[gmx-users] R: Md continuation with cpt

[Anna Marabotti]

 Dear gmx-users, Mark and Justin,
thank you for your previous and precious support, but now I have another
doubt. As I told you previously, looking at my trajectory I can see that the
protein is still not fully equilibrated, then I would like to continue the
simulation. However, now if I use tpbconv with -extend and mdrun with -cpi,
I'm forced to use the file .tpr that still contains the erroneous
information about the init_step. On the other hand, if I make a new .tpr
file using an .mdp file with init_step = 0, this will no longer be an exact
continuation (at least I think so). Is there a way to manage this problem? I
see that in tpbconv options there is the flag -nsteps, but I don't know if
(and how) it would be a good idea to use it for this problem.

BTW, I tried to recover my .edr file using the command 
eneconv -e 1.edr 2.edr 3.edr 4.edr -o full.edr -settime
as Mark suggested, and using option 0 for the first file, and "l" to set the
time as the continuation from the end of the previous one, but it didn't
work: I obtained a new .edr file still with the error message "timestep
don't match", and when I transformed it into a .xvg file, there was the same
error as previously: only few points were saved, at 0, 60, 160, 260, 5000,
1 and 15000 ps (instead of 140, 200, 300 400, 5140, 10140, 15140 ps as
previously). I don't know if I used it incorrectly. However, using the .trr
files and the option mdrun -rerun, I obtained a new .edr file in which I
could obtain a "coarse-grained" (the sampling was every 5 steps) .edr
file in which I could see that the energy values are stable. Any suggestions
on this point?

Many thanks and best regards
Anna

-Messaggio originale-
Da: Anna Marabotti [mailto:anna.marabo...@isa.cnr.it] 
Inviato: giovedì 28 aprile 2011 16.55
A: 'gmx-users@gromacs.org'
Oggetto: R: Md continuation with cpt

Dear Mark,
thank you very much for your hint. It's a relief to know that I haven't to
redo the simulation!
>From now on I will set init_step = 0 for my simulations.
Anna

--

Message: 3
Date: Thu, 28 Apr 2011 20:56:00 +1000
From: Mark Abraham 
Subject: Re: [gmx-users] R: Md continuation with cpt
To: Discussion list for GROMACS users 
Message-ID: <4db947c0.90...@anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

On 4/28/2011 5:47 PM, Anna Marabotti wrote:
> Dear Justin,
> thank you for your precious help. Yes, the problem is what you say and
what
> I was suspecting too (but I was not sure, that's why I was searching for a
> confirmation of my suspects from more expert people). The problem however
is
> present in the NVT->NPT junction. My .mdp settings were
> NVT:
> tinit = 0
> init_step = 0
> nsteps = 1
> dt = 0.002
>
> NPT
> tinit = 0
> init_step = 2 (instead of 1)
> nsteps = 5
> dt = 0.002
>
> That's why I had a last NPT step of 7 instead of 6, and that's why
I
> set init_step = 7 in the production MD.
> What you are saying also explains the anomalous behaviour of the xvg file
> created from the .edr file, in which only few points were saved, therefore
> the graphs created with xmgrace contain only 7 values (at 140, 200, 300
400,
> 5140, 10140, 15140 ps).
> I always set nstep identical to the last step of the previous
equilibration
> MD because I understood that it was necessary to do it to obtain an exact
> continuation, there is no other special reason.

The label on the step number has nothing to do with the physics. 
Instructions for restarts preserving simulation ensembles are on the 
website. IIRC init_step refers to the label given to the step whose time 
is tinit (see manual 7.3.3), and haphazardly changing only one of them 
might lead to such problems.

>   Since you are saying that
> this is no (longer?) necessary (I'm currently using Gromacs 4.0.7 on this
> machine), I'm very happy to set always nsteps = 0, to avoid future
mistakes.

Do that.

