[gmx-users] recognising phos group
Hi ! I am attempting to simulate a protein that is phosphorylated below is a part of the PDF file HETATM 460 P PO3 A 200 14.995 1.523 4.011 1.00 0.89 P HETATM 461 O1 PO3 A 200 14.287 1.882 5.272 1.00 1.16 O HETATM 462 O2 PO3 A 200 15.841 0.179 4.048 1.00 0.77 O HETATM 463 O3 PO3 A 200 14.134 1.500 2.694 1.00 0.97 O HETATM 464 P PO3 A 201 13.207 -1.138 -1.342 1.00 1.31 P HETATM 465 O1 PO3 A 201 12.997 -2.551 -0.914 1.00 1.43 O HETATM 466 O2 PO3 A 201 11.918 -0.211 -1.324 1.00 1.47 O HETATM 467 O3 PO3 A 201 13.927 -0.914 -2.727 1.00 1.41 O but upon executing pdb2gmx of the PDB file I get an error - Fatal error: Residue 'PO3' not found in residue topology database -- I do know that DNA can be simulated in GROMOS (option 0 of pdb2gmx). So I am wondering how to overcome the above error. Awaiting suggestions Thanks Jayant -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) Residence -24935864, cell-9841042164 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] continuation run in parallel with shuffle and, sort option
While the previously posted script seems like a valid approach, the
usefulness of -sort depends entirely on how long your trajectory is. If
you only sort once at the beginning, then after <<10ns your waters will
be mostly redistributed and I think that you will have totally lost the
benifits of sort. The idea behind my usage of -sort is to commonly
re-sort the system. You can find details here outlined by the links
below. However, it's not entirely trivial so you should expect to spend
some time getting this running.
Download g_desort:
http://www.gromacs.org/pipermail/gmx-users/2007-July/028542.html
Follow the usage instructions in g_desort -h or take a look at this
script that iteratively runs gromacs:
http://wiki.gromacs.org/index.php/Checkpointing_Jobs
--- original message ---
Hi,
I was running a DPPC system with 128 DPPC and 3655 water molecules in
16 CPU with -shuffle -sort option. But I am unable to continue the job
in parallel.
I read a lots of posts in mailing list, but could not understand the
proper way, as I don't know the script languages. So whatever is
mentioned in the list, I could not use those properly.
Can anyone explain the procedure in a simpler way such that a poor
scripter like me can follow? The details what I have done are as
follows
1.grompp -f grompp.mdp -c input1.gro -p dppc.top -n index.ndx -np 16
-shuffle -sort
2./opt/lam/gnu/bin/mpirun c0-15 /home/ananya/gromacs/bin/mdrun_mpi -v -nice 0
then I get the output as, say, topol1.tpr, traj1.trr, confout1.gro,
ener1.edr, deshuf1.ndx
--
If I follow the mail as I am going to copy here, I can follow upto
step 3. In step 4, what is shuffled top file? If I undersant
correctly, I have to get that from my original top file, which is
dppc.top for me using that awk script. But how to use that I did not
understand. Any suggestion is highly appreciated.
Thanking you,
Regards,
Ananya.
--
Hi,
Make it simple, to use grompp for exact continuation, you need to have
1. mdp file with "gen_vel = no", "unconstrained-start = yes",
2. shuffled trr (original output)
3. shuffled edr (original output)
4. shuffled top (use below awk script to parse the output from your previous
grompp output which contains the shuffled table) replace the [ molecules ]
section in your top with the output of this script.
