Re: [gmx-users] MPIRUN error while running position restrained MD
Hi Mark, Thanks for the mail. Yes, I solvate the protein and then do a EM with steepest descent and then I proceed to do position restrained MD, first restraining the protein and then the backbone. It is at the backbone restraint step I got this error. Also I assumed that if there are any bad contacts they would get resolved in minimization step, but looks like it hasn't. Please tell me how to solve this problem. Raghu --- Mark Abraham <[EMAIL PROTECTED]> wrote: > Ragothaman Yennamalli wrote: > > HI, > > Since the log files and crashed .pdb files had > filled > > the whole disk space I had to delete them and > start > > again. > > I am simulating a homodimer protein in a water > box. I > > have mutated three residues and want to look the > > behaviour of the protein. I have four setups for > the > > same protein without mutation and with mutation > and > > respective controls. Among the four only one is > > crashing at the position restraint stage. The > other > > three didnt show me this error (except for the one > > line LINCS warning). > > I have run the position restrained dynamics again. > Yes > > as you are saying it starts with LINCS warning. > > This is what it says after the LINCS warning. > > You should be doing some energy minimization before > attempting MD, else > some bad contacts will send badness around the > system, maybe eventually > causing such crashes. Make sure you do EM after > solvating (and before if > you need to!) > > 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 > __ Yahoo! India Answers: Share what you know. Learn something new http://in.answers.yahoo.com/ ___ 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] MPIRUN error while running position restrained MD
Ragothaman Yennamalli wrote: HI, Since the log files and crashed .pdb files had filled the whole disk space I had to delete them and start again. I am simulating a homodimer protein in a water box. I have mutated three residues and want to look the behaviour of the protein. I have four setups for the same protein without mutation and with mutation and respective controls. Among the four only one is crashing at the position restraint stage. The other three didnt show me this error (except for the one line LINCS warning). I have run the position restrained dynamics again. Yes as you are saying it starts with LINCS warning. This is what it says after the LINCS warning. You should be doing some energy minimization before attempting MD, else some bad contacts will send badness around the system, maybe eventually causing such crashes. Make sure you do EM after solvating (and before if you need to!) 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
Re: [gmx-users] MPIRUN error while running position restrained MD
HI,
Since the log files and crashed .pdb files had filled
the whole disk space I had to delete them and start
again.
I am simulating a homodimer protein in a water box. I
have mutated three residues and want to look the
behaviour of the protein. I have four setups for the
same protein without mutation and with mutation and
respective controls. Among the four only one is
crashing at the position restraint stage. The other
three didnt show me this error (except for the one
line LINCS warning).
I have run the position restrained dynamics again. Yes
as you are saying it starts with LINCS warning.
This is what it says after the LINCS warning.
*
Back Off! I just backed up step20672.pdb to
./#step20672.pdb.1#
Sorry couldn't backup step20672.pdb to
./#step20672.pdb.1#
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Step 20673 Warning: pressure scaling more than 1%,
mu: 8.9983e+20 8.9983e+20 8.9983e+20
Step 20673 Warning: pressure scaling more than 1%,
mu: 8.9983e+20 8.9983e+20 8.9983e+20
Step 20673 Warning: pressure scaling more than 1%,
mu: 8.9983e+20 8.9983e+20 8.9983e+20
Step 20673 Warning: pressure scaling more than 1%,
mu: 8.9983e+20 8.9983e+20 8.9983e+20
Step 20673, time 91.346 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 348017441898496.00 (between atoms 7000 and
7002) rms nan
bonds that rotated more than 30 degrees:
**
I am attaching the .mdp file along with this email.
Thanks in advance.
Raghu
--- Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote:
> Hi Ragu,
>
> The tail of the .log file is not very informative
> here. Please try to
> find in the log where it first went wrong. It may
> well start out with
> a LINCS warning.
> Besides, please be more specific in what you're
> trying to simulate,
> and what protocol you used.
>
> Cheers,
>
> Tsjerk
>
> On 1/19/07, Ragothaman Yennamalli
> <[EMAIL PROTECTED]> wrote:
> > Hi,
> > This is the tail of the .log file
> > new box (3x3):
> >new box[0]={-4.13207e+15, 0.0e+00,
> > -0.0e+00}
> >new box[1]={ 0.0e+00, -5.17576e+15,
> > -0.0e+00}
> >new box[2]={ 0.0e+00, 1.51116e+23,
> > -1.14219e+16}
> > Correcting invalid box:
> > old box (3x3):
> >old box[0]={-4.13207e+15, 0.0e+00,
> > -0.0e+00}
> >old box[1]={ 0.0e+00, -5.17576e+15,
> > -0.0e+00}
> >old box[2]={ 0.0e+00, 1.51116e+23,
> > -1.14219e+16}
> > THe log files have generated as huge files (approx
> > 20GB) which have used all the disk space.
> > Raghu
> > --- Mark Abraham <[EMAIL PROTECTED]> wrote:
> >
> > > Ragothaman Yennamalli wrote:
> > > > Dear all,
> > > > I am running gromacs3.2 version. When I am
> running
> > > the
> > > > position restraint md for the protein, the
> process
> > > > stops within 100 steps with the following
> error:
> > > >
> > >
> >
>
-
> > > > One of the processes started by mpirun has
> exited
> > > with
> > > > nonzero exit
> > > > code. This typically indicates that the
> process
> > > > finished in error.
> > > > If your process did not finish in error, be
> sure
> > > to
> > > > include a "return
> > > > 0" or "exit(0)" in your C code before exiting
> the
> > > > application.
> > > >
> > > > PID 16200 failed on node n0 (10.10.0.8) due to
> > > signal
> > > > 9.
> > > >
> > >
> >
>
-
> > > >
> > > > I searched the mailing list and google and
> > > understood
> > > > that the pressure coupling parameter "tau_p"
> value
> > > in
> > > > the .mdp file has to be more than 1.0 and I
> did
> > > the
> > > > same.
> > >
> > > This is likely irrelevant. What do the ends of
> the
> > > .log files say?
> > >
> > > 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
> > >
> >
> >
> >
> >
> >
>
__
> > Yahoo! India Answers: Share what you know. Learn
> something new
> > http://in.answers.yahoo.com/
> > ___
> > 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
> >
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-
[gmx-users] desorting
I still need to run some tests on longer runs to see if things are
working out ok, but here is a procedure that seems to work for me to
deshuffle/desort based on the deshuffledesort script from
http://www.gromacs.org/pipermail/gmx-users/2002-May/001546.html. I have
pasted together the relevant commands from the script that I use to
manage the runs and the scripts that are created for submission to the
queue, but the basic idea is maintained. The only problem that I am
having is that the MW TIP4p dummy atom is right on top of OW, but I am
still not sure how it is positioned during the simulation.
### Basic procedure to run multiple steps of –shuffle –sort
ED=/projects/pomes/cneale/exe/gromacs-3.3.1/exec/fftw-3.1.2/bin
LAM=/tools/lam/lam-7.1.2/bin
DD=/home/cneale/exe
MD=/working/directory
cd ${MD}
MYMOL=sysName
in="_md1"
out="_md2"
#Shuffle the .trr input file correctly. Assume that it is not currently
shuffled
${ED}/grompp -np 4 -shuffle -sort -f ${MYMOL}${out}.mdp -c
${MYMOL}${in}_deshuffleddesorted.gro -p ${MYMOL}.top -n ${MYMOL}.ndx -o
${MYMOL}${out}_a.tpr -deshuf deshuf.ndx> output.${MYMOL}_grompp${out}_a
2> output.${MYMOL}_grompp${out}_e_a
rm -f deshuf.ndx mdout.mdp
echo System | ${ED}/editconf -f ${MYMOL}${out}_a.tpr -o
${MYMOL}${out}_shuffledsortedInit_a.gro
${DD}/deshuffledesort ${MYMOL}${out}_shuffledsortedInit_a.gro
${MYMOL}${in}_deshuffleddesorted.gro > reshuffleresort${out}_a.ndx
${ED}/trjconv -f ${MYMOL}${in}_deshuffleddesorted.trr -o
${MYMOL}${in}_reshuffleresort.trr -n reshuffleresort${out}_a.ndx
#Create the run input file
${ED}/grompp -np 4 -shuffle -sort -f ${MYMOL}${out}.mdp -c
${MYMOL}${in}_deshuffleddesorted.gro -t
${MYMOL}${in}_reshuffleresort.trr -p ${MYMOL}.top -n ${MYMOL}.ndx
-deshuf deshuffle${out}.ndx -e ${MYMOL}${in}.edr -o ${MYMOL}${out}.tpr >
output.${MYMOL}_grompp${out} 2> output.${MYMOL}_grompp${out}_e
#If a new reshuffle.ndx file differs then the run is invalid.
