Re: [gmx-users] Re: Question about parallazing Gromacs (Qiao Baofu)
Hi,Thanks. I have test different cpus. Our institute has two clusters: one is each node has 4 cpu (A), one is one node has only 1 cpu (B). I made different tests on the two clusters and my local computer using the same system. See the following result: A (For 1 hour) # of cpus ; MD steps 4 finished (20steps for 26:21) 8 finished (20steps for 40:57) 12 87950 20 42749 44 5962 ! B (For 1 hour) # of cpu ; MD steps 1 156991 for 56:12 2 179820 3 200,000 for 54:20 4 200,000 for 51:12c. Local(single cpu), 20 steps For 1h52:38One can see that 1. On cluster A, one nodes(4 cpu) is just as 4 times fast as my local computer.2. More than one nodes will decrease the performancs the gromacs, 3. On cluster B, the more cpu used, the faster gromacs runs. But the difference of speed is not apparent.4. Cluster B with 4 cpus is slow as half as that Cluster A with 1 node (4 cpus)I wonder if anyone can tell the bottlenack: the hardware on the cluster or gromacs? 2006/9/14, Mark Abraham [EMAIL PROTECTED]: You have to find your optimum making some tests with your settings. To do that you can start your simulation and interrupt after a while to have some data logged in the log file. Then, from the information in that log file you can estimate the time that the whole task will take and compare using more or less number of processors until you find your optimum value.Of course, that while should be at least of the order of several minutes. There is a set-up cost borne once at the start of the calculationwhich is not proportional to the length of the calculation, so you need torun long enough to get out of the time period during which it dominates the linear component.Mark___gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED] .Can't post? Read http://www.gromacs.org/mailing_lists/users.php-- Sincerely yours,** Baofu Qiao, PhDFrankfurt Institute for Advanced Studies** ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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_order C code
Dear Gromacs users,
Hie,
I am calculating the order parameters for a bilayer
patch using g_order analysis tool in gromacs version
3.3.
I have a total of 48 elements in the patch and I want
the order parameter value for each and every element
i.e. a total of say 48 values for order parameter
alongwith the average which g_order reports.
I tried to fiddle with the code too and tried changing
the following section as follows:
/* average over frames */
for (i = 1; i nr_tails; i++) {
/* svmul(1.0/nr_frames, (*order)[i],
(*order)[i]);*/
fprintf(stderr,Atom %d Tensor: x=%g , y=%g,
z=%g\n,i,(*order)(index[i])[XX],
(*order)(index[i])[YY],
(*order)(index[i])[ZZ]);
and also:
sprintf(buf,Deuterium order parameters);
slOrd = xvgropen(cfile,buf, Atom, Scd);
for (i = 1; i nr_tails; i++) {
fprintf(ord,%12d %12g %12g %12g\n, atom,
order(index[i])[XX],
order(index[i])[YY],
order(index[i])[ZZ]);
fprintf(slOrd,%12d %12g\n, atom, -1 *
(0.6667 * order(index[i])[XX] +
0.333
* order(index[i])[YY]));
The problem is I am not sure if that is the right way
of doing this. Please suggest me something. Also once
these changes have been incorporated in the C program
how do I generate the exe of g_order. Gcc gives many
undefined errors.
Please suggest me something,
regards,
Priyanka.