BEGIN {
begin=0
}
{
if ($1=="Moltype") {
begin=1
for (i=0;ihttp://www.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] x2top, error generating topology
Vitaly Chaban wrote: Hello All, I've got a problem with x2top in gromacs 3.3.3. Trying to obtain atopology from ".pdb" structure I do the following: 1. Add C C 1 C ; CNT Carbon with one bond C C 2 C C ; CNT double bonded Carbon to ffencadv.n2t. 2. Add the following lines [ bondtypes ] ; i j func b0 kb C C 1 0.14210 478900. [ angletypes ] ; i j k func th0 cth C C C 1 120.000 397.480 [ dihedraltypes ] ; i l func q0 cq C C 1 0.000 167.360 to ffgmxbon.itp. that should be ffencadvbon.itp I presume? 3. Then I execute: x2top -f cnt.pdb -o cnt.top where cnt.pdb is from http://turin.nss.udel.edu/research/tubegenonline.html During the processing I select 7: Encad all-atom force field, using scaled-down vacuum charges The output is Looking whether force field files exist Opening library file /usr/local/gromacs/share/gromacs/top/ffencadv.rtp Opening library file ffencadv.n2t WARNING: all CONECT records are ignored Opening library file ffencadv.n2t There are 0 name to type translations Generating bonds from distances... atom 144 Can not find forcefield for atom C-1 with 0 bonds Can not find forcefield for atom C-2 with 0 bonds Can not find forcefield for atom C-3 with 0 bonds Can not find forcefield for atom C-4 with 0 bonds Can not find forcefield for atom C-5 with 0 bonds Can not find forcefield for atom C-6 with 0 bonds Can not find forcefield for atom C-7 with 0 bonds Can not find forcefield for atom C-8 with 0 bonds Can not find forcefield for atom C-9 with 0 bonds Can not find forcefield for atom C-10 with 0 bonds --- Program x2top, VERSION 3.3.3 Source code file: x2top.c, line: 206 Fatal error: Could only find a forcefield type for 0 out of 144 atoms I had not got this error when using version 3.3.1 with this particular task. Why does it consider the carbon has zero bonds...? Any ideas what to do would be gratefully appreciated. Vitaly ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] x2top, error generating topology
Hello All, I've got a problem with x2top in gromacs 3.3.3. Trying to obtain atopology from ".pdb" structure I do the following: 1. Add >> C C 1 C ; CNT Carbon with one bond >> C C 2 C C ; CNT double bonded Carbon to ffencadv.n2t. 2. Add the following lines [ bondtypes ] ; i j func b0 kb C C 1 0.14210 478900. [ angletypes ] ; i j k func th0 cth C C C 1 120.000 397.480 [ dihedraltypes ] ; i l func q0 cq C C 1 0.000 167.360 to ffgmxbon.itp. 3. Then I execute: x2top -f cnt.pdb -o cnt.top where cnt.pdb is from http://turin.nss.udel.edu/research/tubegenonline.html During the processing I select 7: Encad all-atom force field, using scaled-down vacuum charges The output is Looking whether force field files exist Opening library file /usr/local/gromacs/share/gromacs/top/ffencadv.rtp Opening library file ffencadv.n2t WARNING: all CONECT records are ignored Opening library file ffencadv.n2t There are 0 name to type translations Generating bonds from distances... atom 144 Can not find forcefield for atom C-1 with 0 bonds Can not find forcefield for atom C-2 with 0 bonds Can not find forcefield for atom C-3 with 0 bonds Can not find forcefield for atom C-4 with 0 bonds Can not find forcefield for atom C-5 with 0 bonds Can not find forcefield for atom C-6 with 0 bonds Can not find forcefield for atom C-7 with 0 bonds Can not find forcefield for atom C-8 with 0 bonds Can not find forcefield for atom C-9 with 0 bonds Can not find forcefield for atom C-10 with 0 bonds --- Program x2top, VERSION 3.3.3 Source code file: x2top.c, line: 206 Fatal error: Could only find a forcefield type for 0 out of 144 atoms I had not got this error when using version 3.3.1 with this particular task. Why does it consider the carbon has zero bonds...? Any ideas what to do would be gratefully appreciated. Vitaly ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] inconsistent shifts
Bert wrote: Hi all, I use pbc=full in my system, and all runs are ok except for the "inconsistent shifts" warnings when I use some analysis tools, such as g_density, g_densmap, etc. I have searched the whole list related to this problem, and I doubt several analysis tools are not coded with consideration of full pbc. Am I right? If so, how to deal with these warnings? Thanks in advance. make a tpr with pbc=xyz for analysis. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] inconsistent shifts
Hi all, I use pbc=full in my system, and all runs are ok except for the "inconsistent shifts" warnings when I use some analysis tools, such as g_density, g_densmap, etc. I have searched the whole list related to this problem, and I doubt several analysis tools are not coded with consideration of full pbc. Am I right? If so, how to deal with these warnings? Thanks in advance. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] mix solvent
I gave you advice: http://www.gromacs.org/pipermail/gmx-users/2008-April/033307.html So what have you done to help yourself? Asking the same question without demonstrating that you've attempted to respond to the advice given will surely get you nowhere. -Justin Quoting Mahnam <[EMAIL PROTECTED]>: > In God We Trust > Hello GMX users > I want > to equilibrate my protein in a mix solvent, befor this work, I made a > cubic box that it contained 215 spc water and 5 proline molecule (without > > protein) with 20*20*20 angestrom and then I minimized it. when I do > position restrain with NPT ensemble and pressure coupling (for 20 ps) for > > this box, and the box size increase and big holes are created in the box. > > Also I can do MD at 100 K after this step, but MD at 200 K is imposible > > and it says : > > Grid: 25 x 25 x 25 cells > WARNING: your box is > exploding! (ncells = 15625) > > --- > Program mdrun, > VERSION 3.3.1 > Source code file: gmxfio.c, line: 784 > > Fatal > error: > Can not read/write topologies to file type mdp > > I > attached the mdp file for position restrain step to this mail. > > whould you please guide my for solving this poblem. > > Many > thanks in advance for your help and your reply. > Yours truly > Karim > Mahnam > Institute of Biochemistry and Biophysics (IBB) > > Tehran University > Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] continuation run in parallel with shuffle and sort option
Hi,
I was running a DPPC system with 128 DPPC and 3655 water molecules in
16 CPU with -shuffle -sort option. But I am unable to continue the job
in parallel.