echo System | ${ED}/editconf -f ${MYMOL}${out}.tpr -o
${MYMOL}${out}_shuffledsortedInit.gro
${DD}/deshuffledesort ${MYMOL}${out}_shuffledsortedInit.gro
${MYMOL}${in}_deshuffleddesorted.gro > reshuffleresort${out}.ndx
look=`diff -q reshuffleresort${out}_a.ndx reshuffleresort${out}.ndx`
if [ -n "$look" ]; then
echo There was a big problem. reshuffleresort${out}_a.ndx
reshuffleresort${out}.ndx are different.
#Move the .tpr file to a new name to ensure that production halts
mv ${MYMOL}${out}.tpr ${MYMOL}${out}_notValid.tpr
fi
#Create the deshuffle file to properly handle the next run
${DD}/deshuffledesort ${MYMOL}${in}_deshuffleddesorted.gro
${MYMOL}${out}_shuffledsortedInit.gro > deshuffledesort${out}.ndx
rm -f ${MYMOL}${out}_a.tpr ${MYMOL}${out}_shuffledsortedInit_a.gro
reshuffleresort${out}_a.ndx ${MYMOL}${in}_reshuffleresort.trr
${MYMOL}${out}_shuffledsortedInit.gro reshuffleresort${out}.ndx mdout.mdp
mkdir ${IN}_success
sleep 5
mv ${MYMOL}*${IN}* ${MYSYS}_*${IN}* output* ${IN}_success
cp *.top ${IN}_success
#Production dynamics
${LAM}/mpirun C ${ED}/mdrun_mpi -np 4 -s ${MYMOL}${out}.tpr -deffnm
${MYMOL}${out} -v > output.${MYMOL}_mdrun${out} 2>
output.${MYMOL}_mdrun${out}_e
echo "mdrun finished"
#Deshuffle the gro xtc and trr files. The edr file does not need this.
echo System | ${ED}/trjconv -f ${MYMOL}${out}.xtc -s ${MYMOL}${out}.tpr
-n deshuffledesort${out}.ndx -o ${MYMOL}${out}_deshuffleddesorted.xtc
echo System | ${ED}/trjconv -f ${MYMOL}${out}.trr -s ${MYMOL}${out}.tpr
-n deshuffledesort${out}.ndx -o ${MYMOL}${out}_deshuffleddesorted.trr
echo System | ${ED}/trjconv -f ${MYMOL}${out}.gro -s ${MYMOL}${out}.tpr
-n deshuffledesort${out}.ndx -o ${MYMOL}${out}_deshuffleddesorted.gro
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Re: [gmx-users] g_energy
Dmitriy Golubobsky wrote: Dear GMX developers, and the question is: what kind if interactions consists, for example term LJ-(SR) he is equal for =LJ-SR:Poly-Poly+LJ-SR:Poly-SOL+LJ-SR:SOL-SOL or not? If the union of Poly and SOL are the whole system, then yes, the above relation should be true, since LJ-(SR) is computed from a groupwise sum. and what about other? Don't know what you mean. If the same question for electrostatics, then yes. 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
Re: [gmx-users] Comparison of hydrogen bond number
OZGE ENGIN wrote: Hi, I could not understand a point related to the calculation of hydrogen bond numbers. In order to be sure, I wrote a script in which the hydrogen bond numbers were calculated during the whole trajectory. Firstly, I used the 30.0 degrees and 0.35 nm criteria, and I compared the results of two: The numbers were the same. After that, I tried the 60.0 and 0.35 nm criteria, but this time, the numbers were not the same. What is the problem? Somebody is wrong :-) If you can find parameters for which they disagree, find the bonds that they disagree about in a single structure and see what is going on. 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
Re: [gmx-users] N/A
Florian Haberl wrote: hi, On Friday 19 January 2007 15:25, sangeeta wrote: Dear Sir, I have three questions, My protein has +2 charge, so I added two Cl atoms through the program genion and subsequently edited the topol.top file, in spite of that while running mdrun it gave an error that "FATAL error, CL atom type can not be found",I can not understand the problem. You have to add it to your .mdp file, too. I think not. The problem here is that your forcefield doesn't have a CL atom type defined. You will need to #include "ions.itp" in your .top file, and that will need to have a correct definition for Cl- for your force field and match the atom name in your .top file. 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
Re: [gmx-users] how to calculate internal energy for energygroups?
Marc Baaden wrote: Hi Robert, thanks for the hint. Just to make sure I get this right. So I'd use tpbconv with the subselection I'm interested in to make a new tpr file, and I also probably trjcat the trajectory that I want to analyze to write out the trajectory of the subselection. Then I do an mdrun -rerun with this tpr and xtc file and should be able to use g_energy to extract bond, angle and dihedral terms for my subselection. Someone correct me if this is not the way to proceed. Thanks, I'm sure mdrun will require a .tpr that has the same number of atoms as the trajectory you are analyzing. The way to get a subset of the bonded interactions is to only define in the .top file that set in which you are interested. You don't mess with the atom definitions however. For speed, turn off evaluation of all the non-bonded interactions somehow. 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
RE: [gmx-users] 3D-distribution
g_sdf Currently on the website for download, and I believe it is going into one of the future distributions. Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 - When the only tool you own is a hammer, every problem begins to resemble a nail. > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Roman Holomb > Sent: Saturday, 20 January 2007 2:25 AM > To: gmx-users@gromacs.org > Subject: [gmx-users] 3D-distribution > > > Dear GROMACS users, > > I have a question related with 3D-distribution of molecular density > around a central molecule. > Is it possible to get such plots from GROMACS trajectory file? > > Thanks in advance! > > Sincerely > /Roman > ___ > 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
[gmx-users] desorting
I have seen a script to generate a .ndx file for desorting.
http://www.gromacs.org/pipermail/gmx-users/2002-May/001546.html
Many later posts continue to suggest that there is no gromacs tool to
desort. e.g.
http://www.gromacs.org/pipermail/gmx-users/2006-August/023109.html
I realize that the mentioned script is not an official gromacs tool, I
just want to be sure that there are no other problems. Am I correct that
if one could generate the correct .ndx file (i.e. assuming the top
script is correct) the trajectory can be properly deshuffled and desorted?
My basic strategy is this:
make_ndx -o original.ndx (for analysis tools)
loop{
grompp -shuffle -sort -o shuffledsorted.tpr
trjconv -s shuffledsorted.tpr -o shuffledsorted.gro
script original.gro shuffledsorted.gro > deshuffledesort.ndx
mdrun
trjconv -f shuffledsorted.xtc -n deshuffledesort.ndx -o original.xtc
trjcat -f complete_original.xtc original.xtc -o complete_original.xtc
}
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[gmx-users] broken links in online tutorial files
The links for "Getting Started-Main Table of Contents" on the page(www.gromacs.org/blogcategory/page_2.html) are all broken. Does anyone know of a way to access these files? Will ___ 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] MPIRUN error while running position restrained MD
Hi Ragu,
The tail of the .log file is not very informative here. Please try to
find in the log where it first went wrong. It may well start out with
a LINCS warning.
Besides, please be more specific in what you're trying to simulate,
and what protocol you used.
