[gmx-users] gromacs installation in IBM BLUEGENE
Dear all I've tried compiling both version 3.3.1 and 3.3.2 of GROMACS on an IBM Blue Gene/L system but get the same error message with each version. To compile the GROMACS I've used the following settings/configure flags: ./configure\ --enable-mpi \ --enable-float \ --program-suffix=_mpi \ --prefix=/home/phd/04/mbuanjha/soft/gmx332 \ --enable-type-prefix \ --enable-all-static \ --disable-nice \ --disable-shared \ --disable-threads \ --without-motif \ --without-x \ --without-malloc \ --with-fft=fftw3 \ --enable-ppc-altivec \ --build=i686-linux-gnu \ --host=powerpc \ CC=/bgl/BlueLight/ppcfloor/bglsys/bin/mpixlc \ F77=/bgl/BlueLight/ppcfloor/bglsys/bin/mpixlf77 \ CXX=/bgl/BlueLight/ppcfloor/bglsys/bin/mpixlcxx \ MPICC=/bgl/BlueLight/ppcfloor/bglsys/bin/mpixlc \ CFLAGS=-O3 -qarch=440d -qtune=440 -qhot \ FFLAGS=-O3 -qarch=440d -qtune=440 -qhot \ CXXFLAGS=-O3 -qarch=440d -qtune=440 -qhot \ LDFLAGS=-L/home/phd/04/mbuanjha/soft/fftw312/lib/ -L/home/phd/04/mbuanjha/soft/MYINC\ CPPFLAGS=-I/home/phd/04/mbuanjha/soft/fftw312/include/ -I/home/phd/04/mbuanjha/soft/MYINC \ LIBS=-lmpich.rts -lmsglayer.rts -lrts.rts -ldevices.rts -lcxxmpich.rts -lnsl at the time of running this, i got few warning, as: configure:26419: WARNING: Couldn't find XDR headers and/or libraries - using our own configure:26428: checking for working memcmp configure:26517: result: no but when i make mdrun, it gives error: (cd ./src/gmxlib make ; exit 0) make[1]: Entering directory `/home/phd/04/mbuanjha/soft/gromacs-3.3.2/src/gmxlib' Making all in nonbonded make[2]: Entering directory `/home/phd/04/mbuanjha/soft/gromacs-3.3.2/src/gmxlib/nonbonded' Making all in nb_kernel make[3]: Entering directory `/home/phd/04/mbuanjha/soft/gromacs-3.3.2/src/gmxlib/nonbonded/nb_kernel' rm -f kernel-stamp ./mknb -software_invsqrt Gromacs nonbonded kernel generator (-h for help) Generating single precision functions in C. Using Gromacs software version of 1/sqrt(x). Error: Cannot open nb_kernel010_c.c for writing. make[3]: *** [kernel-stamp] Error 1 make[3]: Leaving directory `/home/phd/04/mbuanjha/soft/gromacs-3.3.2/src/gmxlib/nonbonded/nb_kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/phd/04/mbuanjha/soft/gromacs-3.3.2/src/gmxlib/nonbonded' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/phd/04/mbuanjha/soft/gromacs-3.3.2/src/gmxlib' (cd ./src/mdlib make ; exit 0) make[1]: Entering directory `/home/phd/04/mbuanjha/soft/gromacs-3.3.2/src/mdlib' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/home/phd/04/mbuanjha/soft/gromacs-3.3.2/src/mdlib' (cd ./src/kernel make mdrun ; exit 0) make[1]: Entering directory `/home/phd/04/mbuanjha/soft/gromacs-3.3.2/src/kernel' make[1]: *** No rule to make target `../gmxlib/libgmx_mpi.la', needed by `mdrun'. Stop. make[1]: Leaving directory `/home/phd/04/mbuanjha/soft/gromacs-3.3.2/src/kernel' and stops. thanks in advance anupam -- Science is facts; just as houses are made of stone, so is science is made of facts; but a pile of stones is not a house, and a collection of facts is not necessarily science. Anupam Nath Jha Ph. D. Student Saraswathi Vishveshwara Lab Molecular Biophysics Unit IISc,Bangalore-560012 Karnataka Ph. no.-22932611 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ 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
Re: [gmx-users] Gromacs slow and crashes on Leopard.