> In the meantime, what I have to do? I had a look at the .xtc files with
> gmxcheck and apparently all is fine, with no error messages, also the
> trajectory seems to be coherent with my expectations. I run g_rms and
> g_gyrate and the behaviour of the systems appears "normal" (apart from the
> fact that the system is not stabilized yet, so I have to continue the
> trajectory). I can provide you (offlist) the .xvg graphs, if you want.
>
> Based on these data, what do you suggest to do? Do you think that the
> simulation could be considered formally correct (i.e. this is only a
problem
> of erroneous writing of .edr file) or do I have to repeat
> (AARRH) the whole simulation? I saw in the manual that the
> option -rerun of mdrun command allows to recalculate forces and energies
> from a trajectory file, do you think that I can use it to obtain a new
.edr
> file?
>

If it's just a problem of labelling the frames, then trjcat and eneconv 
have -settime to deal with these kinds of scenarios.

Mark



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Re: [gmx-users] R: Md continuation with cpt

[Mark Abraham]

On 4/29/2011 6:45 PM, Anna Marabotti wrote:

  Dear gmx-users, Mark and Justin,
thank you for your previous and precious support, but now I have another
doubt. As I told you previously, looking at my trajectory I can see that the
protein is still not fully equilibrated, then I would like to continue the
simulation. However, now if I use tpbconv with -extend and mdrun with -cpi,
I'm forced to use the file .tpr that still contains the erroneous
information about the init_step. On the other hand, if I make a new .tpr
file using an .mdp file with init_step = 0, this will no longer be an exact
continuation (at least I think so). Is there a way to manage this problem? I
see that in tpbconv options there is the flag -nsteps, but I don't know if
(and how) it would be a good idea to use it for this problem.


Make a new .tpr with grompp -t. See 
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations



BTW, I tried to recover my .edr file using the command
eneconv -e 1.edr 2.edr 3.edr 4.edr -o full.edr -settime
as Mark suggested, and using option 0 for the first file, and "l" to set the
time as the continuation from the end of the previous one, but it didn't
work: I obtained a new .edr file still with the error message "timestep
don't match", and when I transformed it into a .xvg file, there was the same
error as previously: only few points were saved, at 0, 60, 160, 260, 5000,
1 and 15000 ps (instead of 140, 200, 300 400, 5140, 10140, 15140 ps as
previously). I don't know if I used it incorrectly. However, using the .trr
files and the option mdrun -rerun, I obtained a new .edr file in which I
could obtain a "coarse-grained" (the sampling was every 5 steps) .edr
file in which I could see that the energy values are stable. Any suggestions
on this point?


Try to concatenate only two files, while working out how it should be 
done. Simplify, succeed, and then introduce more complexity.


See if you can use eneconv -f in.edr -o out.edr -settime (or something) 
to correct that file before attempting to concatenate in a later stage.


Mark



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[gmx-users] g_rmsdist error hi (-1000.000000) <= lo (0.000000)

[Andrea Carotti]

Hi all,
I'm trying to use this tool with the following command (selecting the 
backbone atoms: 366 atoms in total)

 g_rmsdist -s 1.pdb -f traj_fit.trr -rms

But the programs stop with the following error:
Program g_rmsdist, VERSION 4.5.4
Source code file: matio.c, line: 953

Fatal error:
hi (-1000.00) <= lo (0.00)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Could you please help me?
Thanks
Andrea



--



Andrea Carotti
Dipartimento di Chimica e Tecnologia del Farmaco
Università di Perugia
Via del Liceo, 1
06123 Perugia, Italy
phone: +39 075 585 5169
fax: +39 075 585 5161
www http://gryphus.chimfarm.unipg.it
personal www http://iris.chimfarm.unipg.it/users/andcar


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Re: [gmx-users] g_rmsdist error hi (-1000.000000) <= lo (0.000000)

[David van der Spoel]

On 2011-04-29 16.32, Andrea Carotti wrote:

Hi all,
I'm trying to use this tool with the following command (selecting the
backbone atoms: 366 atoms in total)
g_rmsdist -s 1.