Cheers,
Tsjerk
On 1/19/07, Ragothaman Yennamalli <[EMAIL PROTECTED]> wrote:
Hi,
This is the tail of the .log file
new box (3x3):
new box[0]={-4.13207e+15, 0.0e+00,
-0.0e+00}
new box[1]={ 0.0e+00, -5.17576e+15,
-0.0e+00}
new box[2]={ 0.0e+00, 1.51116e+23,
-1.14219e+16}
Correcting invalid box:
old box (3x3):
old box[0]={-4.13207e+15, 0.0e+00,
-0.0e+00}
old box[1]={ 0.0e+00, -5.17576e+15,
-0.0e+00}
old box[2]={ 0.0e+00, 1.51116e+23,
-1.14219e+16}
THe log files have generated as huge files (approx
20GB) which have used all the disk space.
Raghu
--- Mark Abraham <[EMAIL PROTECTED]> wrote:
> Ragothaman Yennamalli wrote:
> > Dear all,
> > I am running gromacs3.2 version. When I am running
> the
> > position restraint md for the protein, the process
> > stops within 100 steps with the following error:
> >
>
-
> > One of the processes started by mpirun has exited
> with
> > nonzero exit
> > code. This typically indicates that the process
> > finished in error.
> > If your process did not finish in error, be sure
> to
> > include a "return
> > 0" or "exit(0)" in your C code before exiting the
> > application.
> >
> > PID 16200 failed on node n0 (10.10.0.8) due to
> signal
> > 9.
> >
>
-
> >
> > I searched the mailing list and google and
> understood
> > that the pressure coupling parameter "tau_p" value
> in
> > the .mdp file has to be more than 1.0 and I did
> the
> > same.
>
> This is likely irrelevant. What do the ends of the
> .log files say?
>
> 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
>
__
Yahoo! India Answers: Share what you know. Learn something new
http://in.answers.yahoo.com/
___
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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Re: [gmx-users] [Beginner] How can I generate .gro and .top?
Hi Marcelo, Are you actually interested in the characteristics of your polyethyleneimine with four different substituents randomly arranged on each unit? Or is it ok to have something which in a way resembles sort of polyethyleneimine with four different substituents, which may or may not give behaviour correspondent to real chemical substituents? If the former is the case, you can't do with x2top, nor with PRODRG, but you will need to do a proper parameterization. If the topology is a black box to you, don't go there. If the latter is the case, you can try to get separate topologies for your different building blocks and use these to construct the whole chain. You may want to take a good look at one of the ff*.rtp files together with the gromacs manual to get a feel for the definitions of building blocks. Hope it helps, Tsjerk On 1/18/07, Marcelo de Freitas Lima <[EMAIL PROTECTED]> wrote: ** > You may want to try x2top, but it will only work for simple molecules. > > -- > David. ** > The answer is both yes and no. Gromacs can deal with non-proteins but > the force field may not be able to do it. In your case, what's the > monomer? Can you find some literature of it? Can you try pass the > monomer to the PRODRG? > > Yang Ye > > P.S.: From pdb to gro, you can use editconf. *** Thank you both David and Yang Ye, PRODRG can't handle that polymer (at least the one from the web site "The Dundee PRODRG2 Server") because the size is too far from the limit (~300 atoms). So I hadn't tried x2top yet for the same reason. The molecule is a derivative of polyethyleneimine with 4 different monomers distributed randomly. I will try to generate the ".gro" file by editconf, as you said, however the topology file continues a black box for me. If someone could help me... Thank you everybody, all the best, Marcelo This message was sent using IMP, the Internet Messaging Program. ___ 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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] long range energy
I read these sections and this is where I am confused. It is specified that PME cannot be used with rlilst different than rcoulomb but that if they are egal, long range energies would not be defined. However, I am trying to reproduce a simulation done by a former member of our research group and from the input files (.mdp) he used, I found that he used: rlist = 1.05 rcoulomb 1.15 coulombtype = PME From what I gathered from the manual, this combinaison is not possible, however, not only did he get results from this input, but he had the four types of energies: LJ-(SR), LJ-(LR), coulomb-(SR), coulomb-(LR). (I should have been more precise in my first post. I apologies.) You must be using an older version of Gromacs then. In 3.3.1 I have added a check on this in grompp. So now you have the PP (particle-particle) part of PME below rlist in Coulomb-SR, the PP part of PME above rlist (updated only every nstlist steps) in Coulomb-LR and, if your version is not too old, the reciprocal space contribution in Coul.-recip. Berk. -- Having corrected my entry file, I found LJ-(SR), LJ-(LR), coulomb-(SR) and Coul.-recip. I still don't have the Coulomb-LR though. (I am running version 3.3.1 of gromacs, with nstlist=10) Is Coul.-recip equal to the Coulomb-LR? Is it simply that it changed names? thanks, Richard, ___ 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] how to calculate internal energy for energygroups?
Hi Marc, Yes, I get the same Segfault. The way I have calculated bonded energy terms for subsets is to just copy the topology file and then comment out the unwanted terms. Bob On 1/22/07, Marc Baaden <[EMAIL PROTECTED]> wrote: >>> David van der Spoel said: >> > Just to make sure I get this right. So I'd use tpbconv with the subselect ion >> > I'm interested in to make a new tpr file, and I also probably trjcat the >> > trajectory that I want to analyze to write out the trajectory of the >> > subselection. Then I do an mdrun -rerun with this tpr and xtc file and >> > should be able to use g_energy to extract bond, angle and dihedral terms >> > for my subselection.[..] >> This should work. It does up to mdrun -rerun, which yields a segmentation fault :( Marc -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:[EMAIL PROTECTED] - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217 ___ 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: [gmx-users] 3D-distribution
Hi Roman, Depends on what you really want to do. There is a program g_sdf on the contributions page, which can calculate spatial distribution functions. I have a modified version of g_density (somewhere), which can be used to plot time averaged densities of a given selection. If the latter is what you want, you can contact me off-list. Cheers, Tsjerk On 1/19/07, Roman Holomb <[EMAIL PROTECTED]> wrote: Dear GROMACS users, I have a question related with 3D-distribution of molecular density around a central molecule. Is it possible to get such plots from GROMACS trajectory file? Thanks in advance! Sincerely /Roman ___ 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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_rdf
Try "gmxcheck -f full.trr" How many frames are in your .trr file? Why use a .trr anyway, use the .xtc instead (assuming that you save the xtc coords more often than the trr coords) Next, try making an index file with make_ndx and adding "-n index.ndx" to your g_rdf command. It is unclear to me how you were able to select CA CA without providing an index file. Third, take a closer look at your output and perhaps post it here. By at the zero distance, do you mean that you have ... @ subtitle "System-Ststem" 0.001 0.003 0 0.005 0 0.007 0 ... ? Fourth, look at your .trr in VMD. Perhaps the thing has collapsed? Hi there, I have a problem with g_rdf from version 3.3 I want to be sure, that I have crystal structure or liquid, so I used g_rdf -f full.trr -s full.tpr and selected System System or CA CA But instead of normal radial distribution function, I got only 1 sharp peak at the zero distance and zeros in other distances. What I am doing wrong? ___ 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] how to calculate internal energy for energygroups?
>>> David van der Spoel said: >> > Just to make sure I get this right. So I'd use tpbconv with the subselect ion >> > I'm interested in to make a new tpr file, and I also probably trjcat the >> > trajectory that I want to analyze to write out the trajectory of the >> > subselection. Then I do an mdrun -rerun with this tpr and xtc file and >> > should be able to use g_energy to extract bond, angle and dihedral terms >> > for my subselection.[..] >> This should work. It does up to mdrun -rerun, which yields a segmentation fault :( Marc -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:[EMAIL PROTECTED] - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217 ___ 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] how to calculate internal energy for energygroups?
Marc Baaden wrote: Hi Robert, thanks for the hint. Just to make sure I get this right. So I'd use tpbconv with the subselection I'm interested in to make a new tpr file, and I also probably trjcat the trajectory that I want to analyze to write out the trajectory of the subselection. Then I do an mdrun -rerun with this tpr and xtc file and should be able to use g_energy to extract bond, angle and dihedral terms for my subselection. Someone correct me if this is not the way to proceed. Thanks, Marc This should work. -- 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] how to calculate internal energy for energygroups?