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Re: [gmx-users] Re: Question about parallazing Gromacs (Qiao Baofu)
On Thursday 14 September 2006 09:53, Mark Abraham wrote: Qiao Baofu wrote: Hi, Thanks. I have test different cpus. Our institute has two clusters: one is each node has 4 cpu (A), one is one node has only 1 cpu (B). I made different tests on the two clusters and my local computer using the same system. See the following result: A (For 1 hour) # of cpus ;MD steps 4 finished (20steps for 26:21) 8 finished (20steps for 40:57) 12 87950 20 42749 44 5962 ! B (For 1 hour) # of cpu ; MD steps 1156991 for 56:12 2179820 3200,000 for 54:20 4200,000 for 51:12 c. Local(single cpu), 20 steps For 1h52:38 One can see that 1. On cluster A, one nodes(4 cpu) is just as 4 times fast as my local computer. 2. More than one nodes will decrease the performancs the gromacs, 3. On cluster B, the more cpu used, the faster gromacs runs. But the difference of speed is not apparent. 4. Cluster B with 4 cpus is slow as half as that Cluster A with 1 node (4 cpus) I wonder if anyone can tell the bottlenack: the hardware on the cluster or gromacs? Probably your interconnects between nodes are using carrier pigeons or something :-) I expect that 1 cpu on machine A will require around four times as long as 1 4-cpu node, which you can presumably test for yourself. For next time, if you want to compare hardware like this, either use the same length of time or the same number of MD steps for all of your runs. Also when reporting runtimes, make it clear whether you are reporting walltime or some time * number_of_cpus, etc. :-) Search the mailing list i have post several times benchmark results for different systems with standard benchmark suite. http://www.gromacs.org/pipermail/gmx-developers/2006-January/001473.html Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 Greetings, Florian -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26581 Mailto: florian.haberl AT chemie.uni-erlangen.de --- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Re: Re: Re: Question about parallazing Gromacs
-- Message: 7 Date: Thu, 14 Sep 2006 09:27:45 +0200 From: Qiao Baofu [EMAIL PROTECTED] Subject: Re: [gmx-users] Re: Question about parallazing Gromacs (Qiao Baofu) To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=iso-8859-1 Hi, Thanks. I have test different cpus. Our institute has two clusters: one is each node has 4 cpu (A), one is one node has only 1 cpu (B). I made different tests on the two clusters and my local computer using the same system. See the following result: A (For 1 hour) # of cpus ;MD steps 4 finished (20steps for 26:21) 8 finished (20steps for 40:57) 12 87950 20 42749 44 5962 ! B (For 1 hour) # of cpu ; MD steps 1156991 for 56:12 2179820 3200,000 for 54:20 4200,000 for 51:12 c. Local(single cpu), 20 steps For 1h52:38 One can see that 1. On cluster A, one nodes(4 cpu) is just as 4 times fast as my local computer. 2. More than one nodes will decrease the performancs the gromacs, 3. On cluster B, the more cpu used, the faster gromacs runs. But the difference of speed is not apparent. 4. Cluster B with 4 cpus is slow as half as that Cluster A with 1 node (4 cpus) I wonder if anyone can tell the bottlenack: the hardware on the cluster or gromacs? Well, probably it is a combination of bottlenecks in both software and hardware. Both of them should be optimized to guarantee the best performance. From the hardware side the delays in inter-node communication across the network can be the reason. But also, it can be related with software issues related to the operating system and network configuration. I think that the first thing to do is work in cluster setup to achieve the best performance for your hardware configuration. In addition, take into account that inter-node communication between two CPU's inside the same machine should be faster than between two CPU's across the network. From the software side (Gromacs) the algorithms should be optimized with regard to the parallel programming model. David said in a previous answer that they have detected some problems in the software implementation and they are working to solve that issue in the next version of Gromacs. Regards, --- Cesar Araujo, Lic. of Chemistry Department of Molecular Endocrynology Oulu University Hospital FIN-90029 OYS, OULU, FINLAND phone: +358 8 3155632 e-mail: [EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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_order C code
On Thu, 2006-09-14 at 02:21 -0700, priyanka srivastava wrote:
Dear Gromacs users,
Hie,
I am calculating the order parameters for a bilayer
patch using g_order analysis tool in gromacs version
3.3.
I have a total of 48 elements in the patch and I want
the order parameter value for each and every element
i.e. a total of say 48 values for order parameter
alongwith the average which g_order reports.
I tried to fiddle with the code too and tried changing
the following section as follows:
/* average over frames */
for (i = 1; i nr_tails; i++) {
/* svmul(1.0/nr_frames, (*order)[i],
(*order)[i]);*/
fprintf(stderr,Atom %d Tensor: x=%g , y=%g,
z=%g\n,i,(*order)(index[i])[XX],
(*order)(index[i])[YY],
(*order)(index[i])[ZZ]);
and also:
sprintf(buf,Deuterium order parameters);
slOrd = xvgropen(cfile,buf, Atom, Scd);
for (i = 1; i nr_tails; i++) {
fprintf(ord,%12d %12g %12g %12g\n, atom,
order(index[i])[XX],
order(index[i])[YY],
order(index[i])[ZZ]);
fprintf(slOrd,%12d %12g\n, atom, -1 *
(0.6667 * order(index[i])[XX] +
0.333
* order(index[i])[YY]));
The problem is I am not sure if that is the right way
of doing this. Please suggest me something. Also once
these changes have been incorporated in the C program
how do I generate the exe of g_order. Gcc gives many
undefined errors.
In src/tools: make g_order
It may require that various libraries are already compiled, which is why
you should build all of gromacs once too (in gmx: make install). Having
done that once, make g_order should do the trick I think.
