[gmx-users] specifying the direction of Pull in US
Hi all, I am working on steered molecular dynamics and In that I would like to pull the ligand ( already in complex with protein) away from the reference amino acid ( which I've selected so that I can direct the ligand to get closure to my desired amino acid residue). Now the thing is when I used VMD to assign the direction, The desired direction of mine is not along the proper x, y, or in Z axis. So my question is how can i specify the direction in a situation like this. I've seen in other discussions people have used pull_vec. How can I get the values of the pull_vec. Kindly help me . thanks in advance -- View this message in context: http://gromacs.5086.n6.nabble.com/specifying-the-direction-of-Pull-in-US-tp4999140.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re:Shell scripts
Yes,
I was just going over them individually, then cat into a single spread sheet,
which I can use awk to do combos, $1+$2+$16+$233...etc...
Its still alot of files but easier to manipulate with complex .ndx files than
just using g_energy every time...mostly time saving when you exceed 10
simulation or more. Still, having to re-learn some basic awk, gawk, cat and
piping skills from 12 years ago is a pain, but the simple things are invaluable
with gromacs I would say. Without them you would become so bogged one might
hit insanity levels...
Thanks
Stephan Watkins
University of Bern-Inselspital
Original-Nachricht
Datum: Fri, 6 Jul 2012 07:09:16 +0200
Von: Tsjerk Wassenaar tsje...@gmail.com
An: Discussion list for GROMACS users gmx-users@gromacs.org
Betreff: Re: [gmx-users] Re:Shell scripts
Hey,
I'd probably go for something like:
for ((i=1; i...; i++)); do echo $i 0 | g_energy ...; done
Note the additional 0 to make g_energy exit. The (( )) has been in
bash for ages, so that shouldn't be a problem.
I notice that in the working construct you used 'traj_x.edr', while in
the earlier ones, you used 'traj_${i}.edr'. If you try to extract all
energy terms from a single .edr file, you can also use
echo $(seq 1321) 0 | g_energy -f traj_x.edr -o stuff.xvg
and then parse the columns out of the .xvg file.
Cheers,
Tsjerk
On Fri, Jul 6, 2012 at 1:11 AM, Mark Abraham mark.abra...@anu.edu.au
wrote:
On 6/07/2012 7:25 AM, lloyd riggs wrote:
Dear All,
Thank you,
I finally got this to work on the other PC after four hours...
i=1
while [ $i -le 1322 ]
do
g_energy -f traj_x.edr -o ${i}.xvg EOF
${i}
EOF
i=$(($i+1))
done
Still can not figure out the difference, or why one works on one PC and
not the other?
Probably different bash versions, as your Ubuntu could well be more
recent
than some version on a server at work. Try bash --version. If so, poke
your
system admins to make an up-to-date bash available for you, even if not
as
the system default.
Mark
Stephan (in Rainy Switzerland)
Original-Nachricht
Datum: Thu, 5 Jul 2012 22:25:06 +0200
Von: Elton Carvalho elto...@if.usp.br
An: Discussion list for GROMACS users gmx-users@gromacs.org
Betreff: Re: [gmx-users] Re:Shell scripts
On Thu, Jul 5, 2012 at 6:03 PM, lloyd riggs lloyd.ri...@gmx.ch
wrote:
Does any one know why, or have some other scripts...
My suggestion would be something in the lines of
#!/bin/bash
for i in $(seq 2121) ; do
g_energy -f traj_${i}.edr -o ${i}.xvg ${i} 0
done
===
Notice the in keyword right after 'i'.
I used a subshell to invoke the program 'seq', which generates a
sequence from 1 to the given argument, so we don't depent om how these
other constructs with ((; ; )) work among different versions of bash.
I also suggest replacing the here-document by a here-string, but
that's personal taste. You may or may not have problems with older
versions of bash
Greetings from a foggy Groningen,
--
Elton Carvalho
Tel.: +55 11 3091-6985/6922
Dept Física dos Materiais e Mecânica
Instituto de Física
Universidade de São Paulo
P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
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* Only plain
Re: [gmx-users] Re:Shell scripts
Yes,
One is a newer 12. version Vs. 11.10. The one PC at home just ignores the for
loop, and uses it as an infanite loop over everything while the other complains
of syntax (vs.12). The one while loop I posted works on both, and you can
also catch averidges well by $ sh script.sh outterminaloutput.txt If
somone is interested in averidges. For me they're not that important, except
mayby solvent wise. I looked at it with terminal output and realized it went
on for 10,000 or more steps/iterations over g_energy but didnt notice before is
why it threw me off.
Thanks
Stephan Watkins
University of Bern-Inselspital
Original-Nachricht
Datum: Fri, 06 Jul 2012 09:11:22 +1000
Von: Mark Abraham mark.abra...@anu.edu.au
An: Discussion list for GROMACS users gmx-users@gromacs.org
Betreff: Re: [gmx-users] Re:Shell scripts
On 6/07/2012 7:25 AM, lloyd riggs wrote:
Dear All,
Thank you,
I finally got this to work on the other PC after four hours...
i=1
while [ $i -le 1322 ]
do
g_energy -f traj_x.edr -o ${i}.xvg EOF
${i}
EOF
i=$(($i+1))
done
Still can not figure out the difference, or why one works on one PC and
not the other?
Probably different bash versions, as your Ubuntu could well be more
recent than some version on a server at work. Try bash --version. If so,
poke your system admins to make an up-to-date bash available for you,
even if not as the system default.