I read a lots of posts in mailing list, but could not understand the
proper way, as I don't know the script languages. So whatever is
mentioned in the list, I could not use those properly.
Can anyone explain the procedure in a simpler way such that a poor
scripter like me can follow? The details what I have done are as
follows
1.grompp -f grompp.mdp -c input1.gro -p dppc.top -n index.ndx -np 16
-shuffle -sort
2./opt/lam/gnu/bin/mpirun c0-15 /home/ananya/gromacs/bin/mdrun_mpi -v -nice 0
then I get the output as, say, topol1.tpr, traj1.trr, confout1.gro,
ener1.edr, deshuf1.ndx
--
If I follow the mail as I am going to copy here, I can follow upto
step 3. In step 4, what is shuffled top file? If I undersant
correctly, I have to get that from my original top file, which is
dppc.top for me using that awk script. But how to use that I did not
understand. Any suggestion is highly appreciated.
Thanking you,
Regards,
Ananya.
--
Hi,
Make it simple, to use grompp for exact continuation, you need to have
1. mdp file with "gen_vel = no", "unconstrained-start = yes",
2. shuffled trr (original output)
3. shuffled edr (original output)
4. shuffled top (use below awk script to parse the output from your previous
grompp output which contains the shuffled table) replace the [ molecules ]
section in your top with the output of this script.
BEGIN {
begin=0
}
{
if ($1=="Moltype") {
begin=1
for (i=0;ihttp://www.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 interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] mdrun exectutable
On Tue, 08 Apr 2008 15:49:10 +0200 Marilisa Neri <[EMAIL PROTECTED]> wrote: I am trying to compile by hand the mdrun executable. For this reason, I have selected just the routines that I need. Why don't you run the configure and then use "make mdrun" I think it will do what you want! I collected a list of file.c, file.h, and file.s . I compiled the files .c and .s with this command: (i) mpicc -c *.[cs] -I. -I /fftw-2.1.5/include/ -DHAVE_CONFIG_H -DGMXLIBDIR=\"/Software/gromacs-3.3.1/share/gromacs/top/\" Then, I created the executable "my_mdrun" in this way: (ii) mpicc *.o -lm -L /usr/X11R6/lib -lXm -L /home/marilisa/fftw-2.1.5/lib/ -lsfftw -ldrfftw -ldfftw -o my_mdrun This procedure works with a 32-bits architecture. When I running the command (i) with a 64-bits architecture, I have a problem with the routines: x86_3dnow.s, x86_cpuid.s, x86_sse.s. The general error is: x86_3dnow.s:104: Error: suffix or operands invalid for `push' x86_3dnow.s:156: Error: suffix or operands invalid for `pop' x86_sse.s:18151: Error: suffix or operands invalid for `pop' x86_sse.s:18273: Error: suffix or operands invalid for `push' x86_cpuid.s:73: Error: suffix or operands invalid for `push' x86_cpuid.s:84: Error: suffix or operands invalid for `pop' Someone could help me? Thank you very much, Marilisa ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - XAvier Periole - PhD NMR & Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole - ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] mix solvent
In God We Trust Hello GMX users I want to equilibrate my protein in a mix solvent, befor this work, I made a cubic box that it contained 215 spc water and 5 proline molecule (without protein) with 20*20*20 angestrom and then I minimized it. when I do position restrain with NPT ensemble and pressure coupling (for 20 ps) for this box, and the box size increase and big holes are created in the box. Also I can do MD at 100 K after this step, but MD at 200 K is imposible and it says : Grid: 25 x 25 x 25 cells WARNING: your box is exploding! (ncells = 15625) --- Program mdrun, VERSION 3.3.1 Source code file: gmxfio.c, line: 784 Fatal error: Can not read/write topologies to file type mdp I attached the mdp file for position restrain step to this mail. whould you please guide my for solving this poblem. Many thanks in advance for your help and your reply. Yours truly Karim Mahnam Institute of Biochemistry and Biophysics (IBB) Tehran University prmd-npt.mdp Description: Binary data ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] mdrun exectutable
