[gmx-users] water in lipid bilayer
Hi, I'm performing a transmembrane protein simulation in an explicit DPPC bilayer. I manually removed the lipids to accomodate my protein and the system has undergone 15 ns of equilibration. In removing the lipids, I a gap betwteen the protein and membrane resulted. Most of the lipid molecules aggregated around the protein, but I have found that on one side of the protein, there are some water molecules that have found their way between the protein and lipid bilayer. Is there any way of removing these by altering the simulation parameters, or will I have to remove them manually? I already constrained the waters in the z-direction at the start of the simulation, so that didn't work in this case. Thanks for your time, I would appreciate any advice. Max Macaluso ___ 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] water in lipid bilayer
N-J.M. Macaluso wrote: Hi, I'm performing a transmembrane protein simulation in an explicit DPPC bilayer. I manually removed the lipids to accomodate my protein and the system has undergone 15 ns of equilibration. In removing the lipids, I a gap betwteen the protein and membrane resulted. Most of the lipid molecules aggregated around the protein, but I have found that on one side of the protein, there are some water molecules that have found their way between the protein and lipid bilayer. Is there any way of removing these by altering the simulation parameters, or will I have to remove them manually? See http://wiki.gromacs.org/index.php/Membrane_Simulations... these waters may have been present in your initial structure. I already constrained the waters in the z-direction at the start of the simulation, so that didn't work in this case. I don't understand this. Mark ___ 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] water in lipid bilayer
I already constrained the waters in the z-direction at the start of the simulation, so that didn't work in this case. This happened to me as well. Try increasing the force constants on water by an order of magnitude. ___ 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] water in lipid bilayer
Thanks for your response, I'm sorry, but I didn't find any text on the membrane simulation page on the wiki. What I meant by constraining waters in the z-direction is that at the start of the simulation, I constrained waters in the z-direction so that they wouldn't fall into the gap between the protein and membrane. In my case, the gap was large enough that some waters made their way in. I'm just wondering what I could do to make sure that the lipids aggregate around the protein properly. Should I manually delete these waters, or will the waters eventually make their way out during the course of the simulation. Many thanks, Max On Nov 19 2007, Mark Abraham wrote: N-J.M. Macaluso wrote: Hi, I'm performing a transmembrane protein simulation in an explicit DPPC bilayer. I manually removed the lipids to accomodate my protein and the system has undergone 15 ns of equilibration. In removing the lipids, I a gap betwteen the protein and membrane resulted. Most of the lipid molecules aggregated around the protein, but I have found that on one side of the protein, there are some water molecules that have found their way between the protein and lipid bilayer. Is there any way of removing these by altering the simulation parameters, or will I have to remove them manually? See http://wiki.gromacs.org/index.php/Membrane_Simulations... these waters may have been present in your initial structure. I already constrained the waters in the z-direction at the start of the simulation, so that didn't work in this case. I don't understand this. Mark ___ 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] How to add calcium ions at desired position?