Mark
Stephan (in Rainy Switzerland)
Original-Nachricht
Datum: Thu, 5 Jul 2012 22:25:06 +0200
Von: Elton Carvalho elto...@if.usp.br
An: Discussion list for GROMACS users gmx-users@gromacs.org
Betreff: Re: [gmx-users] Re:Shell scripts
On Thu, Jul 5, 2012 at 6:03 PM, lloyd riggs lloyd.ri...@gmx.ch wrote:
Does any one know why, or have some other scripts...
My suggestion would be something in the lines of
#!/bin/bash
for i in $(seq 2121) ; do
g_energy -f traj_${i}.edr -o ${i}.xvg ${i} 0
done
===
Notice the in keyword right after 'i'.
I used a subshell to invoke the program 'seq', which generates a
sequence from 1 to the given argument, so we don't depent om how these
other constructs with ((; ; )) work among different versions of bash.
I also suggest replacing the here-document by a here-string, but
that's personal taste. You may or may not have problems with older
versions of bash
Greetings from a foggy Groningen,
--
Elton Carvalho
Tel.: +55 11 3091-6985/6922
Dept Física dos Materiais e Mecânica
Instituto de Física
Universidade de São Paulo
P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* Please search the archive at
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RE: [gmx-users] Re:Shell scripts
The question was what version of _ bash_ you are using. If this is your login shell a Ctrl-x-v would tell you. Other wise execture /bin/bash and see what you are really using. But what you should have done first is search your particular error message with a search engine of your choice. The first hits with Google for example suggest that you are not using bash at all on that other machine. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of lloyd riggs [lloyd.ri...@gmx.ch] Sent: 06 July 2012 09:32 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Re:Shell scripts Yes, One is a newer 12. version Vs. 11.10. The one PC at home just ignores the for loop, and uses it as an infanite loop over everything while the other complains of syntax (vs.12). The one while loop I posted works on both, and you can also catch averidges well by $ sh script.sh outterminaloutput.txt If somone is interested in averidges. For me they're not that important, except mayby solvent wise. I looked at it with terminal output and realized it went on for 10,000 or more steps/iterations over g_energy but didnt notice before is why it threw me off. Thanks -- Scanned by iCritical. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] specifying the direction of Pull in US
Why not use distance pulling? Then the pull_vec is defined by the vector separating the two pull groups. Best, Erik 6 jul 2012 kl. 08.21 skrev Raj: Hi all, I am working on steered molecular dynamics and In that I would like to pull the ligand ( already in complex with protein) away from the reference amino acid ( which I've selected so that I can direct the ligand to get closure to my desired amino acid residue). Now the thing is when I used VMD to assign the direction, The desired direction of mine is not along the proper x, y, or in Z axis. So my question is how can i specify the direction in a situation like this. I've seen in other discussions people have used pull_vec. How can I get the values of the pull_vec. Kindly help me . thanks in advance -- View this message in context: http://gromacs.5086.n6.nabble.com/specifying-the-direction-of-Pull-in-US-tp4999140.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re:Shell scripts
On 6/07/2012 6:27 PM, lloyd riggs wrote:
Yes,
I was just going over them individually, then cat into a single spread sheet,
which I can use awk to do combos, $1+$2+$16+$233...etc...
With Tsjerk's suggestion, and g_energy -xvg none, you can have such a
spread sheet from one .edr file written in one go.
Mark
Its still alot of files but easier to manipulate with complex .ndx files than
just using g_energy every time...mostly time saving when you exceed 10
simulation or more. Still, having to re-learn some basic awk, gawk, cat and
piping skills from 12 years ago is a pain, but the simple things are invaluable
with gromacs I would say. Without them you would become so bogged one might
hit insanity levels...
Thanks
Stephan Watkins
University of Bern-Inselspital
Original-Nachricht
Datum: Fri, 6 Jul 2012 07:09:16 +0200
Von: Tsjerk Wassenaar tsje...@gmail.com
An: Discussion list for GROMACS users gmx-users@gromacs.org
Betreff: Re: [gmx-users] Re:Shell scripts
Hey,
I'd probably go for something like:
for ((i=1; i...; i++)); do echo $i 0 | g_energy ...; done
Note the additional 0 to make g_energy exit. The (( )) has been in
bash for ages, so that shouldn't be a problem.
I notice that in the working construct you used 'traj_x.edr', while in
the earlier ones, you used 'traj_${i}.edr'. If you try to extract all
energy terms from a single .edr file, you can also use
echo $(seq 1321) 0 | g_energy -f traj_x.edr -o stuff.xvg
and then parse the columns out of the .xvg file.
Cheers,
Tsjerk
On Fri, Jul 6, 2012 at 1:11 AM, Mark Abraham mark.abra...@anu.edu.au
wrote:
On 6/07/2012 7:25 AM, lloyd riggs wrote:
Dear All,
Thank you,
I finally got this to work on the other PC after four hours...
i=1
while [ $i -le 1322 ]
do
g_energy -f traj_x.edr -o ${i}.xvg EOF
${i}
EOF
i=$(($i+1))
done
Still can not figure out the difference, or why one works on one PC and
not the other?
Probably different bash versions, as your Ubuntu could well be more
recent
than some version on a server at work. Try bash --version. If so, poke
your
system admins to make an up-to-date bash available for you, even if not
as
the system default.