Hadas Leonov wrote: After installing with openmpi - I ran some benchmarks for 4 processors on Mac-Pro: d.villin: Leopard performance: 13714 ps/day old OS performance:41143 ps/day. gmx-benchmark : 48000 ps/day. d.poly-ch2 Leopard performance: 8640 ps/day old OS performance:18000 ps/day gmx-benchmark:20571 ps/day old OS refers to OSX 10.4.9. The slow speed also happens when running only on one CPU. d.villin took 6 times slower than usual. So it can't just be open-mpi fault, can it? Can it be due to compiling gromacs while disabling ia32 optimization? Hi Hadas, probably you are running the C inner loops now. You will want to not only disable the Itanium inner loops, but at the same time enable the x86 inner loops. Carsten ___ 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] pdb2gmx error
Hi Tawhid,
The file you got was in the format used by the _program_ GROMOS. But this
format is not supported by pdb2gmx/Gromacs. The GROMOS _forcefield_ is a set
of equations and parameters, which stands apart from the formatting of the
building blocks. You could've at least taken a bit of effort to look at the
other building block definitions, and you would've seen the differences.
Also, the fact that you got complaints about # should have been indicative
to you that you were doing something wrong. In regards the building blocks
(the .rtp file), read Chapter 5 (notably 5.5). This should help you to
convert the GROMOS format building block to a Gromacs format one.
Tsjerk
On Nov 28, 2007 1:34 AM, Justin A. Lemkul [EMAIL PROTECTED] wrote:
Quoting Tawhid Ezaz [EMAIL PROTECTED]:
I am sorry, my previous mail bounced back, as it was over 50 KB.
I changed the ffG43a1 to include the GTP and GDP which I got from a
previous
post here. {
http://www.gromacs.org/pipermail/gmx-users/2005-May/015188.html}
I changed some structure like giving comment with ; as the origicanal #
was
giving error. but now it tells me there is an error that 05* is not
found in
the atom type database.
Program pdb2gmx, VERSION 3.3.1
Source code file: resall.c, line: 148
Fatal error:
Atom type O5* (residue GTP) not found in atomtype database
---
I am including the file here .the GTP residue is at the bottom of the
file.
https://netfiles.uiuc.edu/tezaz2/shared/ffG43a1.rtp
Is there any other GTP and GDP residue for the force field 43a1?
Have a look at the other entries in the .rtp file, and notice how the
formatting
of the GTP molecule you entered looks nothing like the others. Use the
format
of other residues to guide you (paying special attention to similar
molecules,
like ATP, which is already a part of ffG43a1). The information in the
file you
found appears to be in a different format, although you may still be able
to
extract information from it.
Alternatively, you could use the PRODRG beta server to generate a
suitably-formatted topology (which you can include as an .itp file in your
system topology). However, this topology will require editting, as some
of the
parameters (most notably charges) will likely be unsatisfactory.
-Justin
Thanks in advance.
Tawhid
- Original Message
From: Justin A. Lemkul [EMAIL PROTECTED]
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Monday, November 26, 2007 9:14:37 PM
Subject: Re: [gmx-users] pdb2gmx error
Quoting Tawhid Ezaz [EMAIL PROTECTED]:
Thanks a lot Justin. It worked really nice.
now I am stuck with another problem. I need to add the Building block
GTP and
GDP in 43a1, as I need to get the topology of a tubulin monomer. I
got the
file from a old post here.
http://www.gromacs.org/pipermail/gmx-users/2005-May/015188.html
I copied and pasted it into my file, yet, as the structure doesn't
match it
gave several errors.
is there any way to fix this?
