Re: [gmx-users] ngmx in windows

2010-11-10 Thread bharat gupta
No i did not --disbale-x in your configuration ... I was not having that library but now i installed the library now .. -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -6

Re: [gmx-users] ngmx in windows

2010-11-10 Thread Mark Abraham
On 11/11/2010 3:03 PM, bharat gupta wrote: I am trying to run the simulation trajectory using ngmx in windows .. but it seems that the ngmx.exe file doesnot exists .. can anybody tell what shall i do to view the movie of my simulation Did you --disable-x in your configuration? Do you have the

Re: [gmx-users] ngmx in windows

2010-11-10 Thread Roland Schulz
If you compile using cygwin than it should be able to compile ngmx if you have all required X11 libraries. I recommend you to use VMD. On Wed, Nov 10, 2010 at 11:03 PM, bharat gupta wrote: > I am trying to run the simulation trajectory using ngmx in windows .. but > it seems that the ngmx.exe fil

[gmx-users] ngmx in windows

2010-11-10 Thread bharat gupta
I am trying to run the simulation trajectory using ngmx in windows .. but it seems that the ngmx.exe file doesnot exists .. can anybody tell what shall i do to view the movie of my simulation -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of

Re: [gmx-users] on calculation of the atomic covariance

2010-11-10 Thread Vigneshwar Ramakrishnan
Dear All, I tried using the xpm2ps -combine option to plot the two matrices in the same plot. "xpm2ps -f covara_cognate.xpm -f2 covara_G5C.xpm -diag none -combine halves -cmin -0.5 -cmax 0.8" However, I still get two legends and each of the matrices are scaled differently. That is, the output ra

Re: [gmx-users] on calculation of the atomic covariance

2010-11-10 Thread Vigneshwar Ramakrishnan
Thanks very much, Justin. Somehow this thread did not come up during my search. Really appreciate your help. Sincerely, Vignesh On Wed, Nov 10, 2010 at 10:23 PM, Justin A. Lemkul wrote: > > There are two relevant threads on this same topic that will likely provide > some insight (particularly

Re: [gmx-users] Freeze Groups in Gromacs 4.5.x (bug?)!!!

2010-11-10 Thread Mark Abraham
On 11/11/2010 3:14 AM, Miguel Machuqueiro wrote: Dear users and developers, In GROMACS 4.5.x when using "freeze groups" on a Protein in a Protein+Solvent system, I noticed that the coordinates of a few atoms (not many, but a few) are changed after a short period of MD (~0.2 ps). Of course, t

Re: [gmx-users] trjconv, pbc and breaking of multiple peptides

2010-11-10 Thread ms
On 10/11/10 22:28, Justin A. Lemkul wrote: First, let me see if I understand it correctly. From your explanation (and intuition), it seems that the issue is that "center of mass" in a periodic environment is ambiguous -there are always (at least) two alternate configurations that have the center

Re: [gmx-users] trjconv, pbc and breaking of multiple peptides

2010-11-10 Thread Justin A. Lemkul
ms wrote: On 10/11/10 21:34, Justin A. Lemkul wrote: ms wrote: On 09/11/10 21:36, Justin A. Lemkul wrote: There are numerous -pbc options with trjconv; have you tried others? I have never had luck with -pbc nojump actually working, and -pbc atom provides no guarantee that molecules will b

Re: [gmx-users] trjconv, pbc and breaking of multiple peptides

2010-11-10 Thread ms
On 10/11/10 21:34, Justin A. Lemkul wrote: ms wrote: On 09/11/10 21:36, Justin A. Lemkul wrote: There are numerous -pbc options with trjconv; have you tried others? I have never had luck with -pbc nojump actually working, and -pbc atom provides no guarantee that molecules will be properly re

Re: [gmx-users] trjconv, pbc and breaking of multiple peptides

2010-11-10 Thread Justin A. Lemkul
ms wrote: On 09/11/10 21:36, Justin A. Lemkul wrote: There are numerous -pbc options with trjconv; have you tried others? I have never had luck with -pbc nojump actually working, and -pbc atom provides no guarantee that molecules will be properly reconstructed. Using -pbc mol -center is often

Re: [gmx-users] trjconv, pbc and breaking of multiple peptides

2010-11-10 Thread ms
On 09/11/10 21:36, Justin A. Lemkul wrote: There are numerous -pbc options with trjconv; have you tried others? I have never had luck with -pbc nojump actually working, and -pbc atom provides no guarantee that molecules will be properly reconstructed. Using -pbc mol -center is often a much bette