Mark
Stephan (in Rainy Switzerland)
Original-Nachricht
Datum: Thu, 5 Jul 2012 22:25:06 +0200
Von: Elton Carvalho elto...@if.usp.br
An: Discussion list for GROMACS users gmx-users@gromacs.org
Betreff: Re: [gmx-users] Re:Shell scripts
On Thu, Jul 5, 2012 at 6:03 PM, lloyd riggs lloyd.ri...@gmx.ch
wrote:
Does any one know why, or have some other scripts...
My suggestion would be something in the lines of
#!/bin/bash
for i in $(seq 2121) ; do
g_energy -f traj_${i}.edr -o ${i}.xvg ${i} 0
done
===
Notice the in keyword right after 'i'.
I used a subshell to invoke the program 'seq', which generates a
sequence from 1 to the given argument, so we don't depent om how these
other constructs with ((; ; )) work among different versions of bash.
I also suggest replacing the here-document by a here-string, but
that's personal taste. You may or may not have problems with older
versions of bash
Greetings from a foggy Groningen,
--
Elton Carvalho
Tel.: +55 11 3091-6985/6922
Dept Física dos Materiais e Mecânica
Instituto de Física
Universidade de São Paulo
P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* Please search the archive at
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interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
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* Only plain text messages are allowed!
*
[gmx-users] Re: specifying the direction of Pull in US
hi , When i applied distance I cant have control over the direction of the pull. The ligand is not exactly pulled along the direction i meant to pull -- View this message in context: http://gromacs.5086.n6.nabble.com/specifying-the-direction-of-Pull-in-US-tp4999140p4999155.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re:Shell scripts
Thanks,
and thanks to Tsjerk.
Stephan
Original-Nachricht
Datum: Fri, 06 Jul 2012 20:04:48 +1000
Von: Mark Abraham mark.abra...@anu.edu.au
An: Discussion list for GROMACS users gmx-users@gromacs.org
Betreff: Re: [gmx-users] Re:Shell scripts
On 6/07/2012 6:27 PM, lloyd riggs wrote:
Yes,
I was just going over them individually, then cat into a single spread
sheet, which I can use awk to do combos, $1+$2+$16+$233...etc...
With Tsjerk's suggestion, and g_energy -xvg none, you can have such a
spread sheet from one .edr file written in one go.
Mark
Its still alot of files but easier to manipulate with complex .ndx files
than just using g_energy every time...mostly time saving when you exceed
10 simulation or more. Still, having to re-learn some basic awk, gawk, cat
and piping skills from 12 years ago is a pain, but the simple things are
invaluable with gromacs I would say. Without them you would become so bogged
one might hit insanity levels...
Thanks
Stephan Watkins
University of Bern-Inselspital
Original-Nachricht
Datum: Fri, 6 Jul 2012 07:09:16 +0200
Von: Tsjerk Wassenaar tsje...@gmail.com
An: Discussion list for GROMACS users gmx-users@gromacs.org
Betreff: Re: [gmx-users] Re:Shell scripts
Hey,
I'd probably go for something like:
for ((i=1; i...; i++)); do echo $i 0 | g_energy ...; done
Note the additional 0 to make g_energy exit. The (( )) has been in
bash for ages, so that shouldn't be a problem.
I notice that in the working construct you used 'traj_x.edr', while in
the earlier ones, you used 'traj_${i}.edr'. If you try to extract all
energy terms from a single .edr file, you can also use
echo $(seq 1321) 0 | g_energy -f traj_x.edr -o stuff.xvg
and then parse the columns out of the .xvg file.
Cheers,
Tsjerk
On Fri, Jul 6, 2012 at 1:11 AM, Mark Abraham mark.abra...@anu.edu.au
wrote:
On 6/07/2012 7:25 AM, lloyd riggs wrote:
Dear All,
Thank you,
I finally got this to work on the other PC after four hours...
i=1
while [ $i -le 1322 ]
do
g_energy -f traj_x.edr -o ${i}.xvg EOF
${i}
EOF
i=$(($i+1))
done
Still can not figure out the difference, or why one works on one PC
and
not the other?
Probably different bash versions, as your Ubuntu could well be more
recent
than some version on a server at work. Try bash --version. If so, poke
your
system admins to make an up-to-date bash available for you, even if
not
as
the system default.
Mark
Stephan (in Rainy Switzerland)
Original-Nachricht
Datum: Thu, 5 Jul 2012 22:25:06 +0200
Von: Elton Carvalho elto...@if.usp.br
An: Discussion list for GROMACS users gmx-users@gromacs.org
Betreff: Re: [gmx-users] Re:Shell scripts
On Thu, Jul 5, 2012 at 6:03 PM, lloyd riggs lloyd.ri...@gmx.ch
wrote:
Does any one know why, or have some other scripts...
My suggestion would be something in the lines of
#!/bin/bash
for i in $(seq 2121) ; do
g_energy -f traj_${i}.edr -o ${i}.xvg ${i} 0
done
===
Notice the in keyword right after 'i'.
I used a subshell to invoke the program 'seq', which generates a
sequence from 1 to the given argument, so we don't depent om how
these
other constructs with ((; ; )) work among different versions of
bash.