That depends entirely upon what your errors are and what you're trying
to do.
Please provide more details.
-Justin
Thanks a lot for your help.
Tawhid
- Original Message
From: Justin A. Lemkul [EMAIL PROTECTED]
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Monday, November 26, 2007 7:14:43 PM
Subject: Re: [gmx-users] pdb2gmx error
Quoting Tawhid Ezaz [EMAIL PROTECTED]:
Hi,
I have just started to learn gromacs. I am facing a problem to make
topology
file of a myoglobin. I got the pdb file from the csc tutorial.
When i am running the pdb2gmx with
pdb2gmx -f conf.pdb -p topol.top
i get the message, HEME148 CAB1428 0.569
HEME148 CAC1437 0.562 0.820
N-terminus: NH3+
C-terminus: COO-
Now there are 148 residues with 1451 atoms
---
Program pdb2gmx, VERSION 3.3.1
Source code file: pdb2top.c, line: 570
Fatal error:
atom N not found in residue 1ACE while combining tdb and rtp
---
I was using 43a1 force field (0), {but none of them works}.
i read some previous post and got the idea that there should be a N
atom with
should be linked with ACE, but my conf.pdb files does not have any.
I
have
topol.top file from the tutorial but didn't show how I can generate
that.
Use the -ter option with pdb2gmx, and select 'none' when prompted.
That way,
pdb2gmx does not look for an N-terminal nitrogen (which is obviously
absent in
an acetyl group).
-Justin
I am a totally newbie, thus I am wondering what should I do. Which
file I
should correct to get rid of those? Do
Re: [gmx-users] Barcelona vs Xeon
Hi Martin, we have carried out benchmarks on a Barcelona 2.0 GHz versus a 2.3 GHz Clovertown. Here are numbers for an 8 atom system with PME electrostatics and Gromacs 3.3.1. On the Barcelona we get a performance of 0.38, 0.71, 1.27 and 2.40 ns/day for 1, 2, 4, and 8 CPUs, respectively. On the Clovertown we get 0.52, 0.97, 1.75, and 2.74 ns/day. So indeed the scaling on the AMDs is much better on 8 CPUs (80% compared to 66%), but the absolute performance is better on the Intels. For a 2.0 GHz Clovertown the absolute performance on 8 CPUs is probably nearly the same as on a Barcelona, but the single-CPU performance will still be better on the Clovertown. One has to keep in mind, however, that this is just a single benchmark and other MD systems might show a different scaling behaviour. Carsten Martin Höfling wrote: Hi all, Barcelona 1.9GHz vs Xeon 2.0GHz has anyone here benchmarked these two available 8-core solutions? Speed/core wins probably the intel side but what about scaling on 8 cores? Has the NUMA/Hypertransport architecture an advantage here? In price, they are very similar. Xeon is of course available with higher frequencies but also increases in cost/cpu very fast. Best Martin ___ 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Department Am Fassberg 11 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/research/dep/grubmueller/ http://www.gwdg.de/~ckutzne ___ 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] Barcelona vs Xeon
Hi, For Gromacs 4.0, which will come out in a few months, the situation will be quite different. The parallelization has been much improved and automatic sorting of atoms optimizes the memory access a lot. Both these things have much more effect on the Core2 CPUs which don't have hypertransport or a built in memory controller. So both the scaling and the absolute will go up significantly for Core2 and only slightly for AMD CPUs. Berk. From: Carsten Kutzner [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] Barcelona vs Xeon Date: Wed, 28 Nov 2007 09:55:05 +0100 Hi Martin, we have carried out benchmarks on a Barcelona 2.0 GHz versus a 2.3 GHz Clovertown. Here are numbers for an 8 atom system with PME electrostatics and Gromacs 3.3.1. On the Barcelona we get a performance of 0.38, 0.71, 1.27 and 2.40 ns/day for 1, 2, 4, and 8 CPUs, respectively. On the Clovertown we get 0.52, 0.97, 1.75, and 2.74 ns/day. So indeed the scaling on the AMDs is much better on 8 CPUs (80% compared to 66%), but the absolute performance is better on the Intels. For a 2.0 GHz Clovertown the absolute