Re: [gmx-users] DSSP error

2010-11-10 Thread ahmet yıldırım
I do not have any problem. The problem is solved. Thank you very much 10 Kasım 2010 22:45 tarihinde Justin A. Lemkul yazdı: > > > ahmet yıldırım wrote: > >> Dear Justin, >> >> Finally, The problem is solved, Thank you very much for your patience. >> >> Ps: I set *r...@ab-desktop:/home/ab/Deskto

Re: [gmx-users] DSSP error

2010-11-10 Thread Justin A. Lemkul
ahmet yıldırım wrote: Dear Justin, Finally, The problem is solved, Thank you very much for your patience. Ps: I set *r...@ab-desktop:/home/ab/Desktop/dssp# export DSSP=/usr/local/bin/dssp* the instead of 4.step but the do_dssp dont run again.The I don't still understand why the DSSP environ

Re: [gmx-users] DSSP error

2010-11-10 Thread ahmet yıldırım
Dear Justin, Finally, The problem is solved, Thank you very much for your patience. Ps: I set *r...@ab-desktop:/home/ab/Desktop/dssp# export DSSP=/usr/local/bin/dssp* the instead of 4.step but the do_dssp dont run again.The I don't still understand why the DSSP environment variable is not run. T

Re: [gmx-users] DSSP error

2010-11-10 Thread Justin A. Lemkul
ahmet yıldırım wrote: 1.step-r...@ab-desktop:/home/ab/Desktop# tar xvzf dsspcmbi.tar.gz 2.step-r...@ab-desktop:/home/ab/Desktop/dssp#./DsspCompileGCC 3.step-r...@ab-desktop:/home/ab/Desktop/dssp# cp dsspcmbi dssp 4.step-r...@ab-desktop:/home/ab/Desktop/dssp# export DSSP=/usr/local/bin/dssp

Re: [gmx-users] DSSP error

2010-11-10 Thread ahmet yıldırım
1.step-r...@ab-desktop:/home/ab/Desktop# tar xvzf dsspcmbi.tar.gz 2.step-r...@ab-desktop:/home/ab/Desktop/dssp#./DsspCompileGCC 3.step-r...@ab-desktop:/home/ab/Desktop/dssp# cp dsspcmbi dssp 4.step-r...@ab-desktop:/home/ab/Desktop/dssp# export DSSP=/usr/local/bin/dssp Dear Justin, I compiled the p

Re: [gmx-users] DSSP error

2010-11-10 Thread Ali Naqvi
May be the directory you are working in is read only, as Justin mentioned this could be a permissions issue. As an example the super computer that I use, cannot write anything in the home directory, therefore all simulations and analysis are done in scratch. Ali -- gmx-users mailing listgmx-

Re: [gmx-users] DSSP error

2010-11-10 Thread Justin A. Lemkul
Justin A. Lemkul wrote: ahmet yıldırım wrote: Dear Justin, Thanks for your replies a...@ab-desktop:~/Desktop/gromacswork$ dssp protein.pdb bash: /usr/local/bin/dssp: cannot execute binary file That seems to indicate that the dssp executable does not match your architecture. Get rid of

Re: [gmx-users] DSSP error

2010-11-10 Thread Justin A. Lemkul
ahmet yıldırım wrote: Dear Justin, Thanks for your replies a...@ab-desktop:~/Desktop/gromacswork$ dssp protein.pdb bash: /usr/local/bin/dssp: cannot execute binary file That seems to indicate that the dssp executable does not match your architecture. Get rid of this executable and compile

Re: [gmx-users] DSSP error

2010-11-10 Thread ahmet yıldırım
Dear Justin, Thanks for your replies a...@ab-desktop:~/Desktop/gromacswork$ dssp protein.pdb bash: /usr/local/bin/dssp: cannot execute binary file 2010/11/10 Justin A. Lemkul > > > ahmet yıldırım wrote: > >> Dear Justin, I don't undertand you said "you haven't chmod +x dssp)?" >> Please look a

Re: [gmx-users] DSSP error

2010-11-10 Thread Justin A. Lemkul
ahmet yıldırım wrote: Dear Justin, I don't undertand you said "you haven't chmod +x dssp)?" Please look at attached photo? I guess that means it's executable; I'm not used to looking into things with the filesystem browser window. I just couldn't remember if the dssp executable was, by d

