Re: [gmx-users] rigid tetrahedral molecule
On 2011-04-30 00.38, Mark Abraham wrote:
On 4/30/2011 5:05 AM, Sanku M wrote:
Hi David,
Actually, I had tried to use vsites to make this molecule rigid. I
read the manual section 4.7 as well. But, unfortunately, for a 5-site
tetrahedral geometry I was not able to figure out the right vsite type
I should use. So, I was wondering whether you can provide some input
on the details of how to use virtual sites for a tetrahedral molecule.
It would have been helpful.
David suggested using vsites as well as the multiple-constraints
approach, because the molecule needs to have its degrees of freedom
artificially increased to compensate for the artificial decrease.
A vsite could only work if there was some way to take four atoms for the
force calculation, project them into one (say COM), do the MD update
step on the COM, and project the update back out. I've no idea whether
that's sound or can be implemented, however.
It is quite involved. You need to keep the total mass constant and the
moments of inertia.
For instance for methane one could construct 4 mass-particles M on the
C-H bonds which are connected by 6 constraints. Then you can construct
the virtual positions of C and H based on those four masses. A real
methane has 5x3 degrees of freedom. The above construction has 4 masses
* 3 dof - 6 constraints = 6 degrees of freedom left. This would
therefore yield a correct rigid model.
Mark
Sanku
*From:* David van der Spoel sp...@xray.bmc.uu.se
*To:* Discussion list for GROMACS users gmx-users@gromacs.org
*Sent:* Fri, April 29, 2011 11:46:01 AM
*Subject:* Re: [gmx-users] rigid tetrahedral molecule
On 2011-04-29 17.55, gyorgy.han...@fc.up.pt
mailto:gyorgy.han...@fc.up.pt wrote:
Hi Sanku,
I've read about your problem just now, I don't know if it's already
solved but I had the same problem some weeks ago and I also had a lot of
troubles. But, finally I managed to solve it so maybe my experiences can
be helpful for you:
I think you should use SHAKE instead of LINCS. The manual says somewhere
that LINCS cannot be used when constraining triangles (i.e. angles) but
SHAKE works fine. On the other hand, if you use SHAKE you must switch
from domain decomposition to particle decomposition (if you run your
simulations parallel) just by using -pd when you type mdrun ('domain
decomposition = no' in the mdp file is not enough).
Then you must add as many constraints as degrees of freedom you have, so
9 in your case. In my case it was 15 for the PF6 anion. Maybe it'll work
with less than 9 but in my case I had to add 15 contraints. What I did
was the following:
First I constrained all P-F bonds then I constrained fictious F-F bonds
that I thought would make the molecule rigid. But it wasn't enough. Then
I added some more redundant F-F contraints (up to 15 in total) in a bit
arbitrary way until I found the 'magic combination'.
Now my simulations run perfectly.
Please note that if your rigid molecule has less than 6 degrees of
freedom your temperature will be incorrect!
You can achieve a solution with the right number of d.o.f. by using
vsites as well. How to do this is left as an exercise for the reader.
I hope this helps.
best,
Gyorgy
Citando Sanku M msank...@yahoo.com mailto:msank...@yahoo.com:
Thanks. The molecule was developed as a part of OPLS. The authors
used a
software called BOSS( developed in Bill Jorgensen's lab) . I guess this
softwares have way to perform rigid body motion. There are other
softwares like
DL-POLY which can perform rigid body MD. So, I guess, in those cases,
just
declaring a molecule 'rigid' might be good enough.
But, gromacs does not explicitly do rigid body MD. That's why I was
looking for
a trick .
From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
mailto:gmx-users@gromacs.org
Sent: Wed, April 27, 2011 8:25:05 PM
Subject: Re: [gmx-users] rigid tetrahedral molecule
Sanku M wrote:
Hi,
I am interested in simulating a anionic molecule BF4(-) ( Boron
tetrafluoride). In the paper which developed the parameters for this
molecule,
it is mentioned that it has been used as 'rigid' molecule i.e the
molecule only
has non-bonding interaction but there was no intramolecular motion as
the
geometry was fixed.
I am trying to simulate this molecule in gromacs treating it as
rigid. But, I
was looking for best way to 'rigidify' this molecule.
I was wondering whether using LINCS to constrain all B-F and F-F
bonds will be
good enough . Or, Should I use virtual sites ? If I really need to
use virtual
site, will it be something like TIP5P water model ?
Can someone suggest the best wayout ?
Constraints should do the trick, but probably the best approach is to
simply
contact the authors who developed the model and ask how they did it.
Then you
know
Re: [gmx-users] rigid tetrahedral molecule
Hi Sanku,
I've read about your problem just now, I don't know if it's already
solved but I had the same problem some weeks ago and I also had a lot
of troubles. But, finally I managed to solve it so maybe my
experiences can be helpful for you:
I think you should use SHAKE instead of LINCS. The manual says
somewhere that LINCS cannot be used when constraining triangles (i.e.
angles) but SHAKE works fine. On the other hand, if you use SHAKE you
must switch from domain decomposition to particle decomposition (if
you run your simulations parallel) just by using -pd when you type
mdrun ('domain decomposition = no' in the mdp file is not enough).
Then you must add as many constraints as degrees of freedom you have,
so 9 in your case. In my case it was 15 for the PF6 anion. Maybe it'll
work with less than 9 but in my case I had to add 15 contraints. What
I did was the following:
First I constrained all P-F bonds then I constrained fictious F-F
bonds that I thought would make the molecule rigid. But it wasn't
enough. Then I added some more redundant F-F contraints (up to 15 in
total) in a bit arbitrary way until I found the 'magic combination'.
Now my simulations run perfectly.
I hope this helps.
best,
Gyorgy
Citando Sanku M msank...@yahoo.com:
Thanks. The molecule was developed as a part of OPLS. The authors used a
software called BOSS( developed in Bill Jorgensen's lab) . I guess this
softwares have way to perform rigid body motion. There are other
softwares like
DL-POLY which can perform rigid body MD. So, I guess, in those cases, just
declaring a molecule 'rigid' might be good enough.
But, gromacs does not explicitly do rigid body MD. That's why I was
looking for
a trick .
From: Justin A. Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Wed, April 27, 2011 8:25:05 PM
Subject: Re: [gmx-users] rigid tetrahedral molecule
Sanku M wrote:
Hi,
I am interested in simulating a anionic molecule BF4(-) ( Boron
tetrafluoride). In the paper which developed the parameters for
this molecule,
it is mentioned that it has been used as 'rigid' molecule i.e the
molecule only
has non-bonding interaction but there was no intramolecular motion as the
geometry was fixed.
I am trying to simulate this molecule in gromacs treating it as
rigid. But, I
was looking for best way to 'rigidify' this molecule.
I was wondering whether using LINCS to constrain all B-F and F-F
bonds will be
good enough . Or, Should I use virtual sites ? If I really need to
use virtual
site, will it be something like TIP5P water model ?
Can someone suggest the best wayout ?
Constraints should do the trick, but probably the best approach is to simply
contact the authors who developed the model and ask how they did it.
Then you
know you're exactly reproducing what they did.