Please suggest me something,
regards,
Priyanka.
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--
Erik Marklund, PhD Student, Molecular Biopcysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
[EMAIL PROTECTED]
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Re: [gmx-users] Re: Question about parallazing Gromacs (Qiao Baofu)
2006/9/14, Mark Abraham [EMAIL PROTECTED]: Probably your interconnects between nodes are using carrier pigeons orsomething :-) I expect that 1 cpu on machine A will require around fourtimes as long as 1 4-cpu node, which you can presumably test for yourself. It is forbidden to run only one cpu on the cluster A in my inisititute. For next time, if you want to compare hardware like this, either use thesame length of time or the same number of MD steps for all of your runs.Also when reporting runtimes, make it clear whether you are reporting walltime or some time * number_of_cpus, etc. :-)For all the jobs (except the one on my local computer) , I set walltime=1hour, and nsteps= 200,000,dt=0.001.The running time are taken from the end of the .log file. See the following example. NODE (s) Real (s) (%) Time: 1581.000 1581.000 100.0 26:21 (Mnbf/s) (GFlops) (ns/day) (hour/ns)Performance: 56.376 4.515 10.930 2.196Mark___ gmx-users mailing listgmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease 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 -- Sincerely yours,**Baofu Qiao, PhDFrankfurt Institute for Advanced StudiesMax-von-Laue-Str. 160438 Frankfurt am Main, Germany TEL:+49-69-7984-7529 ** ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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_order C code
Thank you for your reply.
I am also curious to know if this is the right way of
doing it. I am not sure of the changes that I have
made in the code.
Any suggestions on that please?
Since, when I say make install it gives the
following error:
cc -DHAVE_CONFIG_H -I. -I. -I../../src
-I/usr/X11R6/include -I../../include
-DGMXLIBDIR=\/usr/local/gromacs/share/top\ -O3
-fomit-frame-pointer -finline-functions -Wall
-Wno-unused -malign-double -funroll-all-loops -MT
gmx_order.lo -MD -MP -MF .deps/gmx_order.Tpo -c
gmx_order.c -o gmx_order.o
gmx_order.c: In function `calc_order':
gmx_order.c:251: called object is not a function
gmx_order.c:252: called object is not a function
gmx_order.c:252: called object is not a function
gmx_order.c: In function `order_plot':
gmx_order.c:300: `i' undeclared (first use in this
function)
gmx_order.c:300: (Each undeclared identifier is
reported only once
gmx_order.c:300: for each function it appears in.)
gmx_order.c:301: called object is not a function
gmx_order.c:302: called object is not a function
gmx_order.c:302: called object is not a function
gmx_order.c:303: called object is not a function
gmx_order.c:304: called object is not a function
make[2]: *** [gmx_order.lo] Error 1
make[2]: Leaving directory
`/home/histidine/gromacs/gromacs-3.3/src/tools'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory
`/home/histidine/gromacs/gromacs-3.3/src'
make: *** [install-recursive] Error 1
thanks and regards,
Priyanka.
--- Erik Marklund [EMAIL PROTECTED] wrote:
On Thu, 2006-09-14 at 02:21 -0700, priyanka
srivastava wrote:
Dear Gromacs users,
Hie,
I am calculating the order parameters for a
bilayer
patch using g_order analysis tool in gromacs
version
3.3.
I have a total of 48 elements in the patch and I
want
the order parameter value for each and every
element
i.e. a total of say 48 values for order parameter
alongwith the average which g_order reports.
I tried to fiddle with the code too and tried
changing
the following section as follows:
/* average over frames */
for (i = 1; i nr_tails; i++) {
/* svmul(1.0/nr_frames, (*order)[i],
(*order)[i]);*/
fprintf(stderr,Atom %d Tensor: x=%g , y=%g,
z=%g\n,i,(*order)(index[i])[XX],
(*order)(index[i])[YY],
(*order)(index[i])[ZZ]);
and also:
sprintf(buf,Deuterium order parameters);
slOrd = xvgropen(cfile,buf, Atom, Scd);
for (i = 1; i nr_tails; i++) {
fprintf(ord,%12d %12g %12g %12g\n,
atom,
order(index[i])[XX],
order(index[i])[YY],
order(index[i])[ZZ]);
fprintf(slOrd,%12d %12g\n, atom, -1 *
(0.6667 * order(index[i])[XX] +
0.333
* order(index[i])[YY]));
The problem is I am not sure if that is the right
way
of doing this. Please suggest me something. Also
once
these changes have been incorporated in the C
program
how do I generate the exe of g_order. Gcc gives
many
undefined errors.
