Re: [gmx-users] Energy units

Cheong Wee Loong, Daniel wrote: Thanks Mark for your reply. So if I understand you correctly, it's not really a mole of anything in particular, it's just an energy value divided by Avogadro's number, and this happens to be consistent with the forcefield parameters as well. So if you have jus

RE: [gmx-users] Energy units

Thanks Mark for your reply. So if I understand you correctly, it's not really a mole of anything in particular, it's just an energy value divided by Avogadro's number, and this happens to be consistent with the forcefield parameters as well. So if you have just a single molecule, that energy v

Re: [gmx-users] simulation broke at 4.0.5 version

Chih-Ying Lin wrote: Hi I am using Gromacs version 4.0.5. I put one protein in a simulation box with water molecules and CL- only. My simulation broke at the step, Relaxation of solvent and hydrogen atom position. Here are the .top file, command, output of the grommp, pr.mdp. anything wro

Re: [gmx-users] Electron Density3

afsaneh maleki wrote: Hi , I want to obtain electron density for solvent in z direction for bilayer. I used following options: ] g_density -f md.xtc -s md.tpr -d z -dens electron -o electrondens.xvg -ei electrons.dat -symm -n index.ndx Atomtapes in md.gro are OH,HW1,HW2 And “electron

Re: [gmx-users] Energy units

Cheong Wee Loong, Daniel wrote: Hi all, This may be a silly and trivial question, but the energy unit given in Gromacs is kJ/mol. What I don’t quite understand is, the energy is per mole of what exactly? In a very real sense, it doesn't matter. It's just a label for a convenient bucke

[gmx-users] Electron Density3

Hi , I want to obtain electron density for solvent in z direction for bilayer. I used following options: ] g_density -f md.xtc -s md.tpr -d z -dens electron -o electrondens.xvg -ei electrons.dat -symm -n index.ndx Atomtapes in md.gro are OH,HW1,HW2 And “electrons.dat” file contains: 3

[gmx-users] simulation broke at 4.0.5 version

Hi I am using Gromacs version 4.0.5. I put one protein in a simulation box with water molecules and CL- only. My simulation broke at the step, Relaxation of solvent and hydrogen atom position. Here are the .top file, command, output of the grommp, pr.mdp. anything wrong here? Thank you Lin *[

Re: [gmx-users] Electron Density2

afsaneh maleki wrote: Dear David van der Spoel, Would you please elaborate on the details? I didn’t underestand about “remove = sign” Please include the previous email in your follow-up. You may only be asking one question, so that you remember your context, but any reader almost certai

[gmx-users] Electron Density2

Dear David van der Spoel, Would you please elaborate on the details? I didn’t underestand about “remove = sign” thanks in advans, Afsaneh Maleki -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.groma

[gmx-users] Energy units

Hi all, This may be a silly and trivial question, but the energy unit given in Gromacs is kJ/mol. What I don't quite understand is, the energy is per mole of what exactly? The energy is system size dependent, so if I double the number of molecules, the energy will double accordingly. But the

Re: [gmx-users] FWD:simulationg a distance restraint with a type 6 bond in gromacs

Thanks Tom, It may easily be that the 6- bond type works in mdrun but not in mdrun-openmm. This would be an explanation for the ridiculous force constants Hans Am Mittwoch, den 06.01.2010, 23:15 + schrieb TJ Piggot: > Please keep all correspondence on the GROMACS mailing list, it gives you

[gmx-users] FWD:simulationg a distance restraint with a type 6 bond in gromacs

Please keep all correspondence on the GROMACS mailing list, it gives you a much greater chance of someone being able to help you. I have used this bond type before and have had no problems (with force constants much smaller than those which you apply). I would make sure that your box is big en

Re: [gmx-users] Added Residue Name [ HFL ] in ffgmx.rtp, still have err message says

On 1/6/10 5:05 PM, Feng Xu wrote: Fatal error: Residue'HFL' not found in residue topology database the portion of ffgmax.rtp file relevant is: If you have a file called "ffgmax.rtp", then none of the changes you made are going to be applied, since pdb2gmx is expecting ffgmx* files. The r

[gmx-users] Added Residue Name [ HFL ] in ffgmx.rtp, still have err message says

Fatal error: Residue 'HFL' not found in residue topology database the portion of ffgmax.rtp file relevant is: . [ HFL ] [ atoms ] HHF HHF 0.725 0 FHF FHF 0.725 0 [ HIS1 ] ... Atom types HHF and FHF are also defined in relevant .atp file. and a simple HF.pdb

Re: [gmx-users] do_dssp

On 1/6/10 7:52 AM, leila karami wrote: Hi dear Justin The executable is dssp leila karami Do you have the correct mode set for the executable (i.e., is it actually executable)? Did you use a pre-compiled binary, or compile it yourself from source? If you issue "which dssp" does your shel

Re: [gmx-users] g_wham .tpr / .xvg / .dat conversion issues

On 1/6/10 1:51 PM, V Hariharan wrote: Hello All, I am trying to use g_wham to view the PMF for my simulation. I read the g_wham -h help menu, and it requires .dat input files for the -if and -it input options. My output files from mdrun for -s and -pf were .tpr and .xvg files, respectively.