I also suggest replacing the here-document by a here-string, but
that's personal taste. You may or may not have problems with older
versions of bash
Greetings from a foggy Groningen,
--
Elton Carvalho
Tel.: +55 11 3091-6985/6922
Dept Física dos Materiais e Mecânica
Instituto de Física
Universidade de São Paulo
P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
--
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Re: [gmx-users] Crashes during protein-ligand simulation
On 7/6/12 1:12 AM, James Starlight wrote: Dear Gromacs users! I have some problems with the simulation of protein-ligand complex embedded in the ccl4-water environment. In addition there are some crystallography waters (xw) embedded in the protein interiour of the protein. I've done equilibration and minimisation of my system and run it in NVT ensemble. Finally I've already simulated this system in the apo form as well as without XW and there were no any problems. In the current case my system always crashed after 10-15 ns of simulation with the errors like Step 6651310, time 13302.6 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.060675, max 1.520945 (between atoms 3132 and 3130) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3148 3147 90.00.1281 0.1483 0.1000 3150 3149 90.00.1084 0.1444 0.1000 3131 3130 90.00.1321 0.1325 0.1000 3132 3130 90.00.1067 0.2521 0.1000 --- Program mdrun_mpi.openmpi, VERSION 4.5.5 Source code file: /tmp/build/gromacs-4.5.5/src/mdlib/constr.c, line: 189 here both atoms 3132 and 3130 are from LIGAND. During data analysing I didnt observed any serious artifacts in that system. In addition RMSD both of protein and ligand were very stable. Finally there are no fluctuations in energy or temperature. So I could understand why this crasshes could occur. If I try to continue this simulation from the crasshed checkpoint my simulation always goon but within next 5-10ns I've always obtain second crash etc. This is the last step from log file DD step 664 vol min/aver 0.758 load imb.: force 1.0% pme mesh/force 0.708 Step Time Lambda 66513300.00.0 Energies (kJ/mol) Angle G96AngleProper Dih. Improper Dih. LJ-14 5.78299e+011.24988e+042.10966e+031.81619e+038.94229e+01 Coulomb-14LJ (SR)LJ (LR) Disper. corr. Coulomb (SR) 4.65481e+048.27301e+04 -6.89535e+03 -2.15286e+03 -7.16722e+05 Coul. recip. PotentialKinetic En. Total Energy Conserved En. -1.72813e+05 -7.52733e+051.46708e+05 -6.06025e+05 -1.37045e+06 Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 3.10968e+02 -9.74796e+012.52993e+021.55693e-05 Could you explain me what could be wrong with that system and what addition data should I provide to help sheld light on that problem ? If the addition of a ligand causes the simulation to crash (and the simulation runs normally in the apo form with and without crystal waters), then that sounds like a problem with the ligand topology or its initial placement. What is the ligand? How did you generate and validate its topology? How did you place it? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: specifying the direction of Pull in US
On 7/6/12 9:52 AM, Raj wrote: hi , When i applied distance I cant have control over the direction of the pull. The ligand is not exactly pulled along the direction i meant to pull You can specify the pull vector using the difference between the COM positions of the pull group and its reference. Set those (x,y,z) values to pull_vec1. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] DNA simulations
Hard to say if this is correct since we don't know what resname A is. Also, we don't know how you manually merged the DNA. Still, you are coming back to the list too early. View your final structure in VMD and see if the ions are in the positions that you desire. Also, make a topology and a .tpr file and run an energy minimization and then a short MD simulation. Does it crash? Chris. -- original message -- Hello Tsjerk, I followed below steps to create a box with DNA and water molecules that are close to it at some distance: 1. g_select -s Test.gro -select 'Close to A resname SOL and within 0.5 of resname A' -on (since I need around DNA molecule, I randomly chose residue A, such that water molecules are around A) 2. trjconv -n index.ndx -f Test.gro -s Test.gro -o Testoutput.gro (Testoutput.gro - has all the water molecules that are close to the A residue at a distance of 0.5 nm) 3. I then merged manually the original file that has DNA molecule dna.gro with the Testoutput.gro. Need some advice if I proceeded in the right direction to have a box that has DNA + water molecules that are close to it. With Regards, Satya. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: bilayers move apart by nanometers upon implementing dihedral restraints on lipid tails
Justin, Vitaly The topology is fine, I double-checked The simulation runs perfectly fine without the restraints. It is not a PBC effect, since the box size along z is 50 nm after a ns or so. Does one need yet another restraint to hold the bilayer together? There has been some discussion about problems with dihedral restrains in the list earlier, but nothing like this. -- View this message in context: http://gromacs.5086.n6.nabble.com/bilayers-move-apart-by-nanometers-upon-implementing-dihedral-restraints-on-lipid-tails-tp4999104p4999160.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Error in Membrane simulations with POPC bilayer
