[gmx-users] applied electric field on the pure water

Dear users The simulation box contains just water molecules Commands pdb2gmx -f water.pdb -posrefc 0 Force Field : AMBER99SB-ILDN  - Water TIP3P editconf -f conf.gro -bt cubic -box 5 5 5 genbox -cp out.gro -cs spc216.gro -o 5.gro -p topol.top grompp -f min.mdp -c 5.gro -p

[gmx-users] Re: applied electric field on the pure water

Dear users The simulation box contains just water molecules Commands pdb2gmx -f water.pdb -posrefc 0 Force Field : AMBER99SB-ILDN  - Water TIP3P editconf -f conf.gro -bt cubic -box 5 5 5 genbox -cp out.gro -cs spc216.gro -o 5.gro -p topol.top grompp -f min.mdp -c 5.gro -p

[gmx-users] Re: gmx-users Digest, Vol 89, Issue 166

Dear All, I am using OPLSAA forcefield for generating methanol solvent box. The methanol.pdb/methnaol216.gro that is available in /tutor directory of gromacs is for united atom. Please tell me where I can get the methanol coordinates for All Atom. Can I use *.gro file that can be

[gmx-users] Regarding OPLSAA

Dear All, I am using OPLSAA forcefield for generating methanol solvent box. The methanol.pdb/methnaol216.gro that is available in /tutor directory of gromacs is for united atom. Please tell me where I can get the methanol coordinates for All Atom. Can I use *.gro file that can

Re: [gmx-users] Regarding OPLSAA

Ravi Kumar Venkatraman wrote: Dear All, I am using OPLSAA forcefield for generating methanol solvent box. The methanol.pdb/methnaol216.gro that is available in /tutor directory of gromacs is for united atom. Please tell me where I can get the methanol

[gmx-users] gromacs tools and namd

Dear All, I'm trying to use some gmx 4.5 tools like g_rdf, g_order, g_msd, g_hbond. To do it I composed a top file using psf and dcd files with topotools1.2 in vmd and generated a tpr file but also I saw some notes below on terminal. Do any of these notes will cause a problem when making

Re: [gmx-users] gromacs tools and namd

On 30/09/2011 12:07 AM, oguz gurbulak wrote: Dear All, I'm trying to use some gmx 4.5 tools like g_rdf, g_order, g_msd, g_hbond. To do it I composed a top file using psf and dcd files with topotools1.2 in vmd and generated a tpr file but also I saw some notes below on terminal. Do any of

[gmx-users] pull code problem: between protofilaments

Dear Gmx users, I am studying the interaction between the tubulin protofilaments arranged in parallel. For this operation, I have considered a tetramer and a dimer from two protofilaments respectively (say PRO-1 and PRO-2), tetramer in PRO-1 and a dimer in PRO-2. I want to move the dimer of

[gmx-users] Re: gmx-users Digest, Vol 89, Issue 167

Dear Justin, Thank you very much for your immediate reply and your help. -- 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!

Re: [gmx-users] REMD problem

After running for more than 12 hours, the REMD simulation is completed and what I get is 50 log, 50 trr, 50 cpt and 50 tpr files. Not sure if the result is reasonable. I tried to analyze the result, and after applying demux.pl, two files replica_index.xvg replica_temp.xvg are obtained. My

Re: [gmx-users] REMD problem

After running for more than 12 hours, the REMD simulation is completed and what I get is 50 log, 50 trr, 50 cpt and 50 tpr files. Not sure if the result is reasonable. I tried to analyze the result, and after applying demux.pl, two files replica_index.xvg replica_temp.xvg are obtained. My

[gmx-users] how to plot the difference between two contact maps

Dear Users I have plotted contact map for protein and ligand bind complex I want to plot the difference map for that. Although I have extracted coordinates from the plot but I am unable to make the two dimesntional plot for the differnce of contact map. Any help regarding this would be useful.