Re: [gmx-users] DSSP error

2010-11-10 Thread Justin A. Lemkul
ahmet yıldırım wrote: Hi, Please tell me which step is wrong:( 1.step-r...@ab-desktop:/home/ab/Desktop# tar xvzf dsspcmbi.tar.gz 2.step-r...@ab-desktop:/home/ab/Desktop/dssp# cp dsspcmbi dssp 3.step-r...@ab-desktop:/home/ab/Desktop/dssp# mv dssp /usr/local/bin 4.step-r...@ab-desktop:/home/ab/

Re: [gmx-users] DSSP error

2010-11-10 Thread ahmet yıldırım
Hi, Please tell me which step is wrong:( 1.step-r...@ab-desktop:/home/ab/Desktop# tar xvzf dsspcmbi.tar.gz 2.step-r...@ab-desktop:/home/ab/Desktop/dssp# cp dsspcmbi dssp 3.step-r...@ab-desktop:/home/ab/Desktop/dssp# mv dssp /usr/local/bin 4.step-r...@ab-desktop:/home/ab/Desktop/dssp# export DSSP=

Re: [gmx-users] Re: which force file has parameters for creatine md simulations?

2010-11-10 Thread Justin A. Lemkul
Olga Ivchenko wrote: Dear All, I have created creating topology file using *prodrg_beta (using gromos 96 ff) *. When I am trying to run energy minimization it writes an error: Please consider carefully the caveats about PRODRG noted

[gmx-users] Re: which force file has parameters for creatine md simulations?

2010-11-10 Thread Olga Ivchenko
Dear All, I have created creating topology file using *prodrg_beta (using gromos 96 ff) *. When I am trying to run energy minimization it writes an error: Syntax error - File creatine.top, line 19 Last line read: '[ moleculetype ]' Invalid

[gmx-users] Freeze Groups in Gromacs 4.5.x (bug?)!!!

2010-11-10 Thread Miguel Machuqueiro
Dear users and developers, In GROMACS 4.5.x when using "freeze groups" on a Protein in a Protein+Solvent system, I noticed that the coordinates of a few atoms (not many, but a few) are changed after a short period of MD (~0.2 ps). Of course, this is wrong! Are there any options in MDP/GROMP

Re: [gmx-users] trjconv, pbc and breaking of multiple peptides

2010-11-10 Thread ms
On 09/11/10 21:36, Justin A. Lemkul wrote: I am doing REMD simulations of multiple homopolymeric peptides in a PBC box, in vacuum (it's a custom coarse grain). GROMACS 4.0.5. I want to analyze features of the system that require to use g_gyrate to find out the moments of inertia of the system, fo

Re: [gmx-users] y-axis label in hbang and hbdist.xvg file

2010-11-10 Thread Justin A. Lemkul
atila petrosian wrote: Dear Justin count = count of hydrogen bonds being in a certain distance (between 0-0.35) and angle (between 0-30)? The output is a histogram. Bins are generated and then counts are done in those bins. The output is count (per bin) vs. middle of the bin, like any

[gmx-users] Re: the charmm force field in gromacs

2010-11-10 Thread Pär Bjelkmar
Hello, I forward your e-mail to the gmx-users mailing list so that other can see and get help from this. I don't fully understand your question but the testing went as this: We took small peptides (tripeptides typically) of arbitrary conformations of the amino acids and compared the energies of

[gmx-users] y-axis label in hbang and hbdist.xvg file

2010-11-10 Thread atila petrosian
Dear Justin count = count of hydrogen bonds being in a certain distance (between 0-0.35) and angle (between 0-30)? -- 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/Sear

Re: [gmx-users] Gromacs 4.5 build problems

2010-11-10 Thread Roland Schulz
Hi, compiling with PGI doesn't currently work. It would not be difficult to get it to compile with PGI but currently it is not supported. Please let us know if their is a compelling reason why you need to use PGI. Their should be no performance advantage. Thus I suggest to use Intel or GNU. Rola

Re: [gmx-users] -don (g-hbond)

2010-11-10 Thread Erik Marklund
Justin A. Lemkul skrev 2010-11-10 14.57: atila petrosian wrote: Dear Justin I confused. number of donors in donor.xvg file is 203. while, when use g_hbond: found 143 donors. I haven't taken a thorough look through the code (which is quite long), but it looks like the number reported in

Re: [gmx-users] y-axis label in hbang and hbdist.xvg file

2010-11-10 Thread Justin A. Lemkul
atila petrosian wrote: Dear Justin very thanks for your attention. I have another question about g_hbond. in manual, -dist and -ang are distance and angle distribution of all hydrogen bonds respectively. I want to know in hbang and hbdist.xvg file, what is y-axis label? For a simple