Hi Robert, thanks for the hint. Just to make sure I get this right. So I'd use tpbconv with the subselection I'm interested in to make a new tpr file, and I also probably trjcat the trajectory that I want to analyze to write out the trajectory of the subselection. Then I do an mdrun -rerun with this tpr and xtc file and should be able to use g_energy to extract bond, angle and dihedral terms for my subselection. Someone correct me if this is not the way to proceed. Thanks, Marc >>> "Robert Johnson" said: >> Hi Marc, >> The only way I know how to do this is to make a copy of the topology >> file that ONLY contains the bonded terms that you want. Then use the >> mdrun -rerun option to recalculate the bonded energies for those >> terms. You must do this because I think that bonded energies are only >> written for the entire system - not for individual energy groups. >> Someone correct me if I'm wrong. >> Bob Johnson -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:[EMAIL PROTECTED] - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217 ___ 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] Signal:11 info.si_errno:0(Success) si_code:1(SEGV_MAPERR)
Mike Hanby wrote: Howdy, a user of a cluster that I manage sent me an output file of their Gromacs 3.3.1 job. It looks like the job runs for approx 11 hours and then abruptly terminates with a SEGV_MAPERR. What could cause this (gromacs, or a system config / resource?). The output of the log file is below, thanks for any suggestions. Mike # STARTED AT: Wed Jan 17 11:40:03 CST 2007 NSLOTS: 16 :-) /share/apps/gromacs/intel/gromacs-3.3.1-s64-openmpi/bin/mdrun_ompi (-: Option Filename Type Description -s production-Npt-300K_16CPU.tpr InputGeneric run input: tpr tpb tpa xml -o production-Npt-300K_16CPU.trr Output Full precision trajectory: trr trj -x production-Npt-300K_16CPU.xtc Output, Opt! Compressed trajectory (portable xdr format) -c production-Npt-300K_16CPU.gro Output Generic structure: gro g96 pdb xml -e ener.edr Output Generic energy: edr ene Getting Loaded... Reading file production-Npt-300K_16CPU.tpr, VERSION 3.3.1 (single precision) Loaded with Money Back Off! I just backed up ener.edr to ./#ener.edr.1# starting mdrun 'Protein in water' 250 steps, 2500.0 ps. .. steps .. step 650170, will finish at Fri Jan 19 06:52:24 2007 step 650180, will finish at Fri Jan 19 06:52:21 2007 Signal:11 info.si_errno:0(Success) si_code:1(SEGV_MAPERR) Failing at addr:0x7c3fefc [0] func:/share/apps/openmpi/intel/openmpi-1.1.2-64/lib/libopal.so.0 [0x2a966102a5] [1] func:/lib64/tls/libpthread.so.0 [0x3793b0c430] [2] func:/share/apps/gromacs/intel/gromacs-3.3.1-s64-openmpi/bin/mdrun_ompi( spread_q_bsplines+0x1c0) [0x45c80c] We've seen quite some problems with MPI libraries previously. I don't know what the current status of openmpi is. As the cluster manager you may have run some mpi tests, if so did they work flawless? The gromacs function (2 in your call tree) could also generate an overflow due to physics like large forces. Hence it is not possible to determine from this output what causes the problem. -- 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] Signal:11 info.si_errno:0(Success) si_code:1(SEGV_MAPERR)
Howdy, a user of a cluster that I manage sent me an output file of their Gromacs 3.3.1 job. It looks like the job runs for approx 11 hours and then abruptly terminates with a SEGV_MAPERR. What could cause this (gromacs, or a system config / resource?). The output of the log file is below, thanks for any suggestions. Mike # STARTED AT: Wed Jan 17 11:40:03 CST 2007 NSLOTS: 16 :-) /share/apps/gromacs/intel/gromacs-3.3.1-s64-openmpi/bin/mdrun_ompi (-: Option Filename Type Description -s production-Npt-300K_16CPU.tpr InputGeneric run input: tpr tpb tpa xml -o production-Npt-300K_16CPU.trr Output Full precision trajectory: trr trj -x production-Npt-300K_16CPU.xtc Output, Opt! Compressed trajectory (portable xdr format) -c production-Npt-300K_16CPU.gro Output Generic structure: gro g96 pdb xml -e ener.edr Output Generic energy: edr ene Getting Loaded... Reading file production-Npt-300K_16CPU.tpr, VERSION 3.3.1 (single precision) Loaded with Money Back Off! I just backed up ener.edr to ./#ener.edr.1# starting mdrun 'Protein in water' 250 steps, 2500.0 ps. .. steps .. step 650170, will finish at Fri Jan 19 06:52:24 2007 step 650180, will finish at Fri Jan 19 06:52:21 2007 Signal:11 info.si_errno:0(Success) si_code:1(SEGV_MAPERR) Failing at addr:0x7c3fefc [0] func:/share/apps/openmpi/intel/openmpi-1.1.2-64/lib/libopal.so.0 [0x2a966102a5] [1] func:/lib64/tls/libpthread.so.0 [0x3793b0c430] [2] func:/share/apps/gromacs/intel/gromacs-3.3.1-s64-openmpi/bin/mdrun_ompi( spread_q_bsplines+0x1c0) [0x45c80c] [3] func:/share/apps/gromacs/intel/gromacs-3.3.1-s64-openmpi/bin/mdrun_ompi( do_pme+0xb5a) [0x45dfea] [4] func:/share/apps/gromacs/intel/gromacs-3.3.1-s64-openmpi/bin/mdrun_ompi( force+0x9ac) [0x43eac2] [5] func:/share/apps/gromacs/intel/gromacs-3.3.1-s64-openmpi/bin/mdrun_ompi( do_force+0xa10) [0x46e69a] [6] func:/share/apps/gromacs/intel/gromacs-3.3.1-s64-openmpi/bin/mdrun_ompi( do_md+0x1a42) [0x429bfe] [7] func:/share/apps/gromacs/intel/gromacs-3.3.1-s64-openmpi/bin/mdrun_ompi( mdrunner+0xc0f) [0x427f87] [8] func:/share/apps/gromacs/intel/gromacs-3.3.1-s64-openmpi/bin/mdrun_ompi( main+0x2d6) [0x42b62a] [9] func:/lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x379321c3fb] [10] func:/share/apps/gromacs/intel/gromacs-3.3.1-s64-openmpi/bin/mdrun_ompi [0x418b8a] *** End of error message *** 11 additional processes aborted (not shown) ENDED AT: Wed Jan 17 22:54:32 CST 2007 # ___ 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] how to calculate internal energy for energygroups?
Robert Johnson wrote: Hi Marc, The only way I know how to do this is to make a copy of the topology file that ONLY contains the bonded terms that you want. Then use the mdrun -rerun option to recalculate the bonded energies for those terms. You must do this because I think that bonded energies are only written for the entire system - not for individual energy groups. Someone correct me if I'm wrong. Bob Johnson Can't post? Read http://www.gromacs.org/mailing_lists/users.php Unfortunately this is correct. It is on the todo list for 4.0. -- 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] how to calculate internal energy for energygroups?