-Justin
Sanku
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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
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Re: [gmx-users] rigid tetrahedral molecule
On 2011-04-29 17.55, gyorgy.han...@fc.up.pt wrote:
Hi Sanku,
I've read about your problem just now, I don't know if it's already
solved but I had the same problem some weeks ago and I also had a lot of
troubles. But, finally I managed to solve it so maybe my experiences can
be helpful for you:
I think you should use SHAKE instead of LINCS. The manual says somewhere
that LINCS cannot be used when constraining triangles (i.e. angles) but
SHAKE works fine. On the other hand, if you use SHAKE you must switch
from domain decomposition to particle decomposition (if you run your
simulations parallel) just by using -pd when you type mdrun ('domain
decomposition = no' in the mdp file is not enough).
Then you must add as many constraints as degrees of freedom you have, so
9 in your case. In my case it was 15 for the PF6 anion. Maybe it'll work
with less than 9 but in my case I had to add 15 contraints. What I did
was the following:
First I constrained all P-F bonds then I constrained fictious F-F bonds
that I thought would make the molecule rigid. But it wasn't enough. Then
I added some more redundant F-F contraints (up to 15 in total) in a bit
arbitrary way until I found the 'magic combination'.
Now my simulations run perfectly.
Please note that if your rigid molecule has less than 6 degrees of
freedom your temperature will be incorrect!
You can achieve a solution with the right number of d.o.f. by using
vsites as well. How to do this is left as an exercise for the reader.
I hope this helps.
best,
Gyorgy
Citando Sanku M msank...@yahoo.com:
Thanks. The molecule was developed as a part of OPLS. The authors used a
software called BOSS( developed in Bill Jorgensen's lab) . I guess this
softwares have way to perform rigid body motion. There are other
softwares like
DL-POLY which can perform rigid body MD. So, I guess, in those cases,
just
declaring a molecule 'rigid' might be good enough.
But, gromacs does not explicitly do rigid body MD. That's why I was
looking for
a trick .
From: Justin A. Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Wed, April 27, 2011 8:25:05 PM
Subject: Re: [gmx-users] rigid tetrahedral molecule
Sanku M wrote:
Hi,
I am interested in simulating a anionic molecule BF4(-) ( Boron
tetrafluoride). In the paper which developed the parameters for this
molecule,
it is mentioned that it has been used as 'rigid' molecule i.e the
molecule only
has non-bonding interaction but there was no intramolecular motion as
the
geometry was fixed.
I am trying to simulate this molecule in gromacs treating it as
rigid. But, I
was looking for best way to 'rigidify' this molecule.
I was wondering whether using LINCS to constrain all B-F and F-F
bonds will be
good enough . Or, Should I use virtual sites ? If I really need to
use virtual
site, will it be something like TIP5P water model ?
Can someone suggest the best wayout ?
Constraints should do the trick, but probably the best approach is to
simply
contact the authors who developed the model and ask how they did it.
Then you
know you're exactly reproducing what they did.
-Justin
Sanku
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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 list gmx-users@gromacs.org
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Please search the archive at
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Please don't post (un)subscribe requests to the list. Use the www
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--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
gmx-users mailing listgmx-users@gromacs.org
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Please search the archive at
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Re: [gmx-users] rigid tetrahedral molecule
Citando David van der Spoel sp...@xray.bmc.uu.se:
On 2011-04-29 17.55, gyorgy.han...@fc.up.pt wrote:
Hi Sanku,
I've read about your problem just now, I don't know if it's already
solved but I had the same problem some weeks ago and I also had a lot of
troubles. But, finally I managed to solve it so maybe my experiences can
be helpful for you:
I think you should use SHAKE instead of LINCS. The manual says somewhere
that LINCS cannot be used when constraining triangles (i.e. angles) but
SHAKE works fine. On the other hand, if you use SHAKE you must switch
from domain decomposition to particle decomposition (if you run your
simulations parallel) just by using -pd when you type mdrun ('domain
decomposition = no' in the mdp file is not enough).
Then you must add as many constraints as degrees of freedom you have, so
9 in your case. In my case it was 15 for the PF6 anion. Maybe it'll work
with less than 9 but in my case I had to add 15 contraints. What I did
was the following:
First I constrained all P-F bonds then I constrained fictious F-F bonds
that I thought would make the molecule rigid. But it wasn't enough. Then
I added some more redundant F-F contraints (up to 15 in total) in a bit
arbitrary way until I found the 'magic combination'.
Now my simulations run perfectly.
Please note that if your rigid molecule has less than 6 degrees of
freedom your temperature will be incorrect!
You can achieve a solution with the right number of d.o.f. by using
vsites as well. How to do this is left as an exercise for the reader.
Hmm, indeed, my average temperature differs slightly (0.068%) from the
prescribed value. So you mean only 3N - 12 d.o.f. can be
constrained..? This number seems insufficient to keep the molecule
rigid. I'll try with virtual sites.
Thanks for pulling my attention to this.
Gyorgy
I hope this helps.
best,
Gyorgy
Citando Sanku M msank...@yahoo.com:
Thanks. The molecule was developed as a part of OPLS. The authors used a
software called BOSS( developed in Bill Jorgensen's lab) . I guess this
softwares have way to perform rigid body motion. There are other
softwares like
DL-POLY which can perform rigid body MD. So, I guess, in those cases,
just
declaring a molecule 'rigid' might be good enough.
But, gromacs does not explicitly do rigid body MD. That's why I was
looking for
a trick .
From: Justin A. Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Wed, April 27, 2011 8:25:05 PM
Subject: Re: [gmx-users] rigid tetrahedral molecule
Sanku M wrote:
Hi,
I am interested in simulating a anionic molecule BF4(-) ( Boron
tetrafluoride). In the paper which developed the parameters for this
molecule,
it is mentioned that it has been used as 'rigid' molecule i.e the
molecule only
has non-bonding interaction but there was no intramolecular motion as
the
geometry was fixed.
I am trying to simulate this molecule in gromacs treating it as
rigid. But, I
was looking for best way to 'rigidify' this molecule.
I was wondering whether using LINCS to constrain all B-F and F-F
bonds will be
good enough . Or, Should I use virtual sites ? If I really need to
use virtual
site, will it be something like TIP5P water model ?
Can someone suggest the best wayout ?
Constraints should do the trick, but probably the best approach is to
simply
contact the authors who developed the model and ask how they did it.
Then you
know you're exactly reproducing what they did.
-Justin
Sanku
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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 list gmx-users@gromacs.org
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Please search the archive at
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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
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
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Re: [gmx-users] rigid tetrahedral molecule
Hi David,
Actually, I had tried to use vsites to make this molecule rigid. I read the
manual section 4.7 as well. But, unfortunately, for a 5-site tetrahedral
geometry I was not able to figure out the right vsite type I should use. So, I
was wondering whether you can provide some input on the details of how to use
virtual sites for a tetrahedral molecule. It would have been helpful.
Sanku
From: David van der Spoel sp...@xray.bmc.uu.se
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Fri, April 29, 2011 11:46:01 AM
Subject: Re: [gmx-users] rigid tetrahedral molecule
On 2011-04-29 17.55, gyorgy.han...@fc.up.pt wrote:
Hi Sanku,
I've read about your problem just now, I don't know if it's already
solved but I had the same problem some weeks ago and I also had a lot of
troubles. But, finally I managed to solve it so maybe my experiences can
be helpful for you:
I think you should use SHAKE instead of LINCS. The manual says somewhere
that LINCS cannot be used when constraining triangles (i.e. angles) but
SHAKE works fine. On the other hand, if you use SHAKE you must switch
from domain decomposition to particle decomposition (if you run your
simulations parallel) just by using -pd when you type mdrun ('domain
decomposition = no' in the mdp file is not enough).