Hi Justin and Anirban, I started a membrane simulation with POPC bilayer after a training with the given KALP peptide and DPPC bilayer. I am following both of your tutorials (mainly the Justin's). I have problem at where I generate a .tpr file for a DPPC (POPC here)-only system using grompp. I see another warning on non-matching number of atoms along with the error that you recommended a safe one. My error is Warning: atom name 3340 in topol_popc.top and popc_128b_H.pdb does not match (C12 - H2) Warning: atom name 3341 in topol_popc.top and popc_128b_H.pdb does not match (C13 - O) Warning: atom name 3342 in topol_popc.top and popc_128b_H.pdb does not match (O14 - H1) Warning: atom name 3343 in topol_popc.top and popc_128b_H.pdb does not match (C15 - H2) Warning: atom name 3344 in topol_popc.top and popc_128b_H.pdb does not match (O16 - O) Warning: atom name 3345 in topol_popc.top and popc_128b_H.pdb does not match (C17 - H1) Warning: atom name 3346 in topol_popc.top and popc_128b_H.pdb does not match (C18 - H2) Warning: atom name 3347 in topol_popc.top and popc_128b_H.pdb does not match (C19 - O) Warning: atom name 3348 in topol_popc.top and popc_128b_H.pdb does not match (C20 - H1) (more than 20 non-matching atom names) WARNING 1 [file topol_popc.top, line 26]: 10708 non-matching atom names atom names from topol_popc.top will be used atom names from popc_128b_H.pdb will be ignored Analysing residue names: There are: 128 Other residues There are: 2460 Water residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 42105.00 Largest charge group radii for Van der Waals: 6.115, 5.932 nm Largest charge group radii for Coulomb: 6.546, 6.115 nm WARNING 2 [file em_st.mdp]: The sum of the two largest charge group radii (12.661407) is larger than rlist (0.90) Calculating fourier grid dimensions for X Y Z Using a fourier grid of 54x56x48, spacing 0.117 0.117 0.119 Estimate for the relative computational load of the PME mesh part: 0.45 This run will generate roughly 34 Mb of data There were 2 warnings --- Program grompp, VERSION 4.5.3 Source code file: grompp.c, line: 1563 Fatal error: Too many warnings (2), grompp terminated. If you are sure all warnings are harmless, use the -maxwarn option. Can any one of you help me move from here? Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/Error-in-Membrane-simulations-with-POPC-bilayer-tp4999161.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error in Membrane simulations with POPC bilayer
On 7/6/12 10:48 AM, J Peterson wrote: Hi Justin and Anirban, I started a membrane simulation with POPC bilayer after a training with the given KALP peptide and DPPC bilayer. I am following both of your tutorials (mainly the Justin's). I have problem at where I generate a .tpr file for a DPPC (POPC here)-only system using grompp. I see another warning on non-matching number of atoms along with the error that you recommended a safe one. My error is Warning: atom name 3340 in topol_popc.top and popc_128b_H.pdb does not match (C12 - H2) Warning: atom name 3341 in topol_popc.top and popc_128b_H.pdb does not match (C13 - O) Warning: atom name 3342 in topol_popc.top and popc_128b_H.pdb does not match (O14 - H1) Warning: atom name 3343 in topol_popc.top and popc_128b_H.pdb does not match (C15 - H2) Warning: atom name 3344 in topol_popc.top and popc_128b_H.pdb does not match (O16 - O) Warning: atom name 3345 in topol_popc.top and popc_128b_H.pdb does not match (C17 - H1) Warning: atom name 3346 in topol_popc.top and popc_128b_H.pdb does not match (C18 - H2) Warning: atom name 3347 in topol_popc.top and popc_128b_H.pdb does not match (C19 - O) Warning: atom name 3348 in topol_popc.top and popc_128b_H.pdb does not match (C20 - H1) (more than 20 non-matching atom names) WARNING 1 [file topol_popc.top, line 26]: 10708 non-matching atom names atom names from topol_popc.top will be used atom names from popc_128b_H.pdb will be ignored Analysing residue names: There are: 128 Other residues There are: 2460 Water residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 42105.00 Largest charge group radii for Van der Waals: 6.115, 5.932 nm Largest charge group radii for Coulomb: 6.546, 6.115 nm WARNING 2 [file em_st.mdp]: The sum of the two largest charge group radii (12.661407) is larger than rlist (0.90) Calculating fourier grid dimensions for X Y Z Using a fourier grid of 54x56x48, spacing 0.117 0.117 0.119 Estimate for the relative computational load of the PME mesh part: 0.45 This run will generate roughly 34 Mb of data There were 2 warnings --- Program grompp, VERSION 4.5.3 Source code file: grompp.c, line: 1563 Fatal error: Too many warnings (2), grompp terminated. If you are sure all warnings are harmless, use the -maxwarn option. Can any one of you help me move from here? The order of your [molecules] directive does not agree with the contents of the coordinate file. What you're seeing is a mismatch between lipid atom names and water (O, H1, and H2). The second warning may or may not be problematic. If your charge groups are split across periodic boundaries, they will be reconstructed properly. If your molecules are already whole, then you have a separate issue. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: bilayers move apart by nanometers upon implementing dihedral restraints on lipid tails
On 7/6/12 10:40 AM, khandelia wrote: Justin, Vitaly The topology is fine, I double-checked The simulation runs perfectly fine without the restraints. It is not a PBC effect, since the box size along z is 50 nm after a ns or so. Does one need yet another restraint to hold the bilayer together? I have never had a need for any restraints to keep a bilayer intact. There has been some discussion about problems with dihedral restrains in the list earlier, but nothing like this. The problem you're observing seems to indicate that your manipulation of the lipid chain causes physical instability. How extensive are the restraints? How many atoms do they involve? You provided an etc in your previous message, so I'm trying to clarify what's going on. Is it even physically possible to orient the lipid chain in such a way? You've got basically all the consecutive dihedrals in a very specific orientation - is that compatible with your system? Can you run a simulation of a single lipid in vacuo using these restraints? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: bilayers move apart by nanometers upon implementing dihedral restraints on lipid tails