Hi Marc, The only way I know how to do this is to make a copy of the topology file that ONLY contains the bonded terms that you want. Then use the mdrun -rerun option to recalculate the bonded energies for those terms. You must do this because I think that bonded energies are only written for the entire system - not for individual energy groups. Someone correct me if I'm wrong. Bob Johnson On 1/22/07, Marc Baaden <[EMAIL PROTECTED]> wrote: Hi, I fear I am overlooking something obvious, but I couldn't yet figure out how to calculate the internal (bond+angle+dihedral) energy of some energy- group, let's say eg a residue in a protein. When I define energy groups, I get additional interaction terms in the .edr file for Lennard-Jones and Coulomb, but none for bonds, angles and dihedrals. Is there another way than using energy groups and g_energy for this purpose? Thanks in advance, Marc Baaden NB: I am using Gromacs 3.3.1 -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:[EMAIL PROTECTED] - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217 ___ 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
[gmx-users] Error using -demux flag in trjcat (development version)
Hello everyone,
I recently ran a replica exchange calculation using the development
version of Gromacs. I used the demux.pl script to generate the two
.xvg files. I am trying to feed the replica_index.xvg file to trjcat,
but I'm getting a strange error message that I don't understand. Here
is the command and error message:
trjcat -f traj[0-9]{,[0-9]}.xtc -demux replica_index.xvg
Program trjcat, VERSION 3.3.99_development_20060330
Source code file: gmx_trjcat.c, line: 296
Fatal error:
Demuxing the same replica 1 twice at time 2.40
An excerpt of the index_replica.xvg file is shown below. I'm saving
coordinates and attempting replica exchange swaps every 0.6 ps. Does
anyone know what this error message means and how I fix it?
Thanks,
Bob Johnson
0 0123456789 10 11
12 13 14 15 16 17 18 19 20 21 22 23 24 25
26 27 28 29 30 31 32 33 34 35 36 37 38 39
40 41 42 43 44 45 46 47 48 49 50 51 52 53
54 55 56 57 58 59 60 61 62 63
0.6 1032456798 10 11
12 13 14 15 16 17 18 19 20 21 22 23 24 25
26 27 28 29 30 31 32 33 35 34 37 36 38 39
40 41 42 43 44 45 46 47 49 48 50 51 53 52
54 55 56 57 58 59 61 60 62 63
1.2 1032456798 10 11
12 13 14 15 16 17 18 19 20 22 21 24 23 25
26 27 28 29 30 31 32 33 35 34 37 38 36 39
40 41 42 43 44 45 46 49 47 48 50 53 51 52
54 56 55 57 58 59 61 60 62 63
1.8 1032456789 10 11
12 13 14 15 16 17 19 18 20 22 21 24 23 25
26 27 28 29 30 31 32 33 35 34 37 38 39 36
40 41 43 42 44 45 46 49 48 47 50 53 52 51
54 56 57 55 58 59 61 60 63 62
2.4 1032456789 10 11
12 13 14 15 16 17 19 18 20 21 22 24 23 25
26 28 27 29 30 32 31 35 33 34 37 38 39 36
40 43 41 44 42 46 45 48 49 50 47 53 52 51
54 56 57 58 55 61 59 60 63 62
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[gmx-users] how to calculate internal energy for energygroups?
Hi, I fear I am overlooking something obvious, but I couldn't yet figure out how to calculate the internal (bond+angle+dihedral) energy of some energy- group, let's say eg a residue in a protein. When I define energy groups, I get additional interaction terms in the .edr file for Lennard-Jones and Coulomb, but none for bonds, angles and dihedrals. Is there another way than using energy groups and g_energy for this purpose? Thanks in advance, Marc Baaden NB: I am using Gromacs 3.3.1 -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:[EMAIL PROTECTED] - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217 ___ 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] Gromacs 3.2.1: catastrophic error: could not opensource file "sfftw.h"
I recompiled FFTW 2.1.5 using the --enable-type-prefix option and now the configure of Gromacs 3.2.1 succeeds. However, now the make fails with the following error, any suggestions? if /bin/sh ../../libtool --mode=compile icc -DHAVE_CONFIG_H -I. -I. -I../../src -I/usr/X11R6/include -I../../include -DGMXLIBDIR=\"/share/apps/gromac s/intel/gromacs-3.2.1-s64/share/top\" -I/share/apps/intel/cce/9.1.042/include -I/share/apps/fftw/intel/fftw-2.1.5-s64/include -I/usr/local/include -I/ usr/include/libxml2 -O3 -I/usr/include/libxml2 -MT widget.lo -MD -MP -MF ".deps/widget.Tpo" \ -c -o widget.lo `test -f 'widget.c' || echo './'`widget.c; \ then mv -f ".deps/widget.Tpo" ".deps/widget.Plo"; \ else rm -f ".deps/widget.Tpo"; exit 1; \ fi icc -DHAVE_CONFIG_H -I. -I. -I../../src -I/usr/X11R6/include -I../../include -DGMXLIBDIR=\"/share/apps/gromacs/intel/gromacs-3.2.1-s64/share/top\" -I/ share/apps/intel/cce/9.1.042/include -I/share/apps/fftw/intel/fftw-2.1.5-s64/include -I/usr/local/include -I/usr/include/libxml2 -O3 -I/usr/include/li bxml2 -MT widget.lo -MD -MP -MF .deps/widget.Tpo -c widget.c -o widget.o /bin/sh ../../libtool --mode=link icc -O3 -I/usr/include/libxml2 -L/share/apps/intel/cce/9.1.042/lib -L/share/apps/fftw/intel/fftw-2.1.5-s64/lib -L/ usr/X11R6/lib -o libgmx.la -rpath /share/apps/gromacs/intel/gromacs-3.2.1-s64/x86_64-unknown-linux-gnu/lib -version-info 3:0:0 3dview.lo atomprop.loblock_tx.lo bondfree.lo calcgrid.lo calch.lo confio.lo copyrite.lo disre.lo do_fit.lo enxio.lo ewald_util.lo fatal.lo ffscanf.lo filenm.lo futil.lo gb util.lo fnbf.lo gmxfio.lo ifunc.lo index.lo cinvsqrtdata.lo invblock.lo macros.lo orires.lo main.lo maths.lo matio.lo mshift.lo mvdata.lo mvxvf.lo nam es.lo network.lo nrama.lo nrjac.lo nrnb.lo pargs.lo pbc.lo pdbio.lo princ.lo rando.lo random.lo gmx_random.lo rbin.lo readinp.lo replace.lo rmpbc.lo s hift_util.lo sortwater.lo smalloc.lo stat.lo statutil.lo strdb.lo string2.lo symtab.lo tpxio.lo trnio.lo trxio.lo txtdump.lo typedefs.lo viewit.lo wgm s.lo wman.lo writeps.lo xdrd.lo xtcio.lo xvgr.lo detectcpu.lo libxdrf.lo vec.lo dihres.lo xmlio.lo innerf.lo f77_wrappers.lo mgmx.lo widget.lo -L/usr/ X11R6/lib64 -lnsl -lsrfftw -lsfftw -lXm -lXt -lSM -lICE -lXext -lXp -lX11 -lxml2 -lz -lpthread -lm -L/share/apps/intel/cce/9.1.042/lib -L/share/ap ps/fftw/intel/fftw-2.1.5-s64/lib -L/usr/X11R6/lib" -L/usr/X11R6/lib -L/share/apps/intel/fce/9.1.036/lib -L/usr/lib/gcc/x86_64-redhat-linux/3.4.6/ -L/u sr/lib/gcc/x86_64-redhat-linux/3.4.6/../../../../lib64 -lsvml -lifport -lifcore -limf -lm -lipgo -lirc -lgcc_s -lirc_s -ldl /bin/sh: -c: line 0: unexpected EOF while looking for matching `"' /bin/sh: -c: line 1: syntax error: unexpected end of file make[3]: *** [libgmx.la] Error 2 make[3]: Leaving directory `/home/makeuser/tmp/gromacs/gromacs-3.2.1_s64/gromacs-3.2.1/src/gmxlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/makeuser/tmp/gromacs/gromacs-3.2.1_s64/gromacs-3.2.1/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/makeuser/tmp/gromacs/gromacs-3.2.1_s64/gromacs-3.2.1/src' make: *** [all-recursive] Error 1 Making install in src make[1]: Entering directory `/home/makeuser/tmp/gromacs/gromacs-3.2.1_s64/gromacs-3.2.1/src' Making install in gmxlib make[2]: Entering directory `/home/makeuser/tmp/gromacs/gromacs-3.2.1_s64/gromacs-3.2.1/src/gmxlib' /bin/sh ../../libtool --mode=link icc -O3 -I/usr/include/libxml2 -L/share/apps/intel/cce/9.1.042/lib -L/share/apps/fftw/intel/fftw-2.1.5-s64/lib -L/ usr/X11R6/lib -o libgmx.la -rpath /share/apps/gromacs/intel/gromacs-3.2.1-s64/x86_64-unknown-linux-gnu/lib -version-info 3:0:0 3dview.lo atomprop.loblock_tx.lo bondfree.lo calcgrid.lo calch.lo confio.lo copyrite.lo disre.lo do_fit.lo enxio.lo ewald_util.lo fatal.lo ffscanf.lo filenm.lo futil.lo gb util.lo fnbf.lo gmxfio.lo ifunc.lo index.lo cinvsqrtdata.lo invblock.lo macros.lo orires.lo main.lo maths.lo matio.lo mshift.lo mvdata.lo mvxvf.lo nam es.lo network.lo nrama.lo nrjac.lo nrnb.lo pargs.lo pbc.lo pdbio.lo princ.lo rando.lo random.lo gmx_random.lo rbin.lo readinp.lo replace.lo rmpbc.lo s hift_util.lo sortwater.lo smalloc.lo stat.lo statutil.lo strdb.lo string2.lo symtab.lo tpxio.lo trnio.lo trxio.lo txtdump.lo typedefs.lo viewit.lo wgm s.lo wman.lo writeps.lo xdrd.lo xtcio.lo xvgr.lo detectcpu.lo libxdrf.lo vec.lo dihres.lo xmlio.lo innerf.lo f77_wrappers.lo mgmx.lo widget.lo -L/usr/ X11R6/lib64 -lnsl -lsrfftw -lsfftw -lXm -lXt -lSM -lICE -lXext -lXp -lX11 -lxml2 -lz -lpthread -lm -L/share/apps/intel/cce/9.1.042/lib -L/share/ap ps/fftw/intel/fftw-2.1.5-s64/lib -L/usr/X11R6/lib" -L/usr/X11R6/lib -L/share/apps/intel/fce/9.1.036/lib -L/usr/lib/gcc/x86_64-redhat-linux/3.4.6/ -L/u sr/lib/gcc/x86_64-redhat-linux/3.4.6/../../../../lib64 -lsvml -lifport -lifcore -limf -lm -lipgo -lirc -lgcc_s -lirc_s -ldl /bin/sh: -c: line 0: unexpected EOF while looki
