Now I want to disturb you again for a command. I have one TFE molecule. I want to make a solvent box with 100 TFE and 600 Water molecules. What are the commands to translate

Re: [gmx-users] water in protein itp file

raja wrote: Dear gmxions, I want to include one crystal water within protein itp, to further restrict it by harmonic bond with metal ion at the active site. In other words, one of the water molecules to be treated just likes another protein residue by pdb2gmx. How to do that? Nobody here

Re: [gmx-users] water in protein itp file

Dear Mark, Thanks for your immediate reply and good solution. But until before yours this mail, I was thinking that inclusion of water and restraining them with metal ion is a very common happening in MD. Since in my short spell of molecular modeling and drug design experience, I have found almost

[gmx-users] error says segnentation fault

Dear All everytime i give the command mdrun...the terminal stops after some steps and says segmentation fault regards nur Find out what India is talking about on - Yahoo! Answers India Send FREE SMS to your friend's mobile from Yahoo! Messenger Version 8. Get it

Re: [gmx-users] water in protein itp file

Dear Mark, Well and thanks again, QM-MM is a good option, as you said for analyzing the energetic of water ligating process. But my case not concerning to that process, rather study a system consists of a macromolecule as a whole, where this water bound zinc is a part of it. If this is a case of

Re: [gmx-users] error says segnentation fault

nur avneet wrote: Dear All everytime i give the command mdrun...the terminal stops after some steps and says segmentation fault Something is catastrophically broken. This would happen if you attempted to move a gromacs installation, messed with some system libraries, or possibly moved a

[gmx-users] error after mdrun

Dear All I am new to gromacs...please help me and let me know how to proceed..when i give the mdrun command he terminal displays the following: /usr/local/gromacs/bin/mdrun -nice 0 -v -s hyb2b_vac_md.tpr -o hyb2b_vac_md_1ns_traj.trr -c hyb2b_vac_md_1ns.gro -e hyb2b_vac_md_1ns_ener.edr -g

Re: [gmx-users] error after mdrun

nur avneet wrote: Dear All I am new to gromacs...please help me and let me know how to proceed..when i give the mdrun command he terminal displays the following: /usr/local/gromacs/bin/mdrun -nice 0 -v -s hyb2b_vac_md.tpr -o hyb2b_vac_md_1ns_traj.trr -c hyb2b_vac_md_1ns.gro -e

Re: [gmx-users] calculating dielectric constant

Hi David, Thanks for your kindly reply.Because I am simulating a pure fluid system, I used the epsilon-r = 1in the .mdp file. _ coulombtype = pme rcoulomb-switch = 0 rcoulomb = 1.1 ; Dielectric constant (DC) for cut-off or DC of reaction field