[gmx-users] Error - please help

Hello, I made a coordinate file of an iron complex and I tried to make the .top file by entering: g_x2top -f LFe.xyz -o LFE.top and the error I got out was: Could only find a forcefield type for 66 out of 74 atoms where 4 out of those 8 are atoms attached to the metal and the metal itself. I

Re: [gmx-users] how to plot the difference between two contact maps

ashutosh shandilya wrote: Dear Users I have plotted contact map for protein and ligand bind complex I want to plot the difference map for that. Although I have extracted coordinates from the plot but I am unable to make the two dimesntional plot for the differnce of contact map. Any help

Re: [gmx-users] Error - please help

Sarina wrote: Hello, I made a coordinate file of an iron complex and I tried to make the .top file by entering: g_x2top -f LFe.xyz -o LFE.top and the error I got out was: Could only find a forcefield type for 66 out of 74 atoms where 4 out of those 8 are atoms attached to the metal and the

[gmx-users] Applied electric field on the pure water

Dear users The simulation box contains just water molecules Commands pdb2gmx -f water.pdb -posrefc 0 Force Field : AMBER99SB-ILDN  - Water TIP3P editconf -f conf.gro -bt cubic -box 5 5 5 genbox -cp out.gro -cs spc216.gro -o 5.gro -p topol.top grompp -f min.mdp -c 5.gro -p topol.top mdrun

[gmx-users] g_cluster -dm option

Hello, I am using g_cluster to cluster trajectories. The exact command I am using is : g_cluster -s protein.pdb -f all.trr -n index.ndx -o rmsd-clust.xpm -method gromos -cutoff 0.07 -wcl 250. This command gives me 145 clusters. This command writes out a rmsd-clust.xpm, which is the RMSD distance

Re: [gmx-users] g_cluster -dm option

Hi santhu, maybe the differecence you observed depend by the xpm format. In the xpm each cell is represented by one character that, in turn, is represented as a color by xpm2ps. Therefore the character count cannot be infinite so each character can represent a range of RMSD cell. In my opinion

Re: [gmx-users] REMD problem

On 30/09/2011 2:50 AM, Liu, Liang wrote: After running for more than 12 hours, the REMD simulation is completed and what I get is 50 log, 50 trr, 50 cpt and 50 tpr files. Yep. One for each simulation. Not sure if the result is reasonable. Justin told you yesterday they would not be,

Re: [gmx-users] REMD problem

Thanks. Actually I applied just because the tutorial said so :( What I need is the structures only, I googled, but did not obtain useful information about Gromacs with REMD. Maybe I need to read the manual again :( I am totally fresh to MD simulation, just worked on this for 1 week ... On Thu,

[gmx-users] tpbconv question

Hello, I'm trying to turn off a Na+ charge using tpbconv in 4.5.4. There is only one Na+ counterion in my simulation. I create an index file, run tpbconv, and my output file looks like the following: [mcharend@xanadu C4_IS]$ tpbconv -s md.tpr -o mdn.tpr -n index.ndx -zeroq

Re: [gmx-users] tpbconv question

Hi Marc, I think that -zeroq ignores the indexing. Using an index will extract a .tpr for the index group only, which is not what you want. There is no simple way to do what you want (using tpbconv). You'll have to modify the charge in the .top file and generate a new .tpr Cheers, Tsjerk On

[gmx-users] Applied electric field on the pure water

The simulation box contains just water molecules ** water.pdb ** ATOM     1   OW  SOL    1       19.350   2.371   0.000  0.00  0.00              ATOM     2   HW1 SOL    1       18.600   2.951   0.000  0.00  0.00              ATOM     3   HW2 SOL    1       20.100   2.951   0.000  0.00  0.00      

[gmx-users] Applied electric field on the pure water

The simulation box contains just water molecules ** water.pdb ** ATOM     1   OW  SOL    1       19.350   2.371   0.000  0.00  0.00              ATOM     2   HW1 SOL    1       18.600   2.951   0.000  0.00  0.00              ATOM     3   HW2 SOL    1       20.100   2.951   0.000  0.00  0.00