In src/tools: make g_order
It may require that various libraries are already
compiled, which is why
you should build all of gromacs once too (in gmx:
make install). Having
done that once, make g_order should do the trick I
think.
Please suggest me something,
regards,
Priyanka.
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--
Erik Marklund, PhD Student, Molecular Biopcysics
group,
Dept. of Cell and Molecular Biology, Uppsala
University.
Husargatan 3, Box 596, 75124 Uppsala,
Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
[EMAIL PROTECTED]
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Fwd: [gmx-users] Hi...
Hi all.. I wrote this mail yesterday. But could not receive any reply till now. So if someone can suggest something about it. That would be nice. Best regardsNavBegin forwarded message:From: Navratna Vajpai [EMAIL PROTECTED]Date: September 13, 2006 10:32:21 AM GMT+02:00To: Discussion list for GROMACS users gmx-users@gromacs.orgSubject: [gmx-users] Hi...Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org Dear AllHi.. This is in regard to your previously replied mail regarding the use of GROMOS96 or OPLS-AA or AMBER force field.As you said it depends upon the users taste which one to use. This means that the three on a broad manner should give convergence of the analyzed data set. Infact from my simulation runs using oplss-aa and gromos96, I didn't found that. I tried using the GROMOS96 and opls-aa force field on my small peptides for a period of 20ns and found that with opls-aa even the phi-psi combination of the individual amino acids were incorrect. Actually this always puzzled me to make a choice for the Force field. The rest of the script was unchanged for the two runs.Could you please comment on the above results? Is there any way really to judge which force field is to be chosen for particular type of analysis?Best regardsNav ***Navratna VajpaiPh. D student in Prof. Grzesiek's laboratoryDepartment of Structural BiologyBiozentrum, University of BaselKlingelbergstrasse 70,CH-4056Basel, Switzerland.Phone- +41 61 267 2080(O) +41 78 744 0810(M)[EMAIL PROTECTED] ___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease 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 ***Navratna VajpaiPh. D student in Prof. Grzesiek's laboratoryDepartment of Structural BiologyBiozentrum, University of BaselKlingelbergstrasse 70,CH-4056Basel, Switzerland.Phone- +41 61 267 2080(O) +41 78 744 0810(M)[EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] short range nonbondeds = 0 in power4
Hi, I've run into a mysterious problem. The versions 3.3. and 3.3.1 compile and execute, but the short range coulomb and LJ energies come out as zero when using the mpi-version. Serial code works ok (mpi version gives zero if run using just one cpu). No errors, no warnings. I've tried using both fftw 2.1.5 and 3.0.1, tried dropping the optimization level to -O1, -qstrict, --disable-ppc-altivec, ... The config options were (e.g.) as follows: setenv CPPFLAGS -I/v/aix52_rs/appl/math/fftw/fftw-3.0.1_32/include setenv LDFLAGS -L/v/aix52_rs/appl/math/fftw/fftw-3.0.1_32/lib setenv MPICC mpcc_r ./configure --prefix=/wrk/gmx --program-suffix=_mpi --enable-mpi --disable-nice --enable-threads -with-fft=fftw3 From the beginning of the config.log: hostname = p690m uname -m = 00105CDA4C00 uname -r = 2 uname -s = AIX uname -v = 5 /usr/bin/uname -p = powerpc /bin/uname -X = unknown /bin/arch = unknown /usr/bin/arch -k = unknown /usr/convex/getsysinfo = unknown hostinfo = unknown /bin/machine = unknown /usr/bin/oslevel = 5.2.0.0 /bin/universe = unknown We don't get the kind of errors described earlier for power4 on the list. I actually managed to make a working mdrun_mpi from 3.3 last year using the same options, but after poe/ppe/... update on the power4 machine I get this odd behaviour also on the 3.3 version. Any ideas? What to tweak, where to look? Cheers, Atte ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] why the backbone can be broken during MD process
Fan, Fenghui wrote: Dear all, Will you please tell me why the backbone can be broken during MD process and how can we fix them? I am looking forward to getting your reply. it can not. please be more specific. Best regards. Fenghui Fan ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [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 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] short range nonbondeds = 0 in power4