Then you must add as many constraints as degrees of freedom you have, so
9 in your case. In my case it was 15 for the PF6 anion. Maybe it'll work
with less than 9 but in my case I had to add 15 contraints. What I did
was the following:
First I constrained all P-F bonds then I constrained fictious F-F bonds
that I thought would make the molecule rigid. But it wasn't enough. Then
I added some more redundant F-F contraints (up to 15 in total) in a bit
arbitrary way until I found the 'magic combination'.
Now my simulations run perfectly.
Please note that if your rigid molecule has less than 6 degrees of
freedom your temperature will be incorrect!
You can achieve a solution with the right number of d.o.f. by using
vsites as well. How to do this is left as an exercise for the reader.
I hope this helps.
best,
Gyorgy
Citando Sanku M msank...@yahoo.com:
Thanks. The molecule was developed as a part of OPLS. The authors used a
software called BOSS( developed in Bill Jorgensen's lab) . I guess this
softwares have way to perform rigid body motion. There are other
softwares like
DL-POLY which can perform rigid body MD. So, I guess, in those cases,
just
declaring a molecule 'rigid' might be good enough.
But, gromacs does not explicitly do rigid body MD. That's why I was
looking for
a trick .
From: Justin A. Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Wed, April 27, 2011 8:25:05 PM
Subject: Re: [gmx-users] rigid tetrahedral molecule
Sanku M wrote:
Hi,
I am interested in simulating a anionic molecule BF4(-) ( Boron
tetrafluoride). In the paper which developed the parameters for this
molecule,
it is mentioned that it has been used as 'rigid' molecule i.e the
molecule only
has non-bonding interaction but there was no intramolecular motion as
the
geometry was fixed.
I am trying to simulate this molecule in gromacs treating it as
rigid. But, I
was looking for best way to 'rigidify' this molecule.
I was wondering whether using LINCS to constrain all B-F and F-F
bonds will be
good enough . Or, Should I use virtual sites ? If I really need to
use virtual
site, will it be something like TIP5P water model ?
Can someone suggest the best wayout ?
Constraints should do the trick, but probably the best approach is to
simply
contact the authors who developed the model and ask how they did it.
Then you
know you're exactly reproducing what they did.
-Justin
Sanku
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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 list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search
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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
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:+46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
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before
Re: [gmx-users] rigid tetrahedral molecule
On 2011-04-29 19.15, gyorgy.han...@fc.up.pt wrote:
Citando David van der Spoel sp...@xray.bmc.uu.se:
On 2011-04-29 17.55, gyorgy.han...@fc.up.pt wrote:
Hi Sanku,
I've read about your problem just now, I don't know if it's already
solved but I had the same problem some weeks ago and I also had a lot of
troubles. But, finally I managed to solve it so maybe my experiences can
be helpful for you:
I think you should use SHAKE instead of LINCS. The manual says somewhere
that LINCS cannot be used when constraining triangles (i.e. angles) but
SHAKE works fine. On the other hand, if you use SHAKE you must switch
from domain decomposition to particle decomposition (if you run your
simulations parallel) just by using -pd when you type mdrun ('domain
decomposition = no' in the mdp file is not enough).
Then you must add as many constraints as degrees of freedom you have, so
9 in your case. In my case it was 15 for the PF6 anion. Maybe it'll work
with less than 9 but in my case I had to add 15 contraints. What I did
was the following:
First I constrained all P-F bonds then I constrained fictious F-F bonds
that I thought would make the molecule rigid. But it wasn't enough. Then
I added some more redundant F-F contraints (up to 15 in total) in a bit
arbitrary way until I found the 'magic combination'.
Now my simulations run perfectly.
Please note that if your rigid molecule has less than 6 degrees of
freedom your temperature will be incorrect!
You can achieve a solution with the right number of d.o.f. by using
vsites as well. How to do this is left as an exercise for the reader.
Hmm, indeed, my average temperature differs slightly (0.068%) from the
prescribed value. So you mean only 3N - 12 d.o.f. can be constrained..?
This number seems insufficient to keep the molecule rigid. I'll try with
virtual sites.
Thanks for pulling my attention to this.
Gyorgy
It is worse than this. If you have e.g. 4 degrees of freedom left after
subtracting the constraints the temperature will be computed as
(Ndf/2) kB T = Ekin
in that case your T will be 6/4 of what it should be, so if you couple
to 200 K, mdrun will print 200K, but the real T will be 300 K (or the
other way around). mdrun prints the number of degrees of freedom to help
you figure this out.
I hope this helps.
best,
Gyorgy
Citando Sanku M msank...@yahoo.com:
Thanks. The molecule was developed as a part of OPLS. The authors
used a
software called BOSS( developed in Bill Jorgensen's lab) . I guess this
softwares have way to perform rigid body motion. There are other
softwares like
DL-POLY which can perform rigid body MD. So, I guess, in those cases,
just
declaring a molecule 'rigid' might be good enough.
But, gromacs does not explicitly do rigid body MD. That's why I was
looking for
a trick .
From: Justin A. Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Wed, April 27, 2011 8:25:05 PM
Subject: Re: [gmx-users] rigid tetrahedral molecule
Sanku M wrote:
Hi,
I am interested in simulating a anionic molecule BF4(-) ( Boron
tetrafluoride). In the paper which developed the parameters for this
molecule,
it is mentioned that it has been used as 'rigid' molecule i.e the
molecule only
has non-bonding interaction but there was no intramolecular motion as
the
geometry was fixed.
I am trying to simulate this molecule in gromacs treating it as
rigid. But, I
was looking for best way to 'rigidify' this molecule.
I was wondering whether using LINCS to constrain all B-F and F-F
bonds will be
good enough . Or, Should I use virtual sites ? If I really need to
use virtual
site, will it be something like TIP5P water model ?
Can someone suggest the best wayout ?
Constraints should do the trick, but probably the best approach is to
simply
contact the authors who developed the model and ask how they did it.
Then you
know you're exactly reproducing what they did.
-Justin
Sanku
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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Dept. of Cell Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
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Re: [gmx-users] rigid tetrahedral molecule
On 4/30/2011 5:05 AM, Sanku M wrote:
Hi David,
Actually, I had tried to use vsites to make this molecule rigid. I
read the manual section 4.7 as well. But, unfortunately, for a 5-site
tetrahedral geometry I was not able to figure out the right vsite type
I should use. So, I was wondering whether you can provide some input
on the details of how to use virtual sites for a tetrahedral molecule.
It would have been helpful.
David suggested using vsites as well as the multiple-constraints
approach, because the molecule needs to have its degrees of freedom
artificially increased to compensate for the artificial decrease.
A vsite could only work if there was some way to take four atoms for the
force calculation, project them into one (say COM), do the MD update
step on the COM, and project the update back out. I've no idea whether
that's sound or can be implemented, however.