Re: [gmx-users] Re: long range energy
Incidentally, if PME has been specified correctly, am I right in assuming there should be an energy term available within g_energy for long range forces? Which one is it? For some reason, I haven't been able to find it yet. - Original Message From: Richard Vadnais <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Monday, January 22, 2007 1:46:52 PM Subject: [gmx-users] Re: long range energy > Richard Vadnais wrote: >> hi all, >> >> I want to find four types of energies from my simulation: LJ and >> Coulomb at long and short range. I use PME for coulomb type and cut-off >> for VdW type with rlist = rcoulomb = 0.9 >> >>However, the LJ (LR) and Coulomb LR are not generated in the output >> nor can I get them with g_energy. > > That's because they aren't defined when rlist = rcoulomb. Have a read of > the relevant manual sections. > > Mark > > I read these sections and this is where I am confused. It is specified that PME cannot be used with rlilst different than rcoulomb but that if they are egal, long range energies would not be defined. However, I am trying to reproduce a simulation done by a former member of our research group and from the input files (.mdp) he used, I found that he used: rlist = 1.05 rcoulomb 1.15 coulombtype = PME From what I gathered from the manual, this combinaison is not possible, however, not only did he get results from this input, but he had the four types of energies: LJ-(SR), LJ-(LR), coulomb-(SR), coulomb-(LR). (I should have been more precise in my first post. I apologies.) thanks for your help, Richard Vadnais, ___ 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 Cheap talk? Check out Yahoo! Messenger's low PC-to-Phone call rates. http://voice.yahoo.com ___ 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] Re: long range energy
From: "Richard Vadnais" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: Subject: [gmx-users] Re: long range energy Date: Mon, 22 Jan 2007 08:46:52 -0500 Richard Vadnais wrote: hi all, I want to find four types of energies from my simulation: LJ and Coulomb at long and short range. I use PME for coulomb type and cut-off for VdW type with rlist = rcoulomb = 0.9 However, the LJ (LR) and Coulomb LR are not generated in the output nor can I get them with g_energy. That's because they aren't defined when rlist = rcoulomb. Have a read of the relevant manual sections. Mark I read these sections and this is where I am confused. It is specified that PME cannot be used with rlilst different than rcoulomb but that if they are egal, long range energies would not be defined. However, I am trying to reproduce a simulation done by a former member of our research group and from the input files (.mdp) he used, I found that he used: rlist = 1.05 rcoulomb 1.15 coulombtype = PME From what I gathered from the manual, this combinaison is not possible, however, not only did he get results from this input, but he had the four types of energies: LJ-(SR), LJ-(LR), coulomb-(SR), coulomb-(LR). (I should have been more precise in my first post. I apologies.) You must be using an older version of Gromacs then. In 3.3.1 I have added a check on this in grompp. So now you have the PP (particle-particle) part of PME below rlist in Coulomb-SR, the PP part of PME above rlist (updated only every nstlist steps) in Coulomb-LR and, if your version is not too old, the reciprocal space contribution in Coul.-recip. Berk. _ 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 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: long range energy
Richard Vadnais wrote: hi all, I want to find four types of energies from my simulation: LJ and Coulomb at long and short range. I use PME for coulomb type and cut-off for VdW type with rlist = rcoulomb = 0.9 However, the LJ (LR) and Coulomb LR are not generated in the output nor can I get them with g_energy. That's because they aren't defined when rlist = rcoulomb. Have a read of the relevant manual sections. Mark I read these sections and this is where I am confused. It is specified that PME cannot be used with rlilst different than rcoulomb but that if they are egal, long range energies would not be defined. However, I am trying to reproduce a simulation done by a former member of our research group and from the input files (.mdp) he used, I found that he used: rlist = 1.05 rcoulomb 1.15 coulombtype = PME From what I gathered from the manual, this combinaison is not possible, however, not only did he get results from this input, but he had the four types of energies: LJ-(SR), LJ-(LR), coulomb-(SR), coulomb-(LR). (I should have been more precise in my first post. I apologies.) thanks for your help, Richard Vadnais, ___ 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_rdf
Hi there, I have a problem with g_rdf from version 3.3 I want to be sure, that I have crystal structure or liquid, so I used g_rdf -f full.trr -s full.tpr and selected System System or CA CA But instead of normal radial distribution function, I got only 1 sharp peak at the zero distance and zeros in other distances. What I am doing wrong? Thank you Karel Berka -- Zdraví zdravý Karel "Krápník" Berka ___ 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] N/A
hi, On Friday 19 January 2007 15:25, sangeeta wrote: > Dear Sir, > > I have three questions, > > My protein has +2 charge, so I added two Cl atoms through the program > genion and subsequently edited the topol.top file, in spite of that while > running mdrun it gave an error that "FATAL error, CL atom type can not be > found",I can not understand the problem. You have to add it to your .mdp file, too. > I wanted to include PBC in my simulation so in the pr.mdp file as well > in md.mdp file I wrote PBC=xyz , am I correct? How can I know that PBC is > being included in my simulation? Yes, take a look at mdout.mdp > In spite of having dssp and running it I can not get the .xpm files. > How can I generate those files? do_dssp -h (set proper path to dssp binary) > Waiting for your reply. > > > regards > SANGEETA > > -- > Open WebMail Project (http://openwebmail.org) > > ___ > 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] problem regarding dssp
Dear Sir, After carrying out one MD simulation of a protein when I went for analysis of secondary structure through dssp the program ran successfully, but no .xpm files were generated.I can not understand the problem , please help. -- Open WebMail Project (http://openwebmail.org) ___ 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] [Beginner] How can I generate .gro and .top?