[gmx-users] Re: g_hbond / hbmap.xpm file

2010-11-10 Thread Thomas Schlesier
>atila petrosian wrote: >> > Dear Justin >> > >> > I confused. >> > number of donors in donor.xvg file is 203. while, when use >g_hbond: >> > found 143 donors. >> > >I haven't taken a thorough look through the code (which is quite >long), but it >looks like the number reported in donor.xvg cons

[gmx-users] y-axis label in hbang and hbdist.xvg file

2010-11-10 Thread atila petrosian
Dear Justin very thanks for your attention. I have another question about g_hbond. in manual, -dist and -ang are distance and angle distribution of all hydrogen bonds respectively. I want to know in hbang and hbdist.xvg file, what is y-axis label? -- gmx-users mailing listgmx-users@gromacs.

Re: [gmx-users] on calculation of the atomic covariance

2010-11-10 Thread Justin A. Lemkul
There are two relevant threads on this same topic that will likely provide some insight (particularly the second): http://lists.gromacs.org/pipermail/gmx-users/2009-November/046846.html http://lists.gromacs.org/pipermail/gmx-users/2009-November/046854.html -Justin Vigneshwar Ramakrishnan wro

RE: [gmx-users] DSSP error

2010-11-10 Thread #ZHAO LINA#
http://biskit.pasteur.fr/install/applications/dssp http://oldwww.gromacs.org/pipermail/gmx-users/2009-April/041004.html http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp?highlight=dssp HTH, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...

Re: [gmx-users] g_hbond / hbmap.xpm file

2010-11-10 Thread Justin A. Lemkul
shahab shariati wrote: Dear Justin Thus, if there are 40 hydrogen bond. Numerical indice 5 on the y-axis of .eps file is same to indice 35 in .ndx file. Is it true? No. Index 5 of the .ndx file corresponds to data line 35 of the .xpm file. The output .eps file is numbered in accordance

[gmx-users] g_hbond / hbmap.xpm file

2010-11-10 Thread shahab shariati
Dear Justin Thus, if there are 40 hydrogen bond. Numerical indice 5 on the y-axis of .eps file is same to indice 35 in .ndx file. 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

[gmx-users] DSSP error

2010-11-10 Thread ahmet yıldırım
Hi, I installed in /usr/local/bin the DSSP program. And I set the environment variable with a command such as “export DSSP=/usr/local/bin/dssp”. a...@ubuntu:/Desktop/work# do_dssp -s run.tpr -f run.xtc ... Selected 1: 'Protein' There are 164 residues in your selected group Opening library file /us

Re: [gmx-users] -don (g-hbond)

2010-11-10 Thread Justin A. Lemkul
atila petrosian wrote: Dear Justin I confused. number of donors in donor.xvg file is 203. while, when use g_hbond: found 143 donors. I haven't taken a thorough look through the code (which is quite long), but it looks like the number reported in donor.xvg considers all donor groups, i

Re: [gmx-users] g_hbond / hbmap.xpm file

2010-11-10 Thread Justin A. Lemkul
shahab shariati wrote: Dear Erik and Justin Thanks for your time and attention. My xpm file is following state: /* XPM */ /* Generated by g_hbond */

[gmx-users] g_hbond / hbmap.xpm file

2010-11-10 Thread shahab shariati
Dear Erik and Justin Thanks for your time and attention. My xpm file is following state: /* XPM */ /* Generated by g_hbond */ /* This file can be converted to EPS by the GROMACS program xpm2ps */ /* title: "Hydrogen Bond Existence Map" */ /* legend: "Hydrogen Bonds" */ /* x-label: "Time (

[gmx-users] -don (g-hbond)

2010-11-10 Thread atila petrosian
Dear Justin I confused. number of donors in donor.xvg file is 203. while, when use g_hbond: found 143 donors. Select a group: 2 Selected 2: 'Protein_A' Select a group: 3 Selected 3: 'Protein_B' Checking for overlap in atoms between Protein_A and Protein_B Calculating hydrogen bonds between Prote

[gmx-users] Gromacs 4.5 build problems

2010-11-10 Thread Miah Wadud Dr (ITCS)
Hello Gromacs users, I am trying to build Gromacs 4.5 using PGI compiler 10.9 and am getting the following error message: mpicc -DHAVE_CONFIG_H -I. -I../../src -I/usr/include/libxml2 -I../../include -DGMXLIBDIR=\"/cvos/apps/gromacs-4.5/share/top\" -I/cvos/shared/apps/fftw/pgi/64/3.1.2/include -Mm