Mark
Sanku
*From:* David van der Spoel sp...@xray.bmc.uu.se
*To:* Discussion list for GROMACS users gmx-users@gromacs.org
*Sent:* Fri, April 29, 2011 11:46:01 AM
*Subject:* Re: [gmx-users] rigid tetrahedral molecule
On 2011-04-29 17.55, gyorgy.han...@fc.up.pt
mailto:gyorgy.han...@fc.up.pt wrote:
Hi Sanku,
I've read about your problem just now, I don't know if it's already
solved but I had the same problem some weeks ago and I also had a lot of
troubles. But, finally I managed to solve it so maybe my experiences can
be helpful for you:
I think you should use SHAKE instead of LINCS. The manual says somewhere
that LINCS cannot be used when constraining triangles (i.e. angles) but
SHAKE works fine. On the other hand, if you use SHAKE you must switch
from domain decomposition to particle decomposition (if you run your
simulations parallel) just by using -pd when you type mdrun ('domain
decomposition = no' in the mdp file is not enough).
Then you must add as many constraints as degrees of freedom you have, so
9 in your case. In my case it was 15 for the PF6 anion. Maybe it'll work
with less than 9 but in my case I had to add 15 contraints. What I did
was the following:
First I constrained all P-F bonds then I constrained fictious F-F bonds
that I thought would make the molecule rigid. But it wasn't enough. Then
I added some more redundant F-F contraints (up to 15 in total) in a bit
arbitrary way until I found the 'magic combination'.
Now my simulations run perfectly.
Please note that if your rigid molecule has less than 6 degrees of
freedom your temperature will be incorrect!
You can achieve a solution with the right number of d.o.f. by using
vsites as well. How to do this is left as an exercise for the reader.
I hope this helps.
best,
Gyorgy
Citando Sanku M msank...@yahoo.com mailto:msank...@yahoo.com:
Thanks. The molecule was developed as a part of OPLS. The authors
used a
software called BOSS( developed in Bill Jorgensen's lab) . I guess this
softwares have way to perform rigid body motion. There are other
softwares like
DL-POLY which can perform rigid body MD. So, I guess, in those cases,
just
declaring a molecule 'rigid' might be good enough.
But, gromacs does not explicitly do rigid body MD. That's why I was
looking for
a trick .
From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
mailto:gmx-users@gromacs.org
Sent: Wed, April 27, 2011 8:25:05 PM
Subject: Re: [gmx-users] rigid tetrahedral molecule
Sanku M wrote:
Hi,
I am interested in simulating a anionic molecule BF4(-) ( Boron
tetrafluoride). In the paper which developed the parameters for this
molecule,
it is mentioned that it has been used as 'rigid' molecule i.e the
molecule only
has non-bonding interaction but there was no intramolecular motion as
the
geometry was fixed.
I am trying to simulate this molecule in gromacs treating it as
rigid. But, I
was looking for best way to 'rigidify' this molecule.
I was wondering whether using LINCS to constrain all B-F and F-F
bonds will be
good enough . Or, Should I use virtual sites ? If I really need to
use virtual
site, will it be something like TIP5P water model ?
Can someone suggest the best wayout ?
Constraints should do the trick, but probably the best approach is to
simply
contact the authors who developed the model and ask how they did it.
Then you
know you're exactly reproducing what they did.
-Justin
Sanku
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu http://vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
-- gmx-users mailing list gmx-users@gromacs.org
mailto:gmx-users@gromacs.org
http://lists.gromacs.org/mailman
Re: [gmx-users] rigid tetrahedral molecule
On 4/30/2011 5:05 AM, Sanku M wrote:
Hi David,
Actually, I had tried to use vsites to make this molecule rigid. I
read the manual section 4.7 as well. But, unfortunately, for a 5-site
tetrahedral geometry I was not able to figure out the right vsite type
I should use. So, I was wondering whether you can provide some input
on the details of how to use virtual sites for a tetrahedral molecule.
It would have been helpful.
David suggested using vsites as well as the multiple-constraints
approach, because the molecule needs to have its degrees of freedom
artificially increased to compensate for the artificial decrease.
A vsite could only work if there was some way to take four atoms for the
force calculation, project them into one (say COM), do the MD update
step on the COM, and project the update back out. I've no idea whether
that's sound or can be implemented, however.
Mark
Sanku
*From:* David van der Spoel sp...@xray.bmc.uu.se
*To:* Discussion list for GROMACS users gmx-users@gromacs.org
*Sent:* Fri, April 29, 2011 11:46:01 AM
*Subject:* Re: [gmx-users] rigid tetrahedral molecule
On 2011-04-29 17.55, gyorgy.han...@fc.up.pt
mailto:gyorgy.han...@fc.up.pt wrote:
Hi Sanku,
I've read about your problem just now, I don't know if it's already
solved but I had the same problem some weeks ago and I also had a lot of
troubles. But, finally I managed to solve it so maybe my experiences can
be helpful for you:
I think you should use SHAKE instead of LINCS. The manual says somewhere
that LINCS cannot be used when constraining triangles (i.e. angles) but
SHAKE works fine. On the other hand, if you use SHAKE you must switch
from domain decomposition to particle decomposition (if you run your
simulations parallel) just by using -pd when you type mdrun ('domain
decomposition = no' in the mdp file is not enough).
Then you must add as many constraints as degrees of freedom you have, so
9 in your case. In my case it was 15 for the PF6 anion. Maybe it'll work
with less than 9 but in my case I had to add 15 contraints. What I did
was the following:
First I constrained all P-F bonds then I constrained fictious F-F bonds
that I thought would make the molecule rigid. But it wasn't enough. Then
I added some more redundant F-F contraints (up to 15 in total) in a bit
arbitrary way until I found the 'magic combination'.
Now my simulations run perfectly.
Please note that if your rigid molecule has less than 6 degrees of
freedom your temperature will be incorrect!
You can achieve a solution with the right number of d.o.f. by using
vsites as well. How to do this is left as an exercise for the reader.
I hope this helps.
best,
Gyorgy
Citando Sanku M msank...@yahoo.com mailto:msank...@yahoo.com:
Thanks. The molecule was developed as a part of OPLS. The authors
used a
software called BOSS( developed in Bill Jorgensen's lab) . I guess this
softwares have way to perform rigid body motion. There are other
softwares like
DL-POLY which can perform rigid body MD. So, I guess, in those cases,
just
declaring a molecule 'rigid' might be good enough.
But, gromacs does not explicitly do rigid body MD. That's why I was
looking for
a trick .
From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
mailto:gmx-users@gromacs.org
Sent: Wed, April 27, 2011 8:25:05 PM
Subject: Re: [gmx-users] rigid tetrahedral molecule
Sanku M wrote:
Hi,
I am interested in simulating a anionic molecule BF4(-) ( Boron
tetrafluoride). In the paper which developed the parameters for this
molecule,
it is mentioned that it has been used as 'rigid' molecule i.e the
molecule only
has non-bonding interaction but there was no intramolecular motion as
the
geometry was fixed.
I am trying to simulate this molecule in gromacs treating it as
rigid. But, I
was looking for best way to 'rigidify' this molecule.
I was wondering whether using LINCS to constrain all B-F and F-F
bonds will be
good enough . Or, Should I use virtual sites ? If I really need to
use virtual
site, will it be something like TIP5P water model ?