Marilisa Neri wrote: I am trying to compile by hand the mdrun executable. For this reason, I have selected just the routines that I need. I collected a list of file.c, file.h, and file.s . I compiled the files .c and .s with this command: (i) mpicc -c *.[cs] -I. -I /fftw-2.1.5/include/ -DHAVE_CONFIG_H -DGMXLIBDIR=\"/Software/gromacs-3.3.1/share/gromacs/top/\" Then, I created the executable "my_mdrun" in this way: (ii) mpicc *.o -lm -L /usr/X11R6/lib -lXm -L /home/marilisa/fftw-2.1.5/lib/ -lsfftw -ldrfftw -ldfftw -o my_mdrun This procedure works with a 32-bits architecture. When I running the command (i) with a 64-bits architecture, I have a problem with the routines: x86_3dnow.s, x86_cpuid.s, x86_sse.s. The general error is: x86_3dnow.s:104: Error: suffix or operands invalid for `push' x86_3dnow.s:156: Error: suffix or operands invalid for `pop' x86_sse.s:18151: Error: suffix or operands invalid for `pop' x86_sse.s:18273: Error: suffix or operands invalid for `push' x86_cpuid.s:73: Error: suffix or operands invalid for `push' x86_cpuid.s:84: Error: suffix or operands invalid for `pop' Someone could help me? You probably need more defines that are generated for you when you use the configure script. You could try to run configure and see what extra defines are generated (src/config.h). Otherwise, you're on your own... Thank you very much, Marilisa ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] mdrun exectutable
I am trying to compile by hand the mdrun executable. For this reason, I have selected just the routines that I need. I collected a list of file.c, file.h, and file.s . I compiled the files .c and .s with this command: (i) mpicc -c *.[cs] -I. -I /fftw-2.1.5/include/ -DHAVE_CONFIG_H -DGMXLIBDIR=\"/Software/gromacs-3.3.1/share/gromacs/top/\" Then, I created the executable "my_mdrun" in this way: (ii) mpicc *.o -lm -L /usr/X11R6/lib -lXm -L /home/marilisa/fftw-2.1.5/lib/ -lsfftw -ldrfftw -ldfftw -o my_mdrun This procedure works with a 32-bits architecture. When I running the command (i) with a 64-bits architecture, I have a problem with the routines: x86_3dnow.s, x86_cpuid.s, x86_sse.s. The general error is: x86_3dnow.s:104: Error: suffix or operands invalid for `push' x86_3dnow.s:156: Error: suffix or operands invalid for `pop' x86_sse.s:18151: Error: suffix or operands invalid for `pop' x86_sse.s:18273: Error: suffix or operands invalid for `push' x86_cpuid.s:73: Error: suffix or operands invalid for `push' x86_cpuid.s:84: Error: suffix or operands invalid for `pop' Someone could help me? Thank you very much, Marilisa ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] (no subject)
Is your simulation box (20*20*20 A^3) big enough? 2008/4/7 Mahnam <[EMAIL PROTECTED]>: > In God We Trust > Hello GMX users > I want to equilibrate my protein in a mix solvent, befor this work, I made > a cubic box that it contained 215 spc water and 5 proline molecule (without > protein) with 20*20*20 angestrom and then I minimized it. when I do position > restrain with NPT ensemble and pressure coupling (for 20 ps) for this box, > and the box size increase and big holes are created in the box. Also I can > do MD at 100 K after this step, but MD at 200 K is imposible and it says : > > Grid: 25 x 25 x 25 cells > WARNING: your box is exploding! (ncells = 15625) > --- > Program mdrun, VERSION 3.3.1 > Source code file: gmxfio.c, line: 784 > > *Fatal error: > Can not read/write topologies to file type mdp* > > I attached the mdp file for position restrain step to this mail. > whould you please guide my for solving this poblem. > > Many thanks in advance for your help and your reply. > Yours truly > Karim Mahnam > Institute of Biochemistry and Biophysics (IBB) > Tehran University > P.O.box 13145-1384 > Tehran > Iran > http://www.ibb.ut.ac.ir/ > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.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 interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] bilayer simulation crashes after 2 ns or 7 ns of stable runs. why does system explode
What will happen if pbc=full is used? 2008/4/4 maria goranovic <[EMAIL PROTECTED]>: > Dear All > > I am running a 128-lipid bilayer simulation with standard parameters. The > simulation abruptly crashed after 2 ns, and a look into the pdb files > suggested that bonds were being broken and eventually the lipids explode. I > tried increasing the cutoffs from 1.0 to 1.4, and this time also, the > simulation exploded, but at a different time point. > > The energy remains nice and stable till the explosion. > > How does one fix this ? What is planting these bombs ? > > Thank you for suggestions. > > -- > Maria G. > Technical University of Denmark > Copenhagen > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.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 interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] AA not present in the ffG43a1.rtp