I am trying to change all lipid acyl tails to a trans orientation, and thought that restraining all tail dihedrals to 180 should work quickest. I have also tried smaller angles (120, 100) and the effect is the same, leaflets drifting apart. In fact, the 180 restraint does work fine in vacuo for a single lipid. But it is possible that the restraints are too loud. I will play with this for a little bit. The dihedrals of ALL lipid acyl tails in a typical lipid bilayer are being restrained. -- View this message in context: http://gromacs.5086.n6.nabble.com/bilayers-move-apart-by-nanometers-upon-implementing-dihedral-restraints-on-lipid-tails-tp4999104p4999164.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Crashes during protein-ligand simulation
Justin, I've done all steps in accordance to your tutorial. I've already done the same systems with another ligands but had no problem. This time I've made topology of the ligand via ATB server. I've only noticed that some cgnr are too big in that topology . This is the example ADN 3 [ atoms ] ; nr type resnr resid atom cgnr chargemasstotal_charge 1NT1ADN N61 -0.844 14.0067 2 H1ADNH1110.422 1.0080 3 H1ADNH1210.422 1.0080 ; 0.000 4 C1ADN C820.097 12.0110 5HC1ADNH0120.177 1.0080 6NR1ADN N32 -0.642 14.0067 7 C1ADN C420.175 12.0110 8 C1ADN C520.092 12.0110 9NR1ADN N72 -0.556 14.0067 10 C1ADN C620.657 12.0110 ; 0.000 11 C1ADNC5'3 -0.677 12.0110 12 C1ADNC4'30.834 12.0110 13OE1ADNO4'3 -0.248 15.9994 14 C1ADNC1'3 -0.558 12.0110 15 C1ADNC2'30.603 12.0110 16 C1ADNC3'3 -0.212 12.0110 17NR1ADN N930.415 14.0067 18OA1ADNO2'3 -0.606 15.9994 19 H1ADNH0830.482 1.0080 20OA1ADNO3'3 -0.606 15.9994 21 H1ADNH0630.482 1.0080 22OA1ADNO5'3 -0.246 15.9994 23 H1ADNH0330.337 1.0080 ; -0.000 24 C1ADN C240.502 12.0110 25HC1ADNH1040.106 1.0080 26NR1ADN N14 -0.608 14.0067 ; 0.000 ; total charge of the molecule: -0.000 2) To the binding pocket I've inserted this ligand manually by means of superimposition with the reference x-ray structure wich include the same protein in the same conformation with the same ligand. I've done some systems already and that aproach was good :) 3) It's strange that the simulation crashes without any reasons ( the system is very stable during calculated 10-15ns trajectory) Also I suppose that such problems could be with the COM groups this is the example from my mdp comm-grps = SOL_NA_CL XW Protein_CCl4_ADN here XW is the water wich were coppied from X-ray structure . Also in that system Ccl4 is the membrane mimicking layer so I've merged it with protein and ligand in the same group. On the current stage I've tried to make changes in the mdp on comm-grps = System to check if the problem was with that COM motion James 2012/7/6, Justin A. Lemkul jalem...@vt.edu: On 7/6/12 1:12 AM, James Starlight wrote: Dear Gromacs users! I have some problems with the simulation of protein-ligand complex embedded in the ccl4-water environment. In addition there are some crystallography waters (xw) embedded in the protein interiour of the protein. I've done equilibration and minimisation of my system and run it in NVT ensemble. Finally I've already simulated this system in the apo form as well as without XW and there were no any problems. In the current case my system always crashed after 10-15 ns of simulation with the errors like Step 6651310, time 13302.6 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.060675, max 1.520945 (between atoms 3132 and 3130) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3148 3147 90.00.1281 0.1483 0.1000 3150 3149 90.00.1084 0.1444 0.1000 3131 3130 90.00.1321 0.1325 0.1000 3132 3130 90.00.1067 0.2521 0.1000 --- Program mdrun_mpi.openmpi, VERSION 4.5.5 Source code file: /tmp/build/gromacs-4.5.5/src/mdlib/constr.c, line: 189 here both atoms 3132 and 3130 are from LIGAND. During data analysing I didnt observed any serious artifacts in that system. In addition RMSD both of protein and ligand were very stable. Finally there are no fluctuations in energy or temperature. So I could understand why this crasshes could occur. If I try to continue this simulation from the crasshed checkpoint my simulation always goon but within next 5-10ns I've always obtain second crash etc. This is the last step from log file DD step 664 vol min/aver 0.758 load imb.: force 1.0% pme mesh/force 0.708 Step Time Lambda 66513300.00.0 Energies (kJ/mol) Angle G96AngleProper Dih. Improper Dih. LJ-14 5.78299e+011.24988e+042.10966e+031.81619e+03 8.94229e+01 Coulomb-14LJ (SR)LJ (LR) Disper. corr. Coulomb (SR) 4.65481e+048.27301e+04 -6.89535e+03
[gmx-users] Boundary
Hi all, Why does GROMACS just provide PBC for boundary condition? However, LAMPPS as an example provides four kind of boundary: periodic, non-periodic and fixed, non-periodic and shrink-wrapped and non-periodic and shrink-wrapped with a minimum value. PBC makes problem when you want to make movie in VMD, even you add some mirror-wise molecule in each direction. Is there anyway to figure out this problem? Thanks, Dariush -- View this message in context: http://gromacs.5086.n6.nabble.com/Boundary-tp4999167.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Calculation of instantaneous dipole moment through Gromacs