Quoting liang [EMAIL PROTECTED]: Never couple solvent and ions separately. Check out: http://wiki.gromacs.org/index.php/Thermostats Try tc-grps = Protein Non-protein excuse me, if the system includes lipid bilayer, how should i set the tc-prgs? Protein + Lipids + Sol and Ion? or Protein + Non-protein ? I think either would work, but I've personally used protein, lipids, solvent + ions. As long as you're not coupling a very small amount of atoms/ions to its own bath then you should avoid problems. -Justin thanks 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] water in lipid bilayer
Do you mean constrain the force constants just in the z-direction? Keep in mind that the water is already in the gap, so it's now a matter of getting it out. Would constraining water in any direction accomplish this? Thanks, Max On Nov 19 2007, himanshu khandelia wrote: I already constrained the waters in the z-direction at the start of the simulation, so that didn't work in this case. This happened to me as well. Try increasing the force constants on water by an order of magnitude. ___ 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] water in lipid bilayer
If the water is already in the gap, delete it, or move it out of the bilayer. What I meant was: If you start the equilibration all over again, try increasing the force constants of the restraints on water along the bilayer normal. On 19 Nov 2007 11:52:49 +, N-J.M. Macaluso [EMAIL PROTECTED] wrote: Do you mean constrain the force constants just in the z-direction? Keep in mind that the water is already in the gap, so it's now a matter of getting it out. Would constraining water in any direction accomplish this? Thanks, Max On Nov 19 2007, himanshu khandelia wrote: I already constrained the waters in the z-direction at the start of the simulation, so that didn't work in this case. This happened to me as well. Try increasing the force constants on water by an order of magnitude. ___ 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 ___ 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] trjconv does not work
Hi all, I want to extract some frames from the whole trajectory. So, I used -trjconv with (b) and (e) options. P.S: I use the Gromacs 3.3.1 version. But I got the following error: Select a group: 0 Selected 0: 'System' Last frame -1 time0.000 Precision of traj.xtc is 0.001 (nm) WARNING no output, trajectory ended at 10 What is the problem? ___ 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] trjconv does not work
Dear Ozge, What was the command line exactly? Ran. OZGE ENGIN wrote: Hi all, I want to extract some frames from the whole trajectory. So, I used -trjconv with (b) and (e) options. P.S: I use the Gromacs 3.3.1 version. But I got the following error: Select a group: 0 Selected 0: 'System' Last frame -1 time0.000 Precision of traj.xtc is 0.001 (nm) WARNING no output, trajectory ended at 10 What is the problem? ___ 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] trjconv does not work
On Mon, 19 Nov 2007 18:02:31 +0200 OZGE ENGIN [EMAIL PROTECTED] wrote: Hi all, I want to extract some frames from the whole trajectory. So, I used -trjconv with (b) and (e) options. P.S: I use the Gromacs 3.3.1 version. But I got the following error: Select a group: 0 Selected 0: 'System' Last frame -1 time0.000 Precision of traj.xtc is 0.001 (nm) WARNING no output, trajectory ended at 10 it looks like you are are asking time frames that do not exist! did you check the trajectory with gmxcheck? XAvier What is the problem? ___ 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 1- Institute of Molecular Assemblies City University of New York - USA 2- 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
Re: Re: [gmx-users] trjconv does not work
The command line ws the following: trjconv -s peptide_b4md.gro -f traj.xtc -b 0.1 -e 0.2 -o file_1.pdb -Original Message- From: Ran Friedman [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Mon, 19 Nov 2007 17:10:51 +0100 Subject: Re: [gmx-users] trjconv does not work Dear Ozge, What was the command line exactly? Ran. OZGE ENGIN wrote: Hi all, I want to extract some frames from the whole trajectory. So, I used -trjconv with (b) and (e) options. P.S: I use the Gromacs 3.3.1 version. But I got the following error: Select a group: 0 Selected 0: 'System' Last frame -1 time0.000 Precision of traj.xtc is 0.001 (nm) WARNING no output, trajectory ended at 10 What is the problem? ___ 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: Re: [gmx-users] trjconv does not work