Atte Sillanpää wrote: Hi, I've run into a mysterious problem. The versions 3.3. and 3.3.1 compile and execute, but the short range coulomb and LJ energies come out as zero when using the mpi-version. Serial code works ok (mpi version gives zero if run using just one cpu). No errors, no warnings. I've tried using both fftw 2.1.5 and 3.0.1, tried dropping the optimization level to -O1, -qstrict, --disable-ppc-altivec, ... The config options were (e.g.) as follows: setenv CPPFLAGS -I/v/aix52_rs/appl/math/fftw/fftw-3.0.1_32/include setenv LDFLAGS -L/v/aix52_rs/appl/math/fftw/fftw-3.0.1_32/lib setenv MPICC mpcc_r ./configure --prefix=/wrk/gmx --program-suffix=_mpi --enable-mpi --disable-nice --enable-threads -with-fft=fftw3 From the beginning of the config.log: hostname = p690m uname -m = 00105CDA4C00 uname -r = 2 uname -s = AIX uname -v = 5 /usr/bin/uname -p = powerpc /bin/uname -X = unknown /bin/arch = unknown /usr/bin/arch -k = unknown /usr/convex/getsysinfo = unknown hostinfo = unknown /bin/machine = unknown /usr/bin/oslevel = 5.2.0.0 /bin/universe = unknown We don't get the kind of errors described earlier for power4 on the list. I actually managed to make a working mdrun_mpi from 3.3 last year using the same options, but after poe/ppe/... update on the power4 machine I get this odd behaviour also on the 3.3 version. Any ideas? What to tweak, where to look? Cheers, Atte ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 if you suspect PME, then try running without it. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [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 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] Hi...
As suggested by you I tried using the g_angle. But got tucked. It asks for a .ndx file. I tried making it using mk_angndx but gave me an error when i used the option -type phi-psi. Although it worked well when I used the option dihedral instead of phi-psi. The .ndx file has strange nomenclature which i didn't followed. [ Phi=180.0_2_33.5 ] or [ Phi=0.0_3_3.77 ] Please suggest.As you said problem with the analysis program g_rama. I looked for g_rama as well as g_chi .. its mentioned in the g_chi option that the phi psi calculation are different from the conventional calculations. Instead of C'(i-1)-Ni-CAi-C'i , H-N-CA-C' is used and similarly its different for the psi as well. But it also states that it is different from the g_rama. I was wondering what other atoms are taken for the phi-psi calculations?Best regards NavOn Sep 14, 2006, at 4:22 PM, David van der Spoel wrote:Navratna Vajpai wrote: Sorry for not so explicitly explaining the things.. Here it goesI have a nona peptide and I ran a MD of 20ns using OPLS-AA force field. when I used the OPLS-AA the phi angles came out to be -ve for three of the amino acids. which is stericaly not allowed. But when I ran it using GROMOS I found all the phi-psi combinations with a negative phi value distribution. But now I am lost as you have said it works only for GROMOS like force field. Why? problem in the anaysis program (assuming you used g_rama). please use g_angle. and if that so I have got -ve phi distribution for the other phi-psi plots. My other question remained unanswered even now. Is there any way really to judge which force field is to be chosen for particular type of analysis?Best regards Thanks what do you mean with -ve ?force field can be evaluated in many ways.Start by checking this paper and references in them:Hydration thermodynamic properties of amino Acid analogues: a systematic comparison of biomolecular force fields and water models. * Hess B, * van der Vegt NF.J Phys Chem B Condens Matter Mater Surf Interfaces Biophys. 2006 Sep 7;110(35):17616-26.-- David.David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,Dept. of Cell and Molecular Biology, Uppsala University.Husargatan 3, Box 596, 75124 Uppsala, Swedenphone: 46 18 471 4205 fax: 46 18 511 755[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease 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 ***Navratna VajpaiPh. D student in Prof. Grzesiek's laboratoryDepartment of Structural BiologyBiozentrum, University of BaselKlingelbergstrasse 70,CH-4056Basel, Switzerland.Phone- +41 61 267 2080(O) +41 78 744 0810(M)[EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] CHARMM force field implementation in Gromacs :
Thanks for your answers (I had forgotten this comment in the script). The problem is that most of dihedral with multiplicity n = 6 don't come alone. For exemple in Arg : HD1 HE || |// --CG--CD--NE--CZ || \ HD2 is defined by 6 dihedral with n=6 (CG-CD-NE-HE, ..., HD2-CD-NE-CZ) They are all of the same type (X-CT2-CT2-X). So, if I understand well, the result should be OK since, for example, CG-CD-NE-HE and CG-CD-NE-CZ are not a combination of different type of dihedrals with n = 6. The problems happen when a combination of different types of dihedral are used (for example if CG-CD-NE-HE is of type A and CG-CD-NE-CZ is of type B). In this case, one possibility is to hack the Gromacs code by allowing a 6th Ryckaert-Bellemans parameter (?) Cheers Nico Hello, I have noticed that both in the Yuguang Mu's and the Mark Abraham's work, the periodic parameters of dihedral angles have been converted into Ryckaert-Bellemans ones. I have tried to find more info about this in the CHARMM and Gromacs documentations but I have not found much. Why exactly this conversion should be done since the periodic potential is implemented