performance on 8 CPUs is probably nearly the same as on a Barcelona, but the single-CPU performance will still be better on the Clovertown. One has to keep in mind, however, that this is just a single benchmark and other MD systems might show a different scaling behaviour. Carsten Martin Höfling wrote: Hi all, Barcelona 1.9GHz vs Xeon 2.0GHz has anyone here benchmarked these two available 8-core solutions? Speed/core wins probably the intel side but what about scaling on 8 cores? Has the NUMA/Hypertransport architecture an advantage here? In price, they are very similar. Xeon is of course available with higher frequencies but also increases in cost/cpu very fast. Best Martin ___ 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Department Am Fassberg 11 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/research/dep/grubmueller/ http://www.gwdg.de/~ckutzne ___ 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 _ Play online games with your friends with Messenger http://www.join.msn.com/messenger/overview ___ 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] Gromacs slow and crashes on Leopard.
Hadas Leonov wrote: When is version 3.3.3 due ? Soon. But meanwhile I put a beta version at the ftp site. ftp://ftp.gromacs.org/pub/gromacs/gromacs_3.3.3_pre1.tar.gz Please use with care, for testing purposes only. -- 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 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] Gromacs slow and crashes on Leopard.
On Wed, 2007-11-28 at 09:20 +0100, Carsten Kutzner wrote: Hadas Leonov wrote: After installing with openmpi - I ran some benchmarks for 4 processors on Mac-Pro: d.villin: Leopard performance:13714 ps/day old OS performance:41143 ps/day. gmx-benchmark : 48000 ps/day. d.poly-ch2 Leopard performance: 8640 ps/day old OS performance:18000 ps/day gmx-benchmark:20571 ps/day old OS refers to OSX 10.4.9. The slow speed also happens when running only on one CPU. d.villin took 6 times slower than usual. So it can't just be open-mpi fault, can it? Can it be due to compiling gromacs while disabling ia32 optimization? Hi Hadas, probably you are running the C inner loops now. You will want to not only disable the Itanium inner loops, but at the same time enable the x86 inner loops. Thanks Carsten, I tried recompliing with --enable-x86-64-sse, but it's still slow as before. Hadas. Carsten ___ 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] Gromacs slow and crashes on Leopard.
Hadas Leonov wrote: On Wed, 2007-11-28 at 09:20 +0100, Carsten Kutzner wrote: Hadas Leonov wrote: After installing with openmpi - I ran some benchmarks for 4 processors on Mac-Pro: d.villin: Leopard performance: 13714 ps/day old OS performance:41143 ps/day. gmx-benchmark : 48000 ps/day. d.poly-ch2 Leopard performance: 8640 ps/day old OS performance:18000 ps/day gmx-benchmark:20571 ps/day old OS refers to OSX 10.4.9. The slow speed also happens when running only on one CPU. d.villin took 6 times slower than usual. So it can't just be open-mpi fault, can it? Can it be due to compiling gromacs while disabling ia32 optimization? Hi Hadas, probably you are running the C inner loops now. You will want to not only disable the Itanium inner loops, but at the same time enable the x86 inner loops. Thanks Carsten, I tried recompliing with --enable-x86-64-sse, but it's still slow as before. Did you try the beta version I put on the ftp site? Hadas. Carsten ___ 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. 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 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] parallel simulation crash on 6 processors
I tried to run a gromacs simulation (gromacs 3.3.1, MD, 18000 atoms) on 2 systems: Intel(R) Pentium(R) CPU 2.40GHz with 100Mbit network and AMD Opteron(tm) Processor 250 with 1Gbit network On both systems I had a crash when I tried to run with more then 5 processors. From 1-5 there was no problem. kind regards, servaas michielssens___ 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] Gromacs slow and crashes on Leopard.