Dear All I want to obtain the instantaneous dipole moment as an output for the OH bond in the pure water molecule simulation. Given the conditions that most of the water models have fixed coordinates and charges during the course of simulation how can I get the same.Is there any possibility of using polarizable water model with flexible charges in GROMACS. -- DeepaK Ojha -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Boundary
On 7/6/12 3:06 PM, dariush wrote: Hi all, Why does GROMACS just provide PBC for boundary condition? However, LAMPPS as an example provides four kind of boundary: periodic, non-periodic and fixed, non-periodic and shrink-wrapped and non-periodic and shrink-wrapped with a minimum value. Gromacs can also do non-periodic systems by setting pbc = no in the .mdp file. A variety of options exist for walls, as well. If there are particular features that users want, they are welcome to implement them and submit them for review in the development code. Otherwise, if no one files a feature request on redmine, the developers aren't going to invest time in the feature unless they need it themselves. I would hazard a guess that 3-D periodic boundary conditions are the most commonly used in simulations of biomolecules. PBC makes problem when you want to make movie in VMD, even you add some mirror-wise molecule in each direction. Is there anyway to figure out this problem? Any trajectory can be fixed for visualization purposes with trjconv. You may need several iterations to achieve the desired effect. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Crashes during protein-ligand simulation
On 7/6/12 2:05 PM, James Starlight wrote: Justin, I've done all steps in accordance to your tutorial. I've already done the same systems with another ligands but had no problem. This time I've made topology of the ligand via ATB server. I've only noticed that some cgnr are too big in that topology . This is the example ADN 3 [ atoms ] ; nr type resnr resid atom cgnr chargemasstotal_charge 1NT1ADN N61 -0.844 14.0067 2 H1ADNH1110.422 1.0080 3 H1ADNH1210.422 1.0080 ; 0.000 4 C1ADN C820.097 12.0110 5HC1ADNH0120.177 1.0080 6NR1ADN N32 -0.642 14.0067 7 C1ADN C420.175 12.0110 8 C1ADN C520.092 12.0110 9NR1ADN N72 -0.556 14.0067 10 C1ADN C620.657 12.0110 ; 0.000 11 C1ADNC5'3 -0.677 12.0110 12 C1ADNC4'30.834 12.0110 13OE1ADNO4'3 -0.248 15.9994 14 C1ADNC1'3 -0.558 12.0110 15 C1ADNC2'30.603 12.0110 16 C1ADNC3'3 -0.212 12.0110 17NR1ADN N930.415 14.0067 18OA1ADNO2'3 -0.606 15.9994 19 H1ADNH0830.482 1.0080 20OA1ADNO3'3 -0.606 15.9994 21 H1ADNH0630.482 1.0080 22OA1ADNO5'3 -0.246 15.9994 23 H1ADNH0330.337 1.0080 ; -0.000 24 C1ADN C240.502 12.0110 25HC1ADNH1040.106 1.0080 26NR1ADN N14 -0.608 14.0067 ; 0.000 ; total charge of the molecule: -0.000 Large charge groups could account for errors in neighbor searching, leading to clashes that cause the simulation to collapse. 2) To the binding pocket I've inserted this ligand manually by means of superimposition with the reference x-ray structure wich include the same protein in the same conformation with the same ligand. I've done some systems already and that aproach was good :) OK, just be ready for reviewers to ask why you didn't do docking ;) 3) It's strange that the simulation crashes without any reasons ( the system is very stable during calculated 10-15ns trajectory) There's always a reason, you just haven't found it yet. The charge group size could indeed be the problem; neighbor searching can fail at any time when some atoms run into one another. Also I suppose that such problems could be with the COM groups this is the example from my mdp comm-grps = SOL_NA_CL XW Protein_CCl4_ADN here XW is the water wich were coppied from X-ray structure . Also in that system Ccl4 is the membrane mimicking layer so I've merged it with protein and ligand in the same group. I see no reason to add such complexity to the system. Breaking the crystal waters into their own COM removal group does not make sense to me. Physically, they are basically part of the protein. On the current stage I've tried to make changes in the mdp on comm-grps = System to check if the problem was with that COM motion And what was the outcome? I see no reason that two COM motion removal groups wouldn't be appropriate (as layers can slide with respect to one another, like a membrane) but three groups does not sound appropriate. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Crashes during protein-ligand simulation
Justin, I've experimented with 2 dirrerent COM groups comm-grps = SOL_NA_CL XW Protein_CCl4_ADN ; 3 groups comm-grps = SOL_NA_CL_XW Protein_CCl4_ADN; 2 groups but the crashes were in both cases after 12- 15ns of simulation this time I've changed to the comm-grps = System and there have not been any crashes yet (to this time I've already calculated addition 20ns after privious crhased simulation using checkpoint file for the last simulation ). But it's posible that it was lucky coincidence :) Could you tell me how I could devide largest group in the above axample into several smaller sub-groups ? Should I do that separation randomly or there are most correct way for that ? (e.g within third cgnr separate all nitrogens and oxygens with corresponded hydrogens in the separate cgrp's from carbons) James 2012/7/6, Justin A. Lemkul jalem...