Can someone suggest the best wayout ?
Constraints should do the trick, but probably the best approach is to
simply
contact the authors who developed the model and ask how they did it.
Then you
know you're exactly reproducing what they did.
-Justin
Sanku
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu http://vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
-- gmx-users mailing list gmx-users@gromacs.org
mailto:gmx-users@gromacs.org
http://lists.gromacs.org/mailman
Re: [gmx-users] rigid tetrahedral molecule
On 4/28/2011 3:49 PM, Sanku M wrote: I went through the LINCS manual . But, I am still struggling with coming up with the idea of putting correct constraint to maintain the rigidity of tetrahedral molecule . I seem to understand from your suggestion that the tetrahedral can be seen as a combination of 4 coupled triangles.( or am I still wrong about it ?) I think it's seven coupled triangles, but that's not a relevant way to think about it. You have 5 atoms, so 3N-6 means 9 degrees of freedom, so you need 9 independent descriptors of relative atomic positions, so 9 constraints. You were trying 10 and 5. Because those constraints form triangles, you may need to take care with LINCS to get a stable simulation. Read up on the details here, I don't remember them. In that case, am I supposed to use multiple settle to keep the molecule in a tetrahedral fashion ? I am sorry but if you can explain it in bit more details, I might get the point. Forget about SETTLE - it was just an example to illustrate that this is not easy to do right. There's a specialised algorithm for rigid water (with three coupled bond constraints) because it is fiddly to get such things right (and fast). Mark *From:* Mark Abraham mark.abra...@anu.edu.au *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Wed, April 27, 2011 11:14:34 PM *Subject:* Re: [gmx-users] rigid tetrahedral molecule On 4/28/2011 1:54 PM, Sanku M wrote: Hi, I tried to keep the geometry of the BF4 fixed by using constraints using lincs. But , unfortunately, my simulation is crashing immediately and if I try minimization with only 2 molecules, it provides a lot of LINCS warning and generate a lot of step*.pdb file . If I try to visualize the minimized snapshot in VMD, it looks like all the distances I tried to constrain decreased drastically. Finally, trying MD run with this minimized configuration results in crashing due to bad contacts. I am sure I am doing something wrong and it might be that my itp file is wrong . So any help will be highly appreciated. Here is the details of what I did. The geometry of the molecule is tetrahedral with B at the center and 4 F atoms is surrounding it in a tetrahedral manner. I first generated a itp file for BF4 which is shown below: I first got the LJ parameters and charges for B and F atom and put them in ffoplsnb.itp file as new atom types opls_1014 and opls_1015 . Initially I tried to put contsraint along all bonds ( i.e among F atoms as well ). But, grompp provides warning that number of constraint is more than number of degrees of freedom. So, I reduced number of constraints by only putting constraint among B and F. But, it did not work either. Sure, you need as many constraints as http://en.wikipedia.org/wiki/Degrees_of_freedom_%28physics_and_chemistry%29 You should also do your homework about using LINCS and coupled triangles of constraints, as I suggested last time. Mark Here is the .itp file I wrote for rigid BF4 . It will be great if someone can point me what I am doing wrong. [ moleculetype ] ; molname nrexcl BF4 3 [ atoms ] #ifdef _FF_OPLS 1 opls_1014 1BF4B 1 0.8276 2 opls_1015 1BF4F1 1 -0.4569 3 opls_1015 1BF4F2 1 -0.4569 4 opls_1015 1BF4F3 1 -0.4569 5 opls_1015 1BF4F4 1 -0.4569 #endif [ constraints ] 1 2 1 0.146 1 3 1 0.146 1 4 1 0.146 1 5 1 0.146 ; 2 3 1 0.238 ; 2 4 1 0.238 ; 2 5 1 0.238 ; 3 4 1 0.238 ; 3 5 1 0.238 ; 4 5 1 0.238 [ exclusions ] 1 2 34 5 2 1 34 5 3 1 24 5 4 1 23 5 5 1 23 4 *From:* Mark Abraham mark.abra...@anu.edu.au *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Wed, April 27, 2011 8:39:23 PM *Subject:* Re: [gmx-users] rigid tetrahedral molecule On 4/28/2011 11:25 AM, Justin A. Lemkul wrote: Sanku M wrote: Hi, I am interested in simulating a anionic molecule BF4(-) ( Boron tetrafluoride). In the paper which developed the parameters for this molecule, it is mentioned that it has been used as 'rigid' molecule i.e the molecule only has non-bonding interaction but there was no intramolecular motion as the geometry was fixed. I am trying to simulate this molecule in gromacs treating it as rigid. But, I was looking for best way to 'rigidify' this molecule. I was wondering whether using LINCS to constrain all B-F and F-F bonds will be good enough . Or, Should I use virtual sites ? If I really need to use virtual site, will it be something like TIP5P water model ? Can someone suggest the best wayout ? Constraints should do
Re: [gmx-users] rigid tetrahedral molecule
Thanks Mark for your comment. But, as far as degrees of freedom is concerned, if there is a tetrahedral molecule as I shown below with atom #1 ( B) being center of the tetrahedron , if we had defined the molecules in terms of bonds and angles ( in stead of constraints ), we would have 4 bonds ( 1-2,1-3,1-4,1-5 ) and 6 angles ( 2-1-3,2-1-4,2-1-5,3-1-4,3-1-5 , 4-1-5 )at 109.45 degrees , thus total ( 4+6)=10 descriptors . In that case, the simulation goes fine . But, then wonder, why, for constraints, we can put only 9 descriptors . Also, I have tried all possible combination to get 9 constraints, but , in each case, gromacs crashes. However, defining 4 bonds and 6 angles using high force-constant lets the simulation go fine. So, on a second thought, I wonder whether defining 9 bond-constraints to get a stable tetrahedral molecule is at all possible. Do I need to go for some sort of compromise, where 4 bonds ( 1-2,1-3,1-4,1-5 ) are defined as constraints and 6 angles with high force-constant are defined to maintain tetrahedral nature ? I am not sure what should be the best possible 9 constraints . 1 opls_1014 1BF4B 1 0.8276 2 opls_1015 1BF4F1 1 -0.4569 3 opls_1015 1BF4F2 1 -0.4569 4 opls_1015 1BF4F3 1 -0.4569 5 opls_1015 1BF4F4 1 -0.4569 From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thu, April 28, 2011 1:00:42 AM Subject: Re: [gmx-users] rigid tetrahedral molecule On 4/28/2011 3:49 PM, Sanku M wrote: I went through the LINCS manual . But, I am still struggling with coming up with the idea of putting correct constraint to maintain the rigidity of tetrahedral molecule .I seem to understand from your suggestion that the tetrahedral can be seen as a combination of 4 coupled triangles.