** You may want to try x2top, but it will only work for simple molecules. -- David. ** The answer is both yes and no. Gromacs can deal with non-proteins but the force field may not be able to do it. In your case, what's the monomer? Can you find some literature of it? Can you try pass the monomer to the PRODRG? Yang Ye P.S.: From pdb to gro, you can use editconf. *** Thank you both David and Yang Ye, PRODRG can't handle that polymer (at least the one from the web site "The Dundee PRODRG2 Server") because the size is too far from the limit (~300 atoms). So I hadn't tried x2top yet for the same reason. The molecule is a derivative of polyethyleneimine with 4 different monomers distributed randomly. I will try to generate the ".gro" file by editconf, as you said, however the topology file continues a black box for me. If someone could help me... Thank you everybody, all the best, Marcelo This message was sent using IMP, the Internet Messaging Program. ___ 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] Gromacs 3.2.1: catastrophic error: could not open source file "sfftw.h"
Howdy, One of my users requested that I compile Gromacs 3.2.1 on our system. I've already compiled and installed 3.3.1 and 3.3 on this system. When I compile 3.2.1, I get the error during config: 'catastrophic error: could not open source file "sfftw.h"' At first I figured Gromacs 3.2.1 must require FFTW 2.1.5 (I have 3.1.2 on the system) so I compiled it and reran the Gromacs 3.2.1 configure. Same error. I searched all of my fftw directories, and I don't see this file anywhere. I'm guessing that the s in sfftw.h stands for single precision? If that's the case, I compiled single precision and double precision versions of fftw in their own separate directories (where single precisions are named fftw.h and doubles are dfftw.h). If that's the case, can I resolve this by simply creating a link called sfftw.h pointing to fftw.h? Also, do I have to use fftw 2.1.5 for Gro 3.2.1, or can I use fftw 3? Thanks, Mike ___ 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] Long range energies
Richard Vadnais wrote: hi all, I want to find four types of energies from my simulation: LJ and Coulomb at long and short range. I use PME for coulomb type and cut-off for VdW type with rlist = rcoulomb = 0.9 However, the LJ (LR) and Coulomb LR are not generated in the output nor can I get them with g_energy. That's because they aren't defined when rlist = rcoulomb. Have a read of the relevant manual sections. 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] N/A
Dear Sir, I have three questions, My protein has +2 charge, so I added two Cl atoms through the program genion and subsequently edited the topol.top file, in spite of that while running mdrun it gave an error that "FATAL error, CL atom type can not be found",I can not understand the problem. I wanted to include PBC in my simulation so in the pr.mdp file as well in md.mdp file I wrote PBC=xyz , am I correct? How can I know that PBC is being included in my simulation? In spite of having dssp and running it I can not get the .xpm files. How can I generate those files? Waiting for your reply. regards SANGEETA -- Open WebMail Project (http://openwebmail.org) ___ 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] MPIRUN error while running position restrained MD
Hi,
This is the tail of the .log file
new box (3x3):
new box[0]={-4.13207e+15, 0.0e+00,
-0.0e+00}
new box[1]={ 0.0e+00, -5.17576e+15,
-0.0e+00}
new box[2]={ 0.0e+00, 1.51116e+23,
-1.14219e+16}
Correcting invalid box:
old box (3x3):
old box[0]={-4.13207e+15, 0.0e+00,
-0.0e+00}
old box[1]={ 0.0e+00, -5.17576e+15,
-0.0e+00}
old box[2]={ 0.0e+00, 1.51116e+23,
-1.14219e+16}
THe log files have generated as huge files (approx
20GB) which have used all the disk space.
Raghu
--- Mark Abraham <[EMAIL PROTECTED]> wrote:
> Ragothaman Yennamalli wrote:
> > Dear all,
> > I am running gromacs3.2 version. When I am running
> the
> > position restraint md for the protein, the process
> > stops within 100 steps with the following error:
> >
>
-
> > One of the processes started by mpirun has exited
> with
> > nonzero exit
> > code. This typically indicates that the process
> > finished in error.
> > If your process did not finish in error, be sure
> to
> > include a "return
> > 0" or "exit(0)" in your C code before exiting the
> > application.
> >
> > PID 16200 failed on node n0 (10.10.0.8) due to
> signal
> > 9.
> >
>
-
> >
> > I searched the mailing list and google and
> understood
> > that the pressure coupling parameter "tau_p" value
> in
> > the .mdp file has to be more than 1.0 and I did
> the
> > same.
>
> This is likely irrelevant. What do the ends of the
> .log files say?
>
> Mark
> ___
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Re: [gmx-users] Replica Exchange Analysis Tools
I'm getting an error message when feeding replica_index.xvg to trjcat. Here is the command and the error message: trjcat -f *.xtc -demux replica_index.xvg Program trjcat, VERSION 3.3.99_development_20060330 Source code file: gmx_trjcat.c, line: 296 Fatal error: Demuxing the same replica 1 twice at time 2.40 Here, the xtc files are the trajectories of only the single stranded DNA (which is just a subset of my system and is the whole reason why I'm doing REMD) - not sure if that matters or not. Also, I saved the ssDNA coordinates at the same frequency as my REMD swaps - one every 0.6 ps. There were 64 replicas total and each replica was running on 32 processors. Also, what will trjcat give me? Will it give trajectories that are at a constant temperature? Thanks, Bob On 1/16/07, David van der Spoel <[EMAIL PROTECTED]> wrote: Robert Johnson wrote: > Hello everyone, > I'm using the current development version of Gromacs to perform > replica exchange MD. Are there any Gromacs tools to aid in the > analysis of the trajectories. For example, are there tools that enable > trajectories grouped by temperature? Is there a way to determine the > temperature of a replica as a function of time? > Thanks, > Bob Johnson > PhD Student > University of Pennsylvania > ___ > 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 There is a script in src/contrib/scripts/demux.pl that will give you this info. Please check and double check. It also gives input to trjcat for demultiplexing trajectories. If you really are using the development version, then do a cvs update, I just added a feature today. -- 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 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 regarding g_sham
Hi to All, I want to use the g_sham command to have the entropy and enthalpy plots of a simulation of a protein in water. I have tried to use the EPot, EKin, and Efree, among others, as input in the graph.xvg file, toghether with the -lsh and -lss options, however the enthalpy.xpm and the entropy.xpm files are not created. Is my input correct? what kind of graph.xvg should I use for input to get the correct output. I am using version 3.3.1. Thanks Afonso __ Fale com seus amigos de graça com o novo Yahoo! Messenger http://br.messenger.yahoo.com/ ___ 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] Comparison of hydrogen bond number
Hi, I could not understand a point related to the calculation of hydrogen bond numbers. In order to be sure, I wrote a script in which the hydrogen bond numbers were calculated during the whole trajectory. Firstly, I used the 30.0 degrees and 0.35 nm criteria, and I compared the results of two: The numbers were the same. After that, I tried the 60.0 and 0.35 nm criteria, but this time, the numbers were not the same. What is the problem? I am so confused. Thanks in advance Özge ENGİN Department of Computational Science and Engineering Koc University, Istanbul ___ 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] 3D-distribution