in both force fields? My problem is that several dihedral angles cannot be easily converted in RB parameters since their multiplicities is equal to 6 and the RB potential implemetation is limited to 5 constants. To quote my own code comment, # We need some elaborate functionality to convert the CHARMM dihedral type # of k * (1 + cos(n * xi - delta ) ) functions summed over n into something # GROMACS can implement. While the above functional form exists in # GROMACS, you can't have more than one function of this type, and # CHARMM has a number of dihedral interactions that require more than # one such function. However for delta = 0 or pi and n = 5, then the above # cosine function can be expanded in powers of cos xi, and the coefficients # of the expansion can be summed in this conversion and presented to # GROMACS as a ready-made Ryckaert-Bellemans dihedral. In practice, this # works because CHARMM only uses such delta and n values for atom type # combinations that need multiple functions of the above form. Warnings # are issued when delta is some other value, and the algorithm dies if # n is 6. In order to simplify GROMACS logfile output so that it only # has to report one sort of dihedral term for most simulations, all # dihedral terms with n = 5 are expressed as R-B, even when not necessary. # Dihedrals with n=6 are left in periodic form, since it is not possible # to convert these to R-B form when the summation is limited to the # fifth power of cos xi. So if you have a single dihedral over a set of atoms that has n=6 then you can leave it in periodic form and the only cost is that you have to remember that the output will likely have both periodic and R-B dihedrals. If you have one such a dihedral in combination with others n6 then you can use a combination of periodic and R-B. If you have multiple dihedrals with n=6 you will need to hack the source code, except in some trivial cases, perhaps. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 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: Fwd: [gmx-users] Hi...
Dongsheng Zhang wrote: On Thu, 2006-09-14 at 06:36 -0700, David van der Spoel wrote: Navratna Vajpai wrote: Hi all.. I wrote this mail yesterday. But could not receive any reply till now. So if someone can suggest something about it. That would be nice. Best regards Nav Begin forwarded message: *From: *Navratna Vajpai [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] *Date: *September 13, 2006 10:32:21 AM GMT+02:00 *To: *Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org *Subject: **[gmx-users] Hi...* *Reply-To: *Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Dear All Hi.. This is in regard to your previously replied mail regarding the use of GROMOS96 or OPLS-AA or AMBER force field. As you said it depends upon the users taste which one to use. This means that the three on a broad manner should give convergence of the analyzed data set. Infact from my simulation runs using oplss-aa and gromos96, I didn't found that. I tried using the GROMOS96 and opls-aa force field on my small peptides for a period of 20ns and found that with opls-aa even the phi-psi combination of the individual amino acids were incorrect. Actually this always puzzled me to make a choice for the Force field. The rest of the script was unchanged for the two runs. Could you please comment on the above results? Is there any way really to judge which force field is to be chosen for particular type of analysis? Best regards Nav what do you mean with incorrect? your question is quite vague. the g_rama program works only for GROMOS like force fields unfortunately but that doesn't mean the phi/psi are wrong. Could you please give more detail why g_rama program works only for GROMOS like force field? To my understanding, the reason to get different values of phi/psi by using g_rama or g_angle is that the definition of phi/psi in g_rama is not in a conventional way. If we define phi/psi in the same way as g_rama, I believe g_angle will give the same answer. No matter which force field is used, these two methods will give different values. Is my understanding correct? because atom names are hardcoded. if you give g_angle the right definitions in the index file it will work correctly. All the best! Dongsheng What would be the correct result anyway? Maybe your peptide unfolds. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [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 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] short range nonbondeds = 0 in power4