Hadas Leonov wrote: Great, thanks! It does solve the ia32 compilation problems, but not the lam-mpi compilation problems - I still get undefined symbols for a few lam variables. So still using open-mpi, Gromacs works a little better now, for d.villin benchmark, the performance are: 1 CPU: 13214 ps/day (compared to 3592 ps/day before, and 18000ps/day on OSX 10.4) 4 CPUs: 38000ps/day (compared to 13714 ps/day before, 41143ps/day on OSX 10.4, and 48000ps/day in the gmx published benchmark). The performance differences might as well have to do with LAM's memory management. For some benchmark systems I have seen a 10% performance improve on a *single* CPU when Gromacs was compiled with LAM-MPI support compared to the non-MPI version. This was on Linux, however. Carsten ___ 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] parallel simulation crash on 6 processors
servaas michielssens wrote: I tried to run a gromacs simulation (gromacs 3.3.1, MD, 18000 atoms) on 2 systems: Intel(R) Pentium(R) CPU 2.40GHz with 100Mbit network and AMD Opteron(tm) Processor 250 with 1Gbit network On both systems I had a crash when I tried to run with more then 5 processors. From 1-5 there was no problem. more details please. kind regards, servaas michielssens ___ 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. 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 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] gromacs installation in IBM BLUEGENE
Dear Anupam, I also obtained a similar error to you when trying to install GROMACS on Blue Gene. I posted a message to the list on Monday but have since found a solution. `/home/phd/04/mbuanjha/soft/gromacs-3.3.2/src/gmxlib/nonbonded/nb_kernel' rm -f kernel-stamp ./mknb -software_invsqrt Gromacs nonbonded kernel generator (-h for help) Generating single precision functions in C. Using Gromacs software version of 1/sqrt(x). Error: Cannot open nb_kernel010_c.c for writing. Essentially the problem is that the executable ./mknb is compiled for the compute nodes on Blue Gene and when the make process attempts to run this executable on the front-end (login nodes running Linux) it fails. I've managed to solve this problem by running ./mknb with the appropriate options, e.g. ./mknb -software_invsqrt for your example on the backend on a single processor. This enables the required kernel_c.c files to be created. Once the kernel files have been created you can continue the make process. At the final link stage you might encounter a number of undefined symbols, e.g. _nss_files_getaliasent_r and others beginning with _nss_* Adding -lnss_files -lnss_dns -lresolv -lc -lnss_files -lnss_dns -lresolv to LDFLAGS should solve this problem. Hope this helps. Fiona ___ 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] opls bonded parameters
Dear gmx users, I am trying to manually make a topology file for a peptide with few substitutions. I had trouble in understanding regarding assignment of dihedral paramaters in opls by grompp. As far as I understood, ffoplsaabond.itp contains all the dihedral parameters where the bond_type from ffoplsaanb.itp are used to define the dihedral angles. If I take an entry from ffoplsaa.rtb for example glycine, [ GLY ] [ atoms ] Nopls_238 -0.500 1 Hopls_2410.300 1 CAopls_223B 0.080 1 HA1opls_1400.060 1 HA2opls_1400.060 1 Copls_2350.500 2 Oopls_236 -0.500 2 And search for a dihedral H-CA-C-O in ffoplsbon.itp, I don't find any entries. Probably, I have to look for the bond_type corresponding to opls_??? entries and then search in ffoplsaabond.itp. It means that the first column entries in rtb file is only used to map PDB atom types to opls atom types and is of no further use. Please let me know if I am wrong. With Regards, Gurpreet Singh - University of Dortmund Department of Chemistry Physical Chemistry I - Biophysical Chemistry Otto-Hahn Str. 6 D-44227 Dortmund Germany Office: C1-06 room 176 Phone: +49 231 755 3916 Fax: +49 231 755 3901 - ___ 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] Compile Gromacs-3.3.2 on HP xxxw9300 Workstation: AMD64 Opteron with Linux