You find those definitions in ffG43a1bon.itp. As far as I know, they are simply placeholders for the explicit data. Probably you can insert the explicit data into the rtp file. Andreas > -Original Message- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] > On Behalf Of Mattia Sturlese > Sent: 08 April 2008 11:54 > To: gmx-users@gromacs.org > Subject: [gmx-users] AA not present in the ffG43a1.rtp > > Dear all, > I have a protein with an oxidated Cys( to sulfinic acid) , this > residue is not present in the residue database. I use PRODGR to obtain > the .itp file of the residue but I don't start grompp > > How I insert this residue in the rtp file?? I trying insert the > parameters manually but I have explicit data of angles, bond, dihedral > and impropersbut ffG43a use Gromos Type definition as ga_XX or > gb_XX.. Where i find a database of this gromos type? Or How I can > insert my .itp file ? > > Thanks folk!! > Mattia Sturlese > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.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 interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] AA not present in the ffG43a1.rtp
Quoting Mattia Sturlese <[EMAIL PROTECTED]>: > Dear all, > I have a protein with an oxidated Cys( to sulfinic acid) , this > residue is not present in the residue database. I use PRODGR to obtain > the .itp file of the residue but I don't start grompp Be aware that the charges given by PRODRG are often unsatisfactory, and usually (if not always) require refining. > > How I insert this residue in the rtp file?? I trying insert the > parameters manually but I have explicit data of angles, bond, dihedral > and impropersbut ffG43a use Gromos Type definition as ga_XX or > gb_XX.. Where i find a database of this gromos type? Or How I can > insert my .itp file ? Use the other entries in the .rtp file as a guide. Bonded parameters are found in ffG43a1bon.itp. -Justin > > Thanks folk!! > Mattia Sturlese > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.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 interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] AA not present in the ffG43a1.rtp
Dear all, I have a protein with an oxidated Cys( to sulfinic acid) , this residue is not present in the residue database. I use PRODGR to obtain the .itp file of the residue but I don't start grompp How I insert this residue in the rtp file?? I trying insert the parameters manually but I have explicit data of angles, bond, dihedral and impropersbut ffG43a use Gromos Type definition as ga_XX or gb_XX.. Where i find a database of this gromos type? Or How I can insert my .itp file ? Thanks folk!! Mattia Sturlese ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g msd freeze
Quoting Kateøina Hyn¹tová <[EMAIL PROTECTED]>: > The simulated system is a carbon chain of 1000 united atom units. Ive tried > bothmaking the system smaller (less units or extracting the trajectory for > one unit)and taking very short time of simulation using the flags -b and -e, > the system response is still the same (even after the run over weekend) The > simulation and all other tools used so far work ok even for much larger > systems.Ive also tried the -msd flag in g_analyze tool, I get the msd graph > "immediatelly". The system im running the simulation on is currently CPU > INTEL Core 2 Quad Q600 (2.4GHz, 8M, 1066MHz), 4x1G DDR2-800 MHz Aeneon BOX. I > have also tried to recompile the g_msd tool.Could I be some problem of e.g. > memory? I appologize if Im not giving the exact or sufficient informationto > about the problem, Im the very begginer. Thank you very much for your > help.Best regards,Katka How was your Gromacs version compiled, and what version are you using? What version of gcc was used? -Justin > >Otherwise, how big is the system, how long is the trajectory and what > >system are you running on? > > > >Mark > > _ > Explore the seven wonders of the world > http://search.msn.com/results.aspx?q=7+wonders+world&mkt=en-US&form=QBRE Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] CPMD and gmx