( or am I still wrong about it ?) I think it's seven coupled triangles, but that's not a relevant way to think about it. You have 5 atoms, so 3N-6 means 9 degrees of freedom, so you need 9 independent descriptors of relative atomic positions, so 9 constraints. You were trying 10 and 5. Because those constraints form triangles, you may need to take care with LINCS to get a stable simulation. Read up on the details here, I don't remember them. In that case, am I supposed to use multiple settle to keep the molecule in a tetrahedral fashion ? I am sorry but if you can explain it in bit more details, I might get the point. Forget about SETTLE - it was just an example to illustrate that this is not easy to do right. There's a specialised algorithm for rigid water (with three coupled bond constraints) because it is fiddly to get such things right (and fast). Mark From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wed, April 27, 2011 11:14:34 PM Subject: Re: [gmx-users] rigid tetrahedral molecule On 4/28/2011 1:54 PM, Sanku M wrote: Hi, I tried to keep the geometry of the BF4 fixed by using constraints using lincs. But , unfortunately, my simulation is crashing immediately and if I try minimization with only 2 molecules, it provides a lot of LINCS warning and generate a lot of step*.pdb file . If I try to visualize the minimized snapshot in VMD, it looks like all the distances I tried to constrain decreased drastically. Finally, trying MD run with this minimized configuration results in crashing due to bad contacts. I am sure I am doing something wrong and it might be that my itp file is wrong . So any help will be highly appreciated. Here is the details of what I did. The geometry of the molecule is tetrahedral with B at the center and 4 F atoms is surrounding it in a tetrahedral manner. I first generated a itp file for BF4 which is shown below: I first got the LJ parameters and charges for B and F atom and put them in ffoplsnb.itp file as new atom types opls_1014 and opls_1015 . Initially I tried to put contsraint along all bonds ( i.e among F atoms as well ). But, grompp provides warning that number of constraint is more than number of degrees of freedom. So, I reduced number of constraints by only putting constraint among B and F. But, it did not work either. Sure, you need as many constraints as http://en.wikipedia.org
Re: [gmx-users] rigid tetrahedral molecule
On 4/28/2011 7:07 PM, Sanku M wrote: Thanks Mark for your comment. But, as far as degrees of freedom is concerned, if there is a tetrahedral molecule as I shown below with atom #1 ( B) being center of the tetrahedron , if we had defined the molecules in terms of bonds and angles ( in stead of constraints ), we would have 4 bonds ( 1-2,1-3,1-4,1-5 ) and 6 angles ( 2-1-3,2-1-4,2-1-5,3-1-4,3-1-5 , 4-1-5 )at 109.45 degrees , thus total ( 4+6)=10 descriptors . Different things happen in each case. A redundant but consistent bonded interaction adds (at most) a small contribution to the energies and forces. Consider what the effect of a suitably-constructed H-H-C angle function of a methylene in an equilibrium configuration would be... nothing significant. However, an implementation of coupled constraints so that they are all mutually satisifed in few iterations is hard enough without having to cope with redundancy also. In that case, the simulation goes fine . But, then wonder, why, for constraints, we can put only 9 descriptors . Also, I have tried all possible combination to get 9 constraints, but , in each case, gromacs crashes. However, defining 4 bonds and 6 angles using high force-constant lets the simulation go fine. So, on a second thought, I wonder whether defining 9 bond-constraints to get a stable tetrahedral molecule is at all possible. So you need to read the LINCS and/or SHAKE literature :-) You say these other codes can do rigid-body simulations, so there must be literature on how to do it. Do I need to go for some sort of compromise, where 4 bonds ( 1-2,1-3,1-4,1-5 ) are defined as constraints and 6 angles with high force-constant are defined to maintain tetrahedral nature ? Maybe. I am not sure what should be the best possible 9 constraints . Don't know. I would start trying four B-F bonds and five F-F bonds, but it shouldn't matter. Mark 1 opls_1014 1BF4B 1 0.8276 2 opls_1015 1BF4F1 1 -0.4569 3 opls_1015 1BF4F2 1 -0.4569 4 opls_1015 1BF4F3 1 -0.4569 5 opls_1015 1BF4F4 1 -0.4569 *From:* Mark Abraham mark.abra...@anu.edu.au *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Thu, April 28, 2011 1:00:42 AM *Subject:* Re: [gmx-users] rigid tetrahedral molecule On 4/28/2011 3:49 PM, Sanku M wrote: I went through the LINCS manual . But, I am still struggling with coming up with the idea of putting correct constraint to maintain the rigidity of tetrahedral molecule . I seem to understand from your suggestion that the tetrahedral can be seen as a combination of 4 coupled triangles.( or am I still wrong about it ?) I think it's seven coupled triangles, but that's not a relevant way to think about it. You have 5 atoms, so 3N-6 means 9 degrees of freedom, so you need 9 independent descriptors of relative atomic positions, so 9 constraints. You were trying 10 and 5. Because those constraints form triangles, you may need to take care with LINCS to get a stable simulation. Read up on the details here, I don't remember them. In that case, am I supposed to use multiple settle to keep the molecule in a tetrahedral fashion ? I am sorry but if you can explain it in bit more details, I might get the point. Forget about SETTLE - it was just an example to illustrate that this is not easy to do right. There's a specialised algorithm for rigid water (with three coupled bond constraints) because it is fiddly to get such things right (and fast). Mark *From:* Mark Abraham mark.abra...@anu.edu.au *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Wed, April 27, 2011 11:14:34 PM *Subject:* Re: [gmx-users] rigid tetrahedral molecule On 4/28/2011 1:54 PM, Sanku M wrote: Hi, I tried to keep the geometry of the BF4 fixed by using constraints using lincs. But , unfortunately, my simulation is crashing immediately and if I try minimization with only 2 molecules, it provides a lot of LINCS warning and generate a lot of step*.pdb file . If I try to visualize the minimized snapshot in VMD, it looks like all the distances I tried to constrain decreased drastically. Finally, trying MD run with this minimized configuration results in crashing due to bad contacts. I am sure I am doing something wrong and it might be that my itp file is wrong . So any help will be highly appreciated. Here is the details of what I did. The geometry of the molecule is tetrahedral with B at the center and 4 F atoms is surrounding it in a tetrahedral manner. I first generated a itp file for BF4 which is shown below: I first got the LJ parameters and charges for B and F atom and put them in ffoplsnb.itp file as new atom types opls_1014
Re: [gmx-users] rigid tetrahedral molecule
Sanku M wrote: Thanks Mark for your comment. But, as far as degrees of freedom is concerned, if there is a tetrahedral molecule as I shown below with atom #1 ( B) being center of the tetrahedron , if we had defined the molecules in terms of bonds and angles ( in stead of constraints ), we would have 4 bonds ( 1-2,1-3,1-4,1-5 ) and 6 angles ( 2-1-3,2-1-4,2-1-5,3-1-4,3-1-5 , 4-1-5 )at 109.45 degrees , thus total ( 4+6)=10 descriptors . In that case, the simulation goes fine . But, then wonder, why, for constraints, we can put only 9 descriptors . Also, I have tried all possible combination to get 9 constraints, but , in each case, gromacs crashes. However, defining 4 bonds and 6 angles using high force-constant lets the simulation go fine. So, on a second thought, I wonder whether defining 9 bond-constraints to get a stable tetrahedral molecule is at all possible. Do I need to go for some sort of compromise, where 4 bonds ( 1-2,1-3,1-4,1-5 ) are defined as constraints and 6 angles with high force-constant are defined to maintain tetrahedral nature ? I am not sure what should be the best possible 9 constraints . For an example, see the CHCL3 definition in the Gromos96 53A6 force field. -Justin 1 opls_1014 1BF4B 1 0.8276 2 opls_1015 1BF4F1 1 -0.4569 3 opls_1015 1BF4F2 1 -0.4569 4 opls_1015 1BF4F3 1 -0.4569 5 opls_1015 1BF4F4 1 -0.4569 *From:* Mark Abraham mark.abra...@anu.edu.au *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Thu, April 28, 2011 1:00:42 AM *Subject:* Re: [gmx-users] rigid tetrahedral molecule On 4/28/2011 3:49 PM, Sanku M wrote: I went through the LINCS manual . But, I am still struggling with coming up with the idea of putting correct constraint to maintain the rigidity of tetrahedral molecule . I seem to understand from your suggestion that the tetrahedral can be seen as a combination of 4 coupled triangles.