Dear ALL; I'm trying to upgrade to GMX-3.3.2 with icc, ifort and mpich2. I used the following command with configure: ./configure --prefix=$HOME/GMX332 --enable-mpi --enable-double --enable-fortran F77=ifort CC=icc The compilation stops after couple of minutes and I get the followinfg error message: nb_kernel_x86_64_sse2.c:98: error: `eNR_NBKERNEL_NR' undeclared here (not in a function) Anyone has an idea of what is going on? I searched the user-list but did not find anything like this. Thanks, Adama ++ Adama Tandia Modeling Simulation Corning INC Corning, NY 14831 USA Tel: 607 248 1036 Fax: 607 974 3405 www.corning.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Compile Gromacs-3.3.2 on HP xxxw9300 Workstation: AMD64 Opteron with Linux
Tandia, Adama wrote: Dear ALL; I'm trying to upgrade to GMX-3.3.2 with icc, ifort and mpich2. I used the following command with configure: ./configure --prefix=$HOME/GMX332 --enable-mpi --enable-double --enable-fortran F77=ifort CC=icc The compilation stops after couple of minutes and I get the followinfg error message: nb_kernel_x86_64_sse2.c:98: error: `eNR_NBKERNEL_NR' undeclared here (not in a function) Anyone has an idea of what is going on? I searched the user-list but did not find anything like this. You can make your life easier by using gcc instead. Fortran doesn't help on x86 or x86_64 chips. Thanks, Adama ++ Adama Tandia Modeling Simulation Corning INC Corning, NY 14831 USA Tel: 607 248 1036 Fax: 607 974 3405 www.corning.com ___ 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. 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 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] Setting up Carbon Nanotube Simulations
Dear Bob Johnson and other users, I am attempting to set up some infinite carbon nanotube simulations. To begin, I want to take a single nanotube with some argon inside and try to simulate it with GROMACS with PBC in the axial direction (it appears I need to use pbc=full). So I have a lot of experience with NAMD, but really nothing with GROMACS So far I can use x2top to generate a topology file from a pdb It seems to work ok as I can make it output all of the dihedrals and seems to match up with what I would get with a psf for NAMD. I am a bit confused on how to include my forcefield with the simulation and to generate the proper *gro file. The x2top generated *top file seems to not have the proper mass for Argon and also doesn't include the parameters for the forcefield. I attempted to generate my own forcefield files in the top directory (ffCNT.itp, ffCNTnb.itp, etc, etc.). It seems from reading the mailing list that I don't need to do this and can just use my pdb file and topology file generated from x2top to start the simulation. How, then would I include my CNT force field (A morse bond, cosine angle, and RB dihedral)? I have created these files already as I stated above. Could I just include this as a separate *itp file as the methanol example shows? Does this file then override the *top file? So I could include it as #include CNT.itp or something in the *top file?This is my main question. I am also a bit confused on the format of this as I don't really have a molecule as for methanol, just atoms for the carbon and argon atoms. Second question (and very naive). Can you start a MD simulation with GROMACS without a *gro file and just a *pdb? I realize that my message here is a bit naive, so I hoping someone will be nice enough to overloook my lack of general knowledge about GROMACS :) Thanks Joshua Moore PS I address Bob Johnson as he seems to be the expert on nanotubes in GROMACS :) -- Joshua D. Moore Graduate Student North Carolina State University Dept. of Chemical and Biomolecular Engineering Box 7905 Centennial Campus Engineering Building I 911 Partners Way Raleigh, NC 27695-7905 Phone: (919) 513-2051 Fax: (919) 513-2470 Email: [EMAIL PROTECTED] ___ 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