The command line was the following: trjconv -s peptide_b4md.gro -f traj.xtc -b 0.1 -e 0.2 -o file_1.pdb -Original Message- From: Ran Friedman [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Mon, 19 Nov 2007 17:10:51 +0100 Subject: Re: [gmx-users] trjconv does not work Dear Ozge, What was the command line exactly? Ran. OZGE ENGIN wrote: Hi all, I want to extract some frames from the whole trajectory. So, I used -trjconv with (b) and (e) options. P.S: I use the Gromacs 3.3.1 version. But I got the following error: Select a group: 0 Selected 0: 'System' Last frame -1 time0.000 Precision of traj.xtc is 0.001 (nm) WARNING no output, trajectory ended at 10 What is the problem? ___ 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] trjconv does not work
I see. Do you have any structure between t=0.1ps and t=0.2ps? Ran. OZGE ENGIN wrote: The command line ws the following: trjconv -s peptide_b4md.gro -f traj.xtc -b 0.1 -e 0.2 -o file_1.pdb ___ 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: Re: [gmx-users] trjconv does not work
Of course, I am performing a 40 ns simulation, and 14 ns of it has been finished. What may be the problem? I know, I can extract specific frames via VMD, but it changes atom types after saving in pdb format. -Original Message- From: Ran Friedman [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Mon, 19 Nov 2007 17:53:16 +0100 Subject: Re: [gmx-users] trjconv does not work I see. Do you have any structure between t=0.1ps and t=0.2ps? Ran. OZGE ENGIN wrote: The command line ws the following: trjconv -s peptide_b4md.gro -f traj.xtc -b 0.1 -e 0.2 -o file_1.pdb ___ 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] trjconv does not work
What I meant is: do you save the trajectory every 0.1ps? The problem seem to be that trjconv isn't able to find any frame between t=0.1ps and t=0.2ps. So, if you save you data every 1ps, there's no data in your .xtc file. This is why Xavier suggested to use gmxcheck, that will tell you both how many steps you have in the xtc and what's the timestep. I agree that trjconv is more convenient than VMD for this. Ran. OZGE ENGIN wrote: Of course, I am performing a 40 ns simulation, and 14 ns of it has been finished. What may be the problem? I know, I can extract specific frames via VMD, but it changes atom types after saving in pdb format. -Original Message- From: Ran Friedman [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Mon, 19 Nov 2007 17:53:16 +0100 Subject: Re: [gmx-users] trjconv does not work I see. Do you have any structure between t=0.1ps and t=0.2ps? Ran. OZGE ENGIN wrote: The command line ws the following: trjconv -s peptide_b4md.gro -f traj.xtc -b 0.1 -e 0.2 -o file_1.pdb ___ 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 ___ 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: Re: [gmx-users] trjconv does not work
The length of your simulation is irrelevant, the frequency of frame output is. If you don't output frames at least 5x per picosecond, asking for the frames in a 0.1ps gap is not going to produce an output - because there probably won't be any. Check your mdp. - Original Message From: OZGE ENGIN [EMAIL PROTECTED] To: gmx-users@gromacs.org Cc: gmx-users@gromacs.org Sent: Monday, November 19, 2007 5:12:51 PM Subject: Re: Re: [gmx-users] trjconv does not work Of course, I am performing a 40 ns simulation, and 14 ns of it has been finished. What may be the problem? I know, I can extract specific frames via VMD, but it changes atom types after saving in pdb format. -Original Message- From: Ran Friedman [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Mon, 19 Nov 2007 17:53:16 +0100 Subject: Re: [gmx-users] trjconv does not work I see. Do you have any structure between t=0.1ps and t=0.2ps? Ran. OZGE ENGIN wrote: The command line ws the following: trjconv -s peptide_b4md.gro -f traj.xtc -b 0.1 -e 0.2 -o file_1.pdb ___ 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 Get easy, one-click access to your favorites. Make Yahoo! your homepage. http://www.yahoo.com/r/hs ___ 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] water in lipid bilayer