[gmx-users] on calculation of the atomic covariance

2010-11-10 Thread Vigneshwar Ramakrishnan
Dear All, I am trying to study the effect of single-point mutations on correlated motions in a protein-DNA system. I am able to calculate the atomic covariance matrix using the g_covar -xpma option. However, when I try to compare the covariance matrices for the two systems (to study the effect of

Re: [gmx-users] -don (g-hbond)

2010-11-10 Thread Justin A. Lemkul
atila petrosian wrote: Hi all I want to know regarding 2nd and 3rd column of donor.xvg output about g_hbond -don. Are there no legends in the header of the file? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Tra

Re: [gmx-users] g_hbond / hbmap.xpm file

2010-11-10 Thread Justin A. Lemkul
shahab shariati wrote: Dear Erik Thanks for your attention. What is your mean of [but keep in mind that the matrix is displayed with the first row at the bottom]. Please clarify that more. The last line of the .xpm file corresponds to the first entry in the H-bonds section of th

Re: [gmx-users] mdrun -rerun: bonded interactions of protein

2010-11-10 Thread Mark Abraham
On 10/11/2010 11:29 PM, NG HUI WEN wrote: Hi Gmxusers, I have been trying to run mdrun --rerun to get the energy of the protein in my protein-lipid system. I know similar questions have been raised on this topic before, I have tried to glean useful information from them to solve my problem b

Re: [gmx-users] -don (g-hbond)

2010-11-10 Thread Justin A. Lemkul
atila petrosian wrote: Dear Justin Header of file is as follow: @title "Donor properties" @xaxis label "Time (ps)" @yaxis label "Number" @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on

Re: [gmx-users] mdrun -rerun: bonded interactions of protein

2010-11-10 Thread Justin A. Lemkul
NG HUI WEN wrote: Hi Gmxusers, I have been trying to run mdrun –rerun to get the energy of the protein in my protein-lipid system. I know similar questions have been raised on this topic before, I have tried to glean useful information from them to solve my problem but unfortunately to n

Re: [gmx-users] g_hbond / hbmap.xpm file

2010-11-10 Thread Erik Marklund
shahab shariati skrev 2010-11-10 10.48: Dear gromacs users I used g_hbond -f *.xtc -s *.tpr -n *.ndx -hbm hbmap.xpm for hydrogen bond analysis. then I used xpm2ps -f hbmap.xpm -o hbmap.eps.the ps file is hydrogen bond index vs time. I don't understand numbers in vertical axis. do these numbe

[gmx-users] mdrun -rerun: bonded interactions of protein

2010-11-10 Thread NG HUI WEN
Hi Gmxusers, I have been trying to run mdrun -rerun to get the energy of the protein in my protein-lipid system. I know similar questions have been raised on this topic before, I have tried to glean useful information from them to solve my problem but unfortunately to no avail. Thanks for your

[gmx-users] -don (g-hbond)

2010-11-10 Thread atila petrosian
Hi all I want to know regarding 2nd and 3rd column of donor.xvg output about g_hbond -don. -- 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! Pleas

Re: [gmx-users] Re: GB-polarization

2010-11-10 Thread Per Larsson
Hi! Sorry for the confusion here. Justin is right. In versions before 4.5.2, the non-polar solvation calculation was done regardless of the sa_algorithm setting. In 4.5.2, this has to be specified explicitly using the setting Ace-approximation, to get the complete solvation free energy. Also, t

[gmx-users] g_hbond / hbmap.xpm file

2010-11-10 Thread shahab shariati
Dear gromacs users I used g_hbond -f *.xtc -s *.tpr -n *.ndx -hbm hbmap.xpm for hydrogen bond analysis. then I used xpm2ps -f hbmap.xpm -o hbmap.eps.the ps file is hydrogen bond index vs time. I don't understand numbers in vertical axis. do these numbers in vertical axis relate to hbond.ndx fil

[gmx-users] -don (g-hbond)

2010-11-10 Thread atila petrosian
Dear Justin Header of file is as follow: @title "Donor properties" @xaxis label "Time (ps)" @yaxis label "Number" @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend "Nbound" @ s1

[gmx-users] g_hbond / hbmap.xpm file

2010-11-10 Thread shahab shariati
Dear Erik Thanks for your attention. What is your mean of [but keep in mind that the matrix is displayed with the first row at the bottom]. Please clarify that more. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the arch