( or am I still wrong about it ?) I think it's seven coupled triangles, but that's not a relevant way to think about it. You have 5 atoms, so 3N-6 means 9 degrees of freedom, so you need 9 independent descriptors of relative atomic positions, so 9 constraints. You were trying 10 and 5. Because those constraints form triangles, you may need to take care with LINCS to get a stable simulation. Read up on the details here, I don't remember them. In that case, am I supposed to use multiple settle to keep the molecule in a tetrahedral fashion ? I am sorry but if you can explain it in bit more details, I might get the point. Forget about SETTLE - it was just an example to illustrate that this is not easy to do right. There's a specialised algorithm for rigid water (with three coupled bond constraints) because it is fiddly to get such things right (and fast). Mark *From:* Mark Abraham mark.abra...@anu.edu.au *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Wed, April 27, 2011 11:14:34 PM *Subject:* Re: [gmx-users] rigid tetrahedral molecule On 4/28/2011 1:54 PM, Sanku M wrote: Hi, I tried to keep the geometry of the BF4 fixed by using constraints using lincs. But , unfortunately, my simulation is crashing immediately and if I try minimization with only 2 molecules, it provides a lot of LINCS warning and generate a lot of step*.pdb file . If I try to visualize the minimized snapshot in VMD, it looks like all the distances I tried to constrain decreased drastically. Finally, trying MD run with this minimized configuration results in crashing due to bad contacts. I am sure I am doing something wrong and it might be that my itp file is wrong . So any help will be highly appreciated. Here is the details of what I did. The geometry of the molecule is tetrahedral with B at the center and 4 F atoms is surrounding it in a tetrahedral manner. I first generated a itp file for BF4 which is shown below: I first got the LJ parameters and charges for B and F atom and put them in ffoplsnb.itp file as new atom types opls_1014 and opls_1015 . Initially I tried to put contsraint along all bonds ( i.e among F atoms as well ). But, grompp provides warning that number of constraint is more than number of degrees of freedom. So, I reduced number of constraints by only putting constraint among B and F. But, it did not work either. Sure, you need as many constraints as http://en.wikipedia.org/wiki/Degrees_of_freedom_%28physics_and_chemistry%29 You should also do your homework about using LINCS and coupled triangles of constraints, as I suggested last time. Mark Here is the .itp file I wrote for rigid BF4 . It will be great if someone can point me what I am doing wrong
[gmx-users] rigid tetrahedral molecule
Hi, I am interested in simulating a anionic molecule BF4(-) ( Boron tetrafluoride). In the paper which developed the parameters for this molecule, it is mentioned that it has been used as 'rigid' molecule i.e the molecule only has non-bonding interaction but there was no intramolecular motion as the geometry was fixed. I am trying to simulate this molecule in gromacs treating it as rigid. But, I was looking for best way to 'rigidify' this molecule. I was wondering whether using LINCS to constrain all B-F and F-F bonds will be good enough . Or, Should I use virtual sites ? If I really need to use virtual site, will it be something like TIP5P water model ? Can someone suggest the best wayout ? Sanku-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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] rigid tetrahedral molecule
Sanku M wrote: Hi, I am interested in simulating a anionic molecule BF4(-) ( Boron tetrafluoride). In the paper which developed the parameters for this molecule, it is mentioned that it has been used as 'rigid' molecule i.e the molecule only has non-bonding interaction but there was no intramolecular motion as the geometry was fixed. I am trying to simulate this molecule in gromacs treating it as rigid. But, I was looking for best way to 'rigidify' this molecule. I was wondering whether using LINCS to constrain all B-F and F-F bonds will be good enough . Or, Should I use virtual sites ? If I really need to use virtual site, will it be something like TIP5P water model ? Can someone suggest the best wayout ? Constraints should do the trick, but probably the best approach is to simply contact the authors who developed the model and ask how they did it. Then you know you're exactly reproducing what they did. -Justin Sanku -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 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] rigid tetrahedral molecule
On 4/28/2011 11:25 AM, Justin A. Lemkul wrote: Sanku M wrote: Hi, I am interested in simulating a anionic molecule BF4(-) ( Boron tetrafluoride). In the paper which developed the parameters for this molecule, it is mentioned that it has been used as 'rigid' molecule i.e the molecule only has non-bonding interaction but there was no intramolecular motion as the geometry was fixed. I am trying to simulate this molecule in gromacs treating it as rigid. But, I was looking for best way to 'rigidify' this molecule. I was wondering whether using LINCS to constrain all B-F and F-F bonds will be good enough . Or, Should I use virtual sites ? If I really need to use virtual site, will it be something like TIP5P water model ? Can someone suggest the best wayout ? Constraints should do the trick, but probably the best approach is to simply contact the authors who developed the model and ask how they did it. Then you know you're exactly reproducing what they did. Yep. Be aware that the coupled constraints make life tricky, and you should read up in the manual and literature for how best to use P-LINCS in such cases. Algorithms like SETTLE for rigid water exist for a reason... Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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] rigid tetrahedral molecule
Thanks. The molecule was developed as a part of OPLS. The authors used a software called BOSS( developed in Bill Jorgensen's lab) . I guess this softwares have way to perform rigid body motion. There are other softwares like DL-POLY which can perform rigid body MD. So, I guess, in those cases, just declaring a molecule 'rigid' might be good enough. But, gromacs does not explicitly do rigid body MD. That's why I was looking for a trick . From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wed, April 27, 2011 8:25:05 PM Subject: Re: [gmx-users] rigid tetrahedral molecule Sanku M wrote: Hi, I am interested in simulating a anionic molecule BF4(-) ( Boron tetrafluoride). In the paper which developed the parameters for this molecule, it is mentioned that it has been used as 'rigid' molecule i.e the molecule only has non-bonding interaction but there was no intramolecular motion as the geometry was fixed. I am trying to simulate this molecule in gromacs treating it as rigid. But, I was looking for best way to 'rigidify' this molecule. I was wondering whether using LINCS to constrain all B-F and F-F bonds will be good enough . Or, Should I use virtual sites ? If I really need to use virtual site, will it be something like TIP5P water model ? Can someone suggest the best wayout ? Constraints should do the trick, but probably the best approach is to simply contact the authors who developed the model and ask how they did it. Then you know you're exactly reproducing what they did. -Justin Sanku -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 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 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] rigid tetrahedral molecule