Dear GROMACS users, I have a question related with 3D-distribution of molecular density around a central molecule. Is it possible to get such plots from GROMACS trajectory file? Thanks in advance! Sincerely /Roman ___ 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] Twin-range neighbour searching (NS) with simple NS algorithm not implemented
hi, Can anyone tell me what does this error mean? ERROR: Twin-range neighbour searching (NS) with simple NS algorithm not implemented my md.mdp file was set: ns_type = grid pbc = xyz Thank you very much! Li,DC Department of Engineering Mechanics Tsinghua University Beijing 100084 China Email address: [EMAIL PROTECTED] 2007-01-22 ___ 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] Gromacs 3.2.1: catastrophic error: could not open source file "sfftw.h"
Sorry if this gets posted twice, I emailed it 18 hours ago and don't see it on the list. Howdy, One of my users requested that I compile Gromacs 3.2.1 on our system. I've already compiled and installed 3.3.1 and 3.3 on this system. When I compile 3.2.1, I get the error during config: 'catastrophic error: could not open source file "sfftw.h"' At first I figured Gromacs 3.2.1 must require FFTW 2.1.5 (I have 3.1.2 on the system) so I compiled it and reran the Gromacs 3.2.1 configure. Same error. I searched all of my fftw directories, and I don't see this file anywhere. I'm guessing that the s in sfftw.h stands for single precision? If that's the case, I compiled single precision and double precision versions of fftw in their own separate directories (where single precisions are named fftw.h and doubles are dfftw.h). If that's the case, can I resolve this by simply creating a link called sfftw.h pointing to fftw.h? Also, do I have to use fftw 2.1.5 for Gro 3.2.1, or can I use fftw 3? Thanks, Mike ___ 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: Gromacs 3.2.1: catastrophic error: could not open source file "sfftw.h"
I recompiled FFTW 2.1.5 using the --enable-type-prefix and this resolved the config issue, however, now I'm getting an error during make: /bin/sh: -c: line 0: unexpected EOF while looking for matching `"' I'm using the following configure command: $ ./configure CC=icc CXX=icpc FC=ifort F77=ifort F90=ifort --enable-sse --enable-fortran --prefix=/share/apps/gromacs/intel/gromacs-3.2.1-s64 Here's the tail of my make log: if /bin/sh ../../libtool --mode=compile icc -DHAVE_CONFIG_H -I. -I. -I../../src -I/usr/X11R6/include -I../../include -DGMXLIBDIR=\"/share/apps/gromacs/intel/gromacs-3.2.1-s64/share/top\" -I/share/apps/intel/cce/9.1.042/include -I/share/apps/fftw/intel/fftw-2.1.5-s64/include -I/usr/local/include -I/usr/include/libxml2 -O3 -I/usr/include/libxml2 -MT widget.lo -MD -MP -MF ".deps/widget.Tpo" \ -c -o widget.lo `test -f 'widget.c' || echo './'`widget.c; \ then mv -f ".deps/widget.Tpo" ".deps/widget.Plo"; \ else rm -f ".deps/widget.Tpo"; exit 1; \ fi icc -DHAVE_CONFIG_H -I. -I. -I../../src -I/usr/X11R6/include -I../../include -DGMXLIBDIR=\"/share/apps/gromacs/intel/gromacs-3.2.1-s64/share/top\" -I/share/apps/intel/cce/9.1.042/include -I/share/apps/fftw/intel/fftw-2.1.5-s64/include -I/usr/local/include -I/usr/include/libxml2 -O3 -I/usr/include/libxml2 -MT widget.lo -MD -MP -MF .deps/widget.Tpo -c widget.c -o widget.o /bin/sh ../../libtool --mode=link icc -O3 -I/usr/include/libxml2 -L/share/apps/intel/cce/9.1.042/lib -L/share/apps/fftw/intel/fftw-2.1.5-s64/lib -L/usr/X11R6/lib -o libgmx.la -rpath /share/apps/gromacs/intel/gromacs-3.2.1-s64/x86_64-unknown-linux-gnu/lib -version-info 3:0:0 3dview.lo atomprop.lo block_tx.lo bondfree.lo calcgrid.lo calch.lo confio.lo copyrite.lo disre.lo do_fit.lo enxio.lo ewald_util.lo fatal.lo ffscanf.lo filenm.lo futil.lo gbutil.lo fnbf.lo gmxfio.lo ifunc.lo index.lo cinvsqrtdata.lo invblock.lo macros.lo orires.lo main.lo maths.lo matio.lo mshift.lo mvdata.lo mvxvf.lo names.lo network.lo nrama.lo nrjac.lo nrnb.lo pargs.lo pbc.lo pdbio.lo princ.lo rando.lo random.lo gmx_random.lo rbin.lo readinp.lo replace.lo rmpbc.lo shift_util.lo sortwater.lo smalloc.lo stat.lo statutil.lo strdb.lo string2.lo symtab.lo tpxio.lo trnio.lo trxio.lo txtdump.lo typedefs.lo viewit.lo wgms.lo wman.lo writeps.lo xdrd.lo xtcio.lo xvgr.lo detectcpu.lo libxdrf.lo vec.lo dihres.lo xmlio.lo innerf.lo f77_wrappers.lo mgmx.lo widget.lo -L/usr/X11R6/lib64 -lnsl -lsrfftw -lsfftw -lXm -lXt -lSM -lICE -lXext -lXp -lX11 -lxml2 -lz -lpthread -lm -L/share/apps/intel/cce/9.1.042/lib -L/share/apps/fftw/intel/fftw-2.1.5-s64/lib -L/usr/X11R6/lib" -L/usr/X11R6/lib -L/share/apps/intel/fce/9.1.036/lib -L/usr/lib/gcc/x86_64-redhat-linux/3.4.6/ -L/usr/lib/gcc/x86_64-redhat-linux/3.4.6/../../../../lib64 -lsvml -lifport -lifcore -limf -lm -lipgo -lirc -lgcc_s -lirc_s -ldl /bin/sh: -c: line 0: unexpected EOF while looking for matching `"' /bin/sh: -c: line 1: syntax error: unexpected end of file make[3]: *** [libgmx.la] Error 2 make[3]: Leaving directory `/home/makeuser/tmp/gromacs/gromacs-3.2.1_s64/gromacs-3.2.1/src/gmxlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/makeuser/tmp/gromacs/gromacs-3.2.1_s64/gromacs-3.2.1/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/makeuser/tmp/gromacs/gromacs-3.2.1_s64/gromacs-3.2.1/src' make: *** [all-recursive] Error 1 -Original Message- From: Mike Hanby Sent: Friday, January 19, 2007 8:26 AM To: 'Discussion list for GROMACS users' Subject: Gromacs 3.2.1: catastrophic error: could not open source file "sfftw.h" Sorry if this gets posted twice, I emailed it 18 hours ago and don't see it on the list. Howdy, One of my users requested that I compile Gromacs 3.2.1 on our system. I've already compiled and installed 3.3.1 and 3.3 on this system. When I compile 3.2.1, I get the error during config: 'catastrophic error: could not open source file "sfftw.h"' At first I figured Gromacs 3.2.1 must require FFTW 2.1.5 (I have 3.1.2 on the system) so I compiled it and reran the Gromacs 3.2.1 configure. Same error. I searched all of my fftw directories, and I don't see this file anywhere. I'm guessing that the s in sfftw.h stands for single precision? If that's the case, I compiled single precision and double precision versions of fftw in their own separate directories (where single precisions are named fftw.h and doubles are dfftw.h). If that's the case, can I resolve this by simply creating a link called sfftw.h pointing to fftw.h? Also, do I have to use fftw 2.1.5 for Gro 3.2.1, or can I use fftw 3? Thanks, Mike ___ 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_energy
Dear GMX developers, I've got a question on the analys tool of gromacs - g_energy during MD I define 2 energy groups for energy calculation. thus after run, I've got values for different interations such us LJ-14 Coulomb-14 LJ-(SR) LJ-(LR) Coulomb-(SR) Coulomb-(LR) Pressure-(bar) Potential Kinetic-En. Total-Energy Coul-SR:Poly-Poly LJ-SR:Poly-Poly Coul-LR:Poly-Poly LJ-LR:Poly-Poly Coul-14:Poly-Poly LJ-14:Poly-Poly Coul-SR:Poly-SOL LJ-SR:Poly-SOL Coul-LR:Poly-SOL LJ-LR:Poly-SOL Coul-14:Poly-SOL LJ-14:Poly-SOL Coul-SR:SOL-SOL LJ-SR:SOL-SOL Coul-LR:SOL-SOL LJ-LR:SOL-SOL Coul-14:SOL-SOL LJ-14:SOL-SOL and the question is: what kind if interactions consists, for example term LJ-(SR) he is equal for =LJ-SR:Poly-Poly+LJ-SR:Poly-SOL+LJ-SR:SOL-SOL or not? and what about other? -- Dmitriy Golubovsky ___ 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