/ I'm performing a transmembrane protein simulation in an explicit DPPC // bilayer. I manually removed the lipids to accomodate my protein and the // system has undergone 15 ns of equilibration. // // In removing the lipids, I a gap betwteen the protein and membrane // resulted. Most of the lipid molecules aggregated around the protein, but // I have found that on one side of the protein, there are some water // molecules that have found their way between the protein and lipid // bilayer. Is there any way of removing these by altering the simulation // parameters, or will I have to remove them manually? // I already // constrained the waters in the z-direction at the start of the // simulation, so that didn't work in this case. I am surprised that 15ns is not enough for those waters to leave on their own. Are you doing anisotropic pressure coupling? If not then this is likely to fix your problem. Also, painful as it may be, I suggest starting over from scratch. It is useful to use make_hole version of gromacs-3.1.2 (search the list for how to get it and use it) or inflategro. Finally, ///how many waters are we talking about? I///f you deeply believe that you have done everything correctly then I suggest at least considering the possibility that there is something interesting going on. Chris. / ___ 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] MPI configure cannot compute sizeof (int)
Hello. I'm trying to get a MPI GROMACS 3.3.2 build for a Cray XT3 (AMD Opteron
cluster). The compute pool runs a linux microkernel called Catamount. You
compile for Catamount with cc or 'ftn, and launch a job with yod. I'm
getting a cannot compute sizeof int error from configure. Here is what I've
done:
module load fftw/3.1.1
setenv CC linux-pgcc
setenv F77 linux-pgf77
setenv MPICC cc
setenv CFLAGS -tp k8-64 -fast -Mscalarsse
setenv FFLAGS -tp k8-64 -fast -Mscalarsse
setenv CPPFLAGS -I${FFTW_INC}
setenv LDFLAGS -L${FFTW_DIR}
./configure --enable-mpi --program-suffix=_mpi --prefix=/usr/local/usp/gromacs
Configure errors here:
checking for int... yes
checking size of int... configure: error: cannot compute sizeof (int)
Config.log output:
configure:7267: checking size of int
configure:7617: cc -o conftest -tp k8-64 -fast -Mscalarsse
-I/opt/fftw/3.1.1/cnos/include -L/opt/fftw/3.1.1/cnos/lib conftest.c 5
/opt/xt-pe/1.5.52/bin/snos64/cc: INFO: catamount target is being used
conftest.c:
configure:7620: $? = 0
configure:7626: ./conftest
./configure: line 1: 5147 Segmentation fault ./conftest$ac_exeext
configure:7629: $? = 139
configure: program exited with status 139
It appears configure is trying to run the MPI job with just
./conftest which doesn't work here (or on many other architectures). Is there
another variable I should set to tell it to use yod to launch the binary? Or
is there a way to skip the int check?
Thanks,
Chris
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Re: [gmx-users] MPI configure cannot compute sizeof (int)
Chris Borchert wrote:
Hello. I'm trying to get a MPI GROMACS 3.3.2 build for a Cray XT3 (AMD Opteron cluster). The compute pool runs a
linux microkernel called Catamount. You compile for Catamount with cc or 'ftn, and launch a job
with yod. I'm getting a cannot compute sizeof int error from configure. Here is what I've
done:
What do you mean by launch a job?
module load fftw/3.1.1
setenv CC linux-pgcc
setenv F77 linux-pgf77
setenv MPICC cc
setenv CFLAGS -tp k8-64 -fast -Mscalarsse
setenv FFLAGS -tp k8-64 -fast -Mscalarsse
setenv CPPFLAGS -I${FFTW_INC}
setenv LDFLAGS -L${FFTW_DIR}
./configure --enable-mpi --program-suffix=_mpi --prefix=/usr/local/usp/gromacs
Configure errors here:
checking for int... yes
checking size of int... configure: error: cannot compute sizeof (int)
Config.log output:
configure:7267: checking size of int
configure:7617: cc -o conftest -tp k8-64 -fast -Mscalarsse
-I/opt/fftw/3.1.1/cnos/include -L/opt/fftw/3.1.1/cnos/lib conftest.c 5
This is not an MPI compilation, unless your cc magically makes all
targets MPI targets.
/opt/xt-pe/1.5.52/bin/snos64/cc: INFO: catamount target is being used
conftest.c:
configure:7620: $? = 0
configure:7626: ./conftest
./configure: line 1: 5147 Segmentation fault ./conftest$ac_exeext
configure:7629: $? = 139
configure: program exited with status 139
It appears configure is trying to run the MPI job with just
./conftest which doesn't work here (or on many other architectures).
What makes you think it's an MPI binary? How do you mean it doesn't work
on many other architectures?
Is there another variable I should set to tell it to use yod to launch the binary?
Not that I'm aware of.
Or is there a way to skip the int check?
configure does scores of such compile-and-test things, so you need to
solve the underlying problem.