@vt.edu: On 7/6/12 2:05 PM, James Starlight wrote: Justin, I've done all steps in accordance to your tutorial. I've already done the same systems with another ligands but had no problem. This time I've made topology of the ligand via ATB server. I've only noticed that some cgnr are too big in that topology . This is the example ADN 3 [ atoms ] ; nr type resnr resid atom cgnr chargemasstotal_charge 1NT1ADN N61 -0.844 14.0067 2 H1ADNH1110.422 1.0080 3 H1ADNH1210.422 1.0080 ; 0.000 4 C1ADN C820.097 12.0110 5HC1ADNH0120.177 1.0080 6NR1ADN N32 -0.642 14.0067 7 C1ADN C420.175 12.0110 8 C1ADN C520.092 12.0110 9NR1ADN N72 -0.556 14.0067 10 C1ADN C620.657 12.0110 ; 0.000 11 C1ADNC5'3 -0.677 12.0110 12 C1ADNC4'30.834 12.0110 13OE1ADNO4'3 -0.248 15.9994 14 C1ADNC1'3 -0.558 12.0110 15 C1ADNC2'30.603 12.0110 16 C1ADNC3'3 -0.212 12.0110 17NR1ADN N930.415 14.0067 18OA1ADNO2'3 -0.606 15.9994 19 H1ADNH0830.482 1.0080 20OA1ADNO3'3 -0.606 15.9994 21 H1ADNH0630.482 1.0080 22OA1ADNO5'3 -0.246 15.9994 23 H1ADNH0330.337 1.0080 ; -0.000 24 C1ADN C240.502 12.0110 25HC1ADNH1040.106 1.0080 26NR1ADN N14 -0.608 14.0067 ; 0.000 ; total charge of the molecule: -0.000 Large charge groups could account for errors in neighbor searching, leading to clashes that cause the simulation to collapse. 2) To the binding pocket I've inserted this ligand manually by means of superimposition with the reference x-ray structure wich include the same protein in the same conformation with the same ligand. I've done some systems already and that aproach was good :) OK, just be ready for reviewers to ask why you didn't do docking ;) 3) It's strange that the simulation crashes without any reasons ( the system is very stable during calculated 10-15ns trajectory) There's always a reason, you just haven't found it yet. The charge group size could indeed be the problem; neighbor searching can fail at any time when some atoms run into one another. Also I suppose that such problems could be with the COM groups this is the example from my mdp comm-grps = SOL_NA_CL XW Protein_CCl4_ADN here XW is the water wich were coppied from X-ray structure . Also in that system Ccl4 is the membrane mimicking layer so I've merged it with protein and ligand in the same group. I see no reason to add such complexity to the system. Breaking the crystal waters into their own COM removal group does not make sense to me. Physically, they are basically part of the protein. On the current stage I've tried to make changes in the mdp on comm-grps = System to check if the problem was with that COM motion And what was the outcome? I see no reason that two COM motion removal groups wouldn't be appropriate (as layers can slide with respect to one another, like a membrane) but three groups does not sound appropriate. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are
Re: [gmx-users] Crashes during protein-ligand simulation
On 7/6/12 3:56 PM, James Starlight wrote: Justin, I've experimented with 2 dirrerent COM groups comm-grps = SOL_NA_CL XW Protein_CCl4_ADN ; 3 groups comm-grps = SOL_NA_CL_XW Protein_CCl4_ADN; 2 groups but the crashes were in both cases after 12- 15ns of simulation this time I've changed to the comm-grps = System and there have not been any crashes yet (to this time I've already calculated addition 20ns after privious crhased simulation using checkpoint file for the last simulation ). But it's posible that it was lucky coincidence :) Could you tell me how I could devide largest group in the above axample into several smaller sub-groups ? Should I do that separation randomly or there are most correct way for that ? (e.g within third cgnr separate all nitrogens and oxygens with corresponded hydrogens in the separate cgrp's from carbons) Look at existing examples in the force field .rtp file. In general, a charge group consists of a functional group (amine, carboxylate, etc) or small CHn units. Generally there are 2-4 atoms per charge group. There is some discussion on these topics in the manual. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: bilayers move apart by nanometers upon implementing dihedral restraints on lipid tails
I am trying to change all lipid acyl tails to a trans orientation, and thought that restraining all tail dihedrals to 180 should work quickest. I have also tried smaller angles (120, 100) and the effect is the same, leaflets drifting apart. In fact, the 180 restraint does work fine in vacuo for a single lipid. But it is possible that the restraints are too loud. I will play with this for a little bit. The dihedrals of ALL lipid acyl tails in a typical lipid bilayer are being restrained. If the force field is coarse-grained, can the problem perhaps be caused by the inconsistency between the restraint force constant and the time-step? Vitaly Dr. Vitaly V. Chaban, 430 Hutchison Hall Dept. Chemistry, University of Rochester 120 Trustee Road, Rochester, NY 14627-0216 THE UNITED STATES OF AMERICA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Calculation of instantaneous dipole moment
Dear All I want to obtain the instantaneous dipole moment as an output for the OH bond in the pure water molecule simulation. Given the conditions that most of the water models have fixed coordinates and charges during the course of simulation how can I get the same.Is there any possibility of using polarizable water model with flexible charges in GROMACS. -- DeepaK Ojha Crazy! Does your water model have equal partial charges on the oxygen and hydrogen? Dr. Vitaly V. Chaban, 430 Hutchison Hall Dept. Chemistry, University of Rochester 120 Trustee Road, Rochester, NY 14627-0216 THE UNITED STATES OF AMERICA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: specifying the direction of Pull in US
Thanks for ur suggestion Justin, I'm facing trouble in setting that vector, actually I cant figure out how can i set up a vector. Is there any easier way with which i can set up a vector. Thanks -- View this message in context: http://gromacs.5086.n6.nabble.com/specifying-the-direction-of-Pull-in-US-tp4999140p4999177.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