Atte Sillanpää wrote: On Thu, 14 Sep 2006, David van der Spoel wrote: I've run into a mysterious problem. The versions 3.3. and 3.3.1 compile and execute, but the short range coulomb and LJ energies come out as zero when using the mpi-version. Serial code works ok (mpi version gives zero if run using just one cpu). No errors, no warnings. ... if you suspect PME, then try running without it. Hi again, the short range energies come out as zero with all electrostatic methods cut-off, PME, shift. But only the short range. Other components get some numbers (and you _can_ continue the simulation for at least thousands of steps). can you try a small water box on one processor? just to eliminate problems. if you can simulate, that means the forces are correct (or zero too...) try printing the forces in other words. just do one step with all output turned on. Cheers, Atte -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone:46 18 471 4205fax: 46 18 511 755 [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 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. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [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 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] Question about use of tpbconv
Hi I have a quick question. When you use tpbconv to continue runs what exactly is taken from the *.edr and *.trr files? For instance if I have to run my simulation in short batches of 1ns is it sufficient to just use the run3 files to continue the run (2ns-3ns) or should thr run1, run2 and run3 files by concatenated and then a run4 file generated using the complete edr and trr files. Thanks Jo Joanne Hanna Department of Chemistry University of Warwick Coventry CV4 7AL (02476) 574623 [EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] CHARMM force field : TIP3 LJ parameters
Hello everybody, sorry to bother you with my problems another time. I have checked the non-bonded parameters from Yuguang Mu's ffcharmmnb.itp. The parameters for TIP3 atoms (CHARMM's water model) are : c6c12 HT 1.008 0.000 A 3.1539699357e-09 1.2921281844e-17 OT15.999 0.000 A 2.4895403920e-03 2.4347673691e-06 I obtain exactly the same thing according to the combination rule #1 and my own version of the charmm ff. The differences happen when the pair HT..OT is combined in [nonbond-params] (using comb-rule #1 and function #1). Yuguang's parameters are : c6c12 HTOT 1 4.3824474706e-05 1.3719498873e-09 while I obtain : c6c12 OTHT 1 2.802131e-06 5.608950e-12 according to chapter 5.6.1, the computation should be C_ij^(M) = sqrt(C_i^(M) . C_j^(M)) with M = [0,6]. So, for the OT..HT pair : C_ij(6) = sqrt( 2.490e-03 x 3.154e-09 ) = sqrt( 7.852e-12 ) = 2.802e-06 C_ij(12)= sqrt( 2.435e-06 x 1.292e-17 ) = sqrt( 3.146e-23 ) = 5.609e-12 Has Someone an idea about this difference? Have I missed something? I have checked several other pairs (with or without CHARMM's 1-4 parameters) : the problem seem to be limited to the OT..HT pair cheers Nicolas -- [ Nicolas Sapay Ph.D. ] University of Calgary, Dept. of Biological Sciences 2500 University Dr. NW, Calgary AB, T2N 1N4, Canada Tel: (403) 220-6869 Fax: (403) 289-9311 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] CHARMM force field implementation in Gromacs :
Nicolas SAPAY wrote: Thanks for your answers (I had forgotten this comment in the script). The problem is that most of dihedral with multiplicity n = 6 don't come alone. For exemple in Arg : HD1 HE || |// --CG--CD--NE--CZ || \ HD2 is defined by 6 dihedral with n=6 (CG-CD-NE-HE, ..., HD2-CD-NE-CZ) They are all of the same type (X-CT2-CT2-X). So, if I understand well, the result should be OK since, for example, CG-CD-NE-HE and CG-CD-NE-CZ are not a combination of different type of dihedrals with n = 6. Correct. A dihedral is defined by the four atoms, the functional form and the parameters. The energy profile of rotation about the CD-NE bond is a linear combination of however many dihedrals it is, which is a quite different thing. The problems happen when a combination of different types of dihedral are used (for example if CG-CD-NE-HE is of type A and CG-CD-NE-CZ is of type B). In this case, one possibility is to hack the Gromacs code by allowing a 6th Ryckaert-Bellemans parameter (?) This is not a problem. None of these dihedral functions occupy the same space, in that (by the above definition) they have a different set of four atoms despite having the same functional form and central atoms. The potential problem comes because the [ dihedraltypes ] section of either the .top file (or the *bon.itp file that is #included) does not allow multiple dihedral functions of the same functional form to apply to the same set of four atom types - grompp just uses the last one defined. As David correctly points out (and I learned something here!), you can define multiple dihedrals of the same form for the same set of four *atoms* (not atom types) in the [ dihedrals ] section of the .top file. You have to read chapter 5 closely to pick that up though (5.6.1 and 5.7.2). So yet another solution to the general problem would be for a script to post-process the CHARMM .top file to correct the dihedrals where multiple periodic functions apply to given set of four atom types. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Why RMSFs of some protein chains in my system are unreasonably large?