Mark
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[gmx-users] Adding polarizability
Dear gromacs community, I've been trying to switch over from AMBER and I'm running into a few issues that the manual doesn't clarify well enough for me. Can anyone point me to information on adding in polarizability to atoms? In amber it was a simple matter of adjusting the frcmod file, but I can't find the location to add that info in for gromacs. Additionally, what do I need to do in terms of the run-parameters and topology/force-field to enable polarizability (the equivalent in AMBER would be IPOL=1)? Secondly, if I'm looking to use the flexible SPC water (a la Ferguson) I've found that I can specify the '-water spc' option during the pdb2gmx conversion while choosing the gromacs 53a6 force field (not sure that it makes a difference), and I add in the -DFLEX_SPC keyword under the 'define' section of the grompp.mdp run-parameter file. Is that all I need to do, or is there a missing or incorrectly done step before I can actually use the flexible SPC? Lastly, I would also like to use the anharmonic (cubic) term for the OH stretching as per ferguson. What do I need to do to enable this? Thank you, -- ~Eric Shamay ___ 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] Adding polarizability
Eric Shamay wrote: Dear gromacs community, I've been trying to switch over from AMBER and I'm running into a few issues that the manual doesn't clarify well enough for me. Can anyone point me to information on adding in polarizability to atoms? In amber it was a simple matter of adjusting the frcmod file, but I can't find the location to add that info in for gromacs. Additionally, what do I need to do in terms of the run-parameters and topology/force-field to enable polarizability (the equivalent in AMBER would be IPOL=1)? As Mark answered there is no out of thebox polarizability. AFAIK there is no complete force field like that in Amber either, only Tinker has one. Secondly, if I'm looking to use the flexible SPC water (a la Ferguson) I've found that I can specify the '-water spc' option during the pdb2gmx conversion while choosing the gromacs 53a6 force field (not sure that it makes a difference), and I add in the -DFLEX_SPC keyword under the 'define' section of the grompp.mdp run-parameter file. Is that all I need to do, or is there a missing or incorrectly done step before I can actually use the flexible SPC? Lastly, I would also like to use the anharmonic (cubic) term for the OH stretching as per ferguson. What do I need to do to enable this? there is flexspc.itp with this model. There is also TIP4P/Flex. Thank you, -- ~Eric Shamay ___ 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] Creating .ndx for TIP5Pwater
JMandumpal wrote: Dear David, I didn't get the desired box length when I tried to use editconf command ( I took the tip5p box from gromacs/tutor directory) . Then, I tried editconf command to generate .gro file using myown water box. It worked!! Still, there is a problem. How can I create .ndx file?- I tried make_ndx -n tip5p_W.pdb, but it resulted in a message: input/output error. probably the pdb file doesn't exist or you're not allowed to write in this directory. Could you suggest an alternative way for builing up ndx files? regards Jestin -- 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] Why so many energy minimization and position restrained simulation steps?
Hi, I am new to Gromacs. I am following this tutorial: http://www.nmr.chem.uu.nl/~abonvin/tutorials/MD-Data/index.html. My question is: why it has multiple steps of energy minimization and position restrained simulation? Is that a common practice? What's the key difference among these steps? Thanks! Peggy ___ 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] How to add calcium ions at desired position?