Thanks, Vasilii. >From publ it's clear that 5 a.u. is standart for all CP MD simulations, I was confused by examples from Biswas page :) It's time to start cp md and will go deeper in theory :) On Mon, Apr 7, 2008 at 9:39 PM, Vasilii Artyukhov <[EMAIL PROTECTED]> wrote: > Dear Andrey, > > The maximum time step depends on whether you're doing Born-Oppenheimer or > Car-Parrinello MD. In the case of usual BO MD, you normally want a time step > of 0.5-1.0 fs, possibly 2 fs, if you use rigid molecules. In the CP case, > you have to use a much smaller time step to make sure that the electronic > degrees of freedom remain decoupled from the atomic motion (the whole idea > of CP approach is to do more time steps, but with only a single iteration > for the electronic structure at each step instead of a full SCF > minimization). You can find some introductory reading on this, e.g., at the > Dominik Marx group website: > http://www.theochem.ruhr-uni-bochum.de/home.en.html > > 2008/4/7, Andrey V Golovin <[EMAIL PROTECTED]>: > > > > > > > > Dear all, > > We successfully passed all test with CPMD-gmx and now the time to do > > md production runs, In examples from interface home page timestep is > > 1fs but in CPMD papers time step is much less, about 0.12 fs. Could > > you please advise some papers to read? I found only one paper > > referencing to CPMD-gmx interface publication. Is any common settings > > for metal cations? > > The best that I found is links from > http://www.cpmd.org/cpmd_publications.html. > > Thanks for any comment. > > -- > > Best regards, Andrey > > > > > Andrey V. Golovin > > Ph.D, Assistant professor tel: +7 (495) 939-5305 > > Bioengineering and > > Bioinformatics Department > > Moscow State University fax: +7 (495) 939-3181 > > 119992 Moscow E-mail: [EMAIL PROTECTED] > > Russia web: http://rnp-group.genebee.msu.su > > > > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.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 interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.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 interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Best regards, Andrey Andrey V. Golovin Ph.D, Assistant professor tel: +7 (495) 939-5305 Bioengineering and Bioinformatics Department Moscow State University fax: +7 (495) 939-3181 119992 Moscow E-mail: [EMAIL PROTECTED] Russia web: http://rnp-group.genebee.msu.su ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g msd freeze
>Kateřina Hynštová wrote: >> Dear users, >> >> >> >> I would like to calculate the mean square displacement. >> >> Using the >> >> >> >> g_msd -f traj.xtc -s input.tpr -n index.ndx -o msd.xvg >> >> >> >> I get >> >> >> >> Reading file input.tpr, VERSION 3.3.2(single precision) >> >> Reading file input.tpr, VERSION 3.3.2(single precision) >> >> Group 0( C) has 1 elements >> >> There is one group in the index >> >> Reading frame 0 time 0.000 >> >> >> >> The system always freezes here without any warning or error. I have > >If your simulation is long and/or computer slow, then it's possible the >calculation is still running. If so, you can experiment with the -b, -e, >and -dt flags to make the calculation shorter. See g_msd -h. You can >also use other analysis tools to check if the problem is localised or not. The simulated system is a carbon chain of 1000 united atom units. Ive tried bothmaking the system smaller (less units or extracting the trajectory for one unit)and taking very short time of simulation using the flags -b and -e, the system response is still the same (even after the run over weekend) The simulation and all other tools used so far work ok even for much larger systems.Ive also tried the -msd flag in g_analyze tool, I get the msd graph "immediatelly". The system im running the simulation on is currently CPU INTEL Core 2 Quad Q600 (2.4GHz, 8M, 1066MHz), 4x1G DDR2-800 MHz Aeneon BOX. I have also tried to recompile the g_msd tool.Could I be some problem of e.g. memory? I appologize if Im not giving the exact or sufficient informationto about the problem, Im the very begginer. Thank you very much for your help.Best regards,Katka >Otherwise, how big is the system, how long is the trajectory and what >system are you running on? > >Mark _ Explore the seven wonders of the world http://search.msn.com/results.aspx?q=7+wonders+world&mkt=en-US&form=QBRE___ gmx-users mailing listgmx-users@gromacs.org http://www.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 interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