Dear all, I finish a 10-ns MD simulations for a system including 16 lysozyme molecule chains, some solvents H2O molecules and 128 Cl- counter ions under PBC. When I use the command to calculate the RMSF of residues as follows: g_rmsf -f ***.xtc -s ***.tpr -o rmsf_res.xvg (I selected 3 for groups) The results showed that 3rd and 14the chain had RMSF 1.2-2nm, which is obviously unreasonable. But compared with other chains, these 2 chains have the basically same peak places. The difference is that RMSFs of residues in these 2 chains are systematically much higher. Is there a bugresulting ina systematic error orany other reasons?Any suggestions are welcome. Thanks, Zhongqiao Hu Dept of Chemical and Biomolecular Engineering National University of Singapore ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Surface Tension Calculation
I posted a question a few days ago regarding the calculation of the surface tension of a lipid bilayer in Gromacs. The response that I got was to use the option #Surf*SurfTens in g_energy. I am not really sure how to do this. I have looked at the g-energy file in Gromacs, and I don't see any option that is #Surf*SurfTens. Maybe the file name is wrong, or I am running an older version of Gromacs or something. Let me know if is there is a way to calculate the surface tension of a lipid bilayer within the Gromacs program, or if it is necessary for me to modify the code. (The more detailed the better. I am new to Gromacs) I case no-one else responds by the sound of it, whether the surf term is present within the energy file will depend on the type of pressure coupling you are using. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] periodic boundary condition
Cherry Y. Yates wrote: Dear gromacs developers and users, I am calculating a nanotube which has periodic boundary condition along one direction. I wonder how to make an itp file for this system. The difficulty lies in describing the bond between two end atoms, e.g., two atoms are bonded in an infinite length system, but are located on the bottom and top of a unit cell. use x2top and in your mdp file use pbc=full Thanks, Cherry Get your email and more, right on the new Yahoo.com http://us.rd.yahoo.com/evt=42973/*http://www.yahoo.com/preview ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [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 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] Surface Tension Calculation
toma0052 wrote: Hi, I posted a question a few days ago regarding the calculation of the surface tension of a lipid bilayer in Gromacs. The response that I got was to use the option #Surf*SurfTens in g_energy. I am not really sure how to do this. I have looked at the g-energy file in Gromacs, and I don't see any option that is #Surf*SurfTens. Maybe the file name is wrong, or I am running an older version of Gromacs or something. Let me know if is there is a way to calculate the surface tension of a lipid bilayer within the Gromacs program, or if it is necessary for me to modify the code. (The more detailed the better. I am new to Gromacs) yes, print the diagonal terms of the pressure tensor, and assuming you surface is normal to the Z-axis you have gamma = (Pzz - (Pxx+Pyy)/2) / Lz where Lz is the box length. If you have two surfaces you have to divide by two. Thanks, Mike Tomasini ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [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 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] mdp wrong
hi followthe lastproblem ,i checked my gro,itp and modifid,but this time ,"invalid command line argument",what's that mean? is still my mdp'wrong?but this mdp that i test well in other gro ,and itp in ffgrom96,and this time ,my forcefield is ffoplsaa,is there any different in the mdp? 3G 时 代 来 临 了，坚 决 对 传 统 邮 箱 说 不 ！ 新 一 代 极 速 3G 邮 箱 闪 亮 登 场 ，280 兆 网 盘 免 费 送 ！ 点 击 此 处 注 册 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Re: gmx-users Digest, Vol 29, Issue 49
Hi Joanna, You can use your last *.tpr/trr/edr files to continue a simulation. The only thing to be aware is if the integrity of the last files is conserved. If not (for example after a system crash), you should exclude the last frame in order to avoid inconsistencies. Regards, César.- --- Cesar Araujo, Lic. of Chemistry Department of Molecular Endocrynology Oulu University Hospital FIN-90029 OYS, OULU, FINLAND phone: +358 8 3155632 e-mail: [EMAIL PROTECTED] Message: 1 Date: Thu, 14 Sep 2006 22:10:18 +0100 From: Joanne Hanna [EMAIL PROTECTED] Subject: [gmx-users] Question about use of tpbconv To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=US-ASCII Hi I have a quick question. When you use tpbconv to continue runs what exactly is taken from the *.edr and *.trr files? For instance if I have to run my simulation in short batches of 1ns is it sufficient to just use the run3 files to continue the run (2ns-3ns) or should thr run1, run2 and run3 files by concatenated and then a run4 file generated using the complete edr and trr files. Thanks Jo Joanne Hanna Department of Chemistry University of Warwick Coventry CV4 7AL (02476) 574623 [EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