Thank all of you for the suggestions! I then ran the procedures described at (http://www.nmr.chem.uu.nl/~abonvin/tutorials/MD-Data/index.html), where it adds water before energy minimization, and it also has position restraint step. But when I came to the step: grompp -f dyna/pr1_SOLV.mdp -po X_pr1.mdp -c X_em3.gro -r X_em3.gro -t X_em3.trr -n X.ndx -p X.top -o X_pr1.tpr mdrun -v -deffnm X_pr1 I got the following error: --- Program mdrun, VERSION 3.3.2 Source code file: network.c, line: 437 Routine should not have been called: gmx_sumi --- I used exactly the same .mdp files as in the tutorial, with the only modification in pr1.mdp to set T-coupling to Protein Non-Protein. Does anybody know what might be the problem? Thanks! Peggy On Nov 19, 2007 3:41 AM, Justin A. Lemkul [EMAIL PROTECTED] wrote: Quoting liang [EMAIL PROTECTED]: Never couple solvent and ions separately. Check out: http://wiki.gromacs.org/index.php/Thermostats Try tc-grps = Protein Non-protein excuse me, if the system includes lipid bilayer, how should i set the tc-prgs? Protein + Lipids + Sol and Ion? or Protein + Non-protein ? I think either would work, but I've personally used protein, lipids, solvent + ions. As long as you're not coupling a very small amount of atoms/ions to its own bath then you should avoid problems. -Justin thanks 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 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] Adding polarizability
Eric Shamay wrote: Dear gromacs community, I've been trying to switch over from AMBER and I'm running into a few issues that the manual doesn't clarify well enough for me. Can anyone point me to information on adding in polarizability to atoms? In amber it was a simple matter of adjusting the frcmod file, but I can't find the location to add that info in for gromacs. Additionally, what do I need to do in terms of the run-parameters and topology/force-field to enable polarizability (the equivalent in AMBER would be IPOL=1)? GROMACS only does polarizability using shell functions (see various sections of the GROMACS manual), and there's no out-of-the-box AMBER equivalence implemented. Secondly, if I'm looking to use the flexible SPC water (a la Ferguson) I've found that I can specify the '-water spc' option during the pdb2gmx conversion while choosing the gromacs 53a6 force field (not sure that it makes a difference), and I add in the -DFLEX_SPC keyword under the 'define' section of the grompp.mdp run-parameter file. Is that all I need to do, or is there a missing or incorrectly done step before I can actually use the flexible SPC? Don't know. Please put different subjects in a different email, so that people can usefully use the email subject line to discard emails of no interest to them. This means you increase your chances that someone who knows your answer will read your email :-) Lastly, I would also like to use the anharmonic (cubic) term for the OH stretching as per ferguson. What do I need to do to enable this? Don't know. Chapters 45 of the manual treat such topics, if they can be treated. Mark ___ 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] interaction energy of bulk TIP3P
i see. i reran the trajectory with reaction field electrostatics and that gave a more negative energy value which was closer to what i was expecting. i guess the missing reciprocal space contributions explains this discrepancy. is there a way to get the full interaction energy with PME ? thnx for the reply -sandeep On Nov 17, 2007 8:18 PM, Mark Abraham [EMAIL PROTECTED] wrote: Hi All I simulated a cubic box of 2180 TIP3P water molecules using gmx 3.3 and PME for 400 ps and extracted the interaction energy of a randomly picked water molecule with rest of the system. Simulation was done at 298K and 1bar and usual procedure for generating a water box and equilibration were used. Average interaction energy reported in the log file was Epot (kJ/mol)Coul-SR LJ-SR WAT-rest -8.13828e+011.21886e+01 giving a total of -8.13828e+01 + 1.21886e+01 = -69.194 kJ/mol Comparing with published numbers using other MD programs this should be in the range of -81 +/- 1 kJ/mol i.e. ~11 kJ/mol less. any clues on origin of this discrepancy ? relevant .top , .mdp files are below. The PME algorithm does an approximation to the full periodic Coulomb summation, but does so with a calculation in direct space, as above, and another in reciprocal space, where your energy groups are not meaningful. So you're only getting the direct-space component of the interaction energy. Mark ___ 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: Re: [gmx-users] Creating .ndx for TIP5Pwater
Dear David, I didn't get the desired box length when I tried to use editconf command ( I took the tip5p box from gromacs/tutor directory) . Then, I tried editconf command to generate .gro file using myown water box. It worked!! Still, there is a problem. How can I create .ndx file?- I tried make_ndx -n tip5p_W.pdb, but it resulted in a message: input/output error. Could you suggest an alternative way for builing up ndx files? regards Jestin ___ 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] How to specify .mdp file for position restrained simulation?
Hi, How to specify the .mdp file in order to run position restrained simulation? From the examples I found on the internet, it seems that the only difference between the .mdp file for position restrained simulation and the one for actual MD simulation is the simulation time -- the position restrained simulation is much shorter. Is this observation true in general? If yes, usually, how long is enough for the position restrained simulation? If not, how to specify the .mdp file for position restrained simulation then? Thanks a lot! Peggy ___ 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