On 4/28/2011 1:54 PM, Sanku M wrote: Hi, I tried to keep the geometry of the BF4 fixed by using constraints using lincs. But , unfortunately, my simulation is crashing immediately and if I try minimization with only 2 molecules, it provides a lot of LINCS warning and generate a lot of step*.pdb file . If I try to visualize the minimized snapshot in VMD, it looks like all the distances I tried to constrain decreased drastically. Finally, trying MD run with this minimized configuration results in crashing due to bad contacts. I am sure I am doing something wrong and it might be that my itp file is wrong . So any help will be highly appreciated. Here is the details of what I did. The geometry of the molecule is tetrahedral with B at the center and 4 F atoms is surrounding it in a tetrahedral manner. I first generated a itp file for BF4 which is shown below: I first got the LJ parameters and charges for B and F atom and put them in ffoplsnb.itp file as new atom types opls_1014 and opls_1015 . Initially I tried to put contsraint along all bonds ( i.e among F atoms as well ). But, grompp provides warning that number of constraint is more than number of degrees of freedom. So, I reduced number of constraints by only putting constraint among B and F. But, it did not work either. Sure, you need as many constraints as http://en.wikipedia.org/wiki/Degrees_of_freedom_(physics_and_chemistry) http://en.wikipedia.org/wiki/Degrees_of_freedom_%28physics_and_chemistry%29 You should also do your homework about using LINCS and coupled triangles of constraints, as I suggested last time. Mark Here is the .itp file I wrote for rigid BF4 . It will be great if someone can point me what I am doing wrong. [ moleculetype ] ; molname nrexcl BF4 3 [ atoms ] #ifdef _FF_OPLS 1 opls_1014 1BF4B 1 0.8276 2 opls_1015 1BF4F1 1 -0.4569 3 opls_1015 1BF4F2 1 -0.4569 4 opls_1015 1BF4F3 1 -0.4569 5 opls_1015 1BF4F4 1 -0.4569 #endif [ constraints ] 1 2 1 0.146 1 3 1 0.146 1 4 1 0.146 1 5 1 0.146 ; 2 3 1 0.238 ; 2 4 1 0.238 ; 2 5 1 0.238 ; 3 4 1 0.238 ; 3 5 1 0.238 ; 4 5 1 0.238 [ exclusions ] 1 2 34 5 2 1 34 5 3 1 24 5 4 1 23 5 5 1 23 4 *From:* Mark Abraham mark.abra...@anu.edu.au *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Wed, April 27, 2011 8:39:23 PM *Subject:* Re: [gmx-users] rigid tetrahedral molecule On 4/28/2011 11:25 AM, Justin A. Lemkul wrote: Sanku M wrote: Hi, I am interested in simulating a anionic molecule BF4(-) ( Boron tetrafluoride). In the paper which developed the parameters for this molecule, it is mentioned that it has been used as 'rigid' molecule i.e the molecule only has non-bonding interaction but there was no intramolecular motion as the geometry was fixed. I am trying to simulate this molecule in gromacs treating it as rigid. But, I was looking for best way to 'rigidify' this molecule. I was wondering whether using LINCS to constrain all B-F and F-F bonds will be good enough . Or, Should I use virtual sites ? If I really need to use virtual site, will it be something like TIP5P water model ? Can someone suggest the best wayout ? Constraints should do the trick, but probably the best approach is to simply contact the authors who developed the model and ask how they did it. Then you know you're exactly reproducing what they did. Yep. Be aware that the coupled constraints make life tricky, and you should read up in the manual and literature for how best to use P-LINCS in such cases. Algorithms like SETTLE for rigid water exist for a reason... Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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 mailto: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 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] rigid tetrahedral molecule
I went through the LINCS manual . But, I am still struggling with coming up with the idea of putting correct constraint to maintain the rigidity of tetrahedral molecule . I seem to understand from your suggestion that the tetrahedral can be seen as a combination of 4 coupled triangles.( or am I still wrong about it ?) In that case, am I supposed to use multiple settle to keep the molecule in a tetrahedral fashion ? I am sorry but if you can explain it in bit more details, I might get the point. From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wed, April 27, 2011 11:14:34 PM Subject: Re: [gmx-users] rigid tetrahedral molecule On 4/28/2011 1:54 PM, Sanku M wrote: Hi, I tried to keep the geometry of the BF4 fixed by using constraints using lincs. But , unfortunately, my simulation is crashing immediately and if I try minimization with only 2 molecules, it provides a lot of LINCS warning and generate a lot of step*.pdb file . If I try to visualize the minimized snapshot in VMD, it looks like all the distances I tried to constrain decreased drastically. Finally, trying MD run with this minimized configuration results in crashing due to bad contacts. I am sure I am doing something wrong and it might be that my itp file is wrong . So any help will be highly appreciated. Here is the details of what I did. The geometry of the molecule is tetrahedral with B at the center and 4 F atoms is surrounding it in a tetrahedral manner. I first generated a itp file for BF4 which is shown below: I first got the LJ parameters and charges for B and F atom and put them in ffoplsnb.itp file as new atom types opls_1014 and opls_1015 . Initially I tried to put contsraint along all bonds ( i.e among F atoms as well ). But, grompp provides warning that number of constraint is more than number of degrees of freedom. So, I reduced number of constraints by only putting constraint among B and F. But, it did not work either. Sure, you need as many constraints as http://en.wikipedia.org/wiki/Degrees_of_freedom_%28physics_and_chemistry%29 You should also do your homework about using LINCS and coupled triangles of constraints, as I suggested last time. Mark Here is the .itp file I wrote for rigid BF4 . It will be great if someone can point me what I am doing wrong. [ moleculetype ] ; molname nrexcl BF4 3 [ atoms ] #ifdef _FF_OPLS 1 opls_1014 1BF4B 1 0.8276 2 opls_1015 1BF4F1 1 -0.4569 3 opls_1015 1BF4F2 1 -0.4569 4 opls_1015 1BF4F3 1 -0.4569 5 opls_1015 1BF4F4 1 -0.4569 #endif [ constraints ] 1 2 1 0.146 1 3 1 0.146 1 4 1 0.146 1 5 1 0.146 ; 2 3 1 0.238 ; 2 4 1 0.238 ; 2 5 1 0.238 ; 3 4 1 0.238 ; 3 5 1 0.238 ; 4 5 1 0.238 [ exclusions ] 1 2 34 5 2 1 34 5 3 1 24 5 4 1 23 5 5 1 23 4 From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wed, April 27, 2011 8:39:23 PM Subject: Re: [gmx-users] rigid tetrahedral molecule On 4/28/2011 11:25 AM, Justin A. Lemkul wrote: Sanku M wrote: Hi, I am interested in simulating a anionic molecule BF4(-) ( Boron tetrafluoride). In the paper which developed the parameters for this molecule, it is mentioned that it has been used as 'rigid' molecule i.e the molecule only has non-bonding interaction but there was no intramolecular motion as the geometry was fixed. I am trying to simulate this molecule in gromacs treating it as rigid. But, I was looking for best way to 'rigidify' this molecule. I was wondering whether using LINCS to constrain all B-F and F-F bonds will be good enough . Or, Should I use virtual sites ? If I really need to use virtual site, will it be something like TIP5P water model ? Can someone suggest the best wayout ? Constraints should do the trick, but probably the best approach is to simply contact the authors who developed the model and ask how they did it. Then you know you're exactly reproducing what they did. Yep. Be aware that the coupled constraints make life tricky, and you should read up in the manual and literature for how best to use P-LINCS in such cases. Algorithms like SETTLE