[gmx-users] g_wham .tpr / .xvg / .dat conversion issues

Hello All, I am trying to use g_wham to view the PMF for my simulation. I read the g_wham -h help menu, and it requires .dat input files for the -if and -it input options. My output files from mdrun for -s and -pf were .tpr and .xvg files, respectively. How to I convert my .tpr and .xvg files i

Re: [gmx-users] Electron Density

afsaneh maleki wrote: Hi, I want to obtain electron density for solvent in z direction for bilayer. I used following options: ] g_density -f md.xtc -s md.tpr -d z -dens electron -o electrondens.xvg -ei electrons.dat -symm -n index.ndx Atomtapes in md.gro are OH,HW1,HW2 And “electro

[gmx-users] Electron Density

Hi, I want to obtain electron density for solvent in z direction for bilayer. I used following options: ] g_density -f md.xtc -s md.tpr -d z -dens electron -o electrondens.xvg -ei electrons.dat -symm -n index.ndx Atomtapes in md.gro are OH,HW1,HW2 And “electrons.dat” file contains: 3

[gmx-users] do_dssp

Hi dear Justin The executable is dssp leila karami -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www

Re: [gmx-users] do_dssp

Hi Leila! Can I add just one more note? The file dssp, that you put in the right place, has the permissions to be executed? Nuno Azoia On Wed, 2010-01-06 at 15:35 +0330, leila karami wrote: > dear Rasoul > > I put executable DSSP in /usr/local/bin and gromacs is > in /usr/local/gromacs. > >

Re: [gmx-users] do_dssp

OK. you are right! Rasoul On Wed, Jan 6, 2010 at 1:09 PM, Justin A. Lemkul wrote: > > > On 1/6/10 7:05 AM, leila karami wrote: > >> dear Rasoul >> I put executable DSSP in /usr/local/bin and gromacs is >> in /usr/local/gromacs. >> is it true? >> >> > Is the executable named DSSP, or dssp? Case

Re: [gmx-users] do_dssp

yes. Could you perform do_dssp properly? Rasoul On Wed, Jan 6, 2010 at 1:05 PM, leila karami wrote: > dear Rasoul > > I put executable DSSP in /usr/local/bin and gromacs is > in /usr/local/gromacs. > > is it true? > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.o

Re: [gmx-users] do_dssp

On 1/6/10 7:05 AM, leila karami wrote: dear Rasoul I put executable DSSP in /usr/local/bin and gromacs is in /usr/local/gromacs. is it true? Is the executable named DSSP, or dssp? Case matters. DSSP is the environment variable that must be set, while dssp is the name of the executable its

[gmx-users] do_dssp

dear Rasoul I put executable DSSP in /usr/local/bin and gromacs is in /usr/local/gromacs. is it true? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't pos

Re: [gmx-users] do_dssp

On 1/6/10 6:57 AM, rasoul nasiri wrote: Then your executable has problem. Gromacs tool can not find DSSP for doing d_dssp. Do you put executable DSSP in the path of gromacs is installed? This is not necessary. One needs to set the environment variable DSSP correctly, since the default loca

Re: [gmx-users] do_dssp

On 1/6/10 5:58 AM, leila karami wrote: dear Rasoul I had executable dssp program, already. Then have you set your PATH appropriately, as well as the DSSP environment variable? See the help information for do_dssp to see the assumptions that the program is making regarding the location of t

Re: [gmx-users] do_dssp

Then your executable has problem. Gromacs tool can not find DSSP for doing d_dssp. Do you put executable DSSP in the path of gromacs is installed? Rasoul. On Wed, Jan 6, 2010 at 11:58 AM, leila karami wrote: > dear Rasoul > > I had executable dssp program, already. > > leila karami > > -- > gmx-

Re: [gmx-users] define a new covalent bond in gromacs

I'll try and let you know about results Hans Am Mittwoch, den 06.01.2010, 11:15 + schrieb TJ Piggot: > How about using bond type 6 to restrain the distance without actually > creating a bond between the atoms? > > Tom > > --On Tuesday, January 05, 2010 22:57:32 +0100 David van der Spoel >

Re: [gmx-users] define a new covalent bond in gromacs

How about using bond type 6 to restrain the distance without actually creating a bond between the atoms? Tom --On Tuesday, January 05, 2010 22:57:32 +0100 David van der Spoel wrote: Hans HEINDL wrote: mdrun-openmm does not yet support any restraints But gromacs does. Therefore, it seems

[gmx-users] do_dssp

dear Rasoul I had executable dssp program, already. leila karami -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list.

Re: [gmx-users] do_dssp

Do you have a DSSP program on your system? If no, please install executable DSSP program from http://swift.cmbi.kun.nl/gv/dssp/ website. Rasoul On Wed, Jan 6, 2010 at 11:34 AM, leila karami wrote: > Hi > > I apply following command: > > do_dssp -f rrr.xtc -s .tpr -n n.ndx -map ss.map > > but

[gmx-users] do_dssp

Hi I apply following command: do_dssp -f rrr.xtc -s .tpr -n n.ndx -map ss.map but following error is came up: Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddal9qL4 ddRvmyo0 > /dev/null 2> /dev/null Any help will highly appreciated! -- gmx-users mailing listgmx-user

Re: [gmx-users] grompp segmentation error

Dear Justin, I am having grompp segmentation error only for the drug-enzyme complex tutorial, all other executables are ok, can this occur due to the any other reasons like following the tutorial improperly. Thanks, Ram On Tue, Jan 5, 2010 at 1:24 PM, Justin A. Lemkul wrote: > > > ram bio wrot

Re: [gmx-users] Problems with calculating Cv and Cp

Lum Nforbi wrote: Hi Andrew Paluch, You had asked me to supply the formulas that I attempted using to calculate Cv. The formula from J. M. Haile is labelled isometric heat capacity and given by Cv = Nk/(N-NT*(3(N/2)-1)) and the one in Allen and Tildesley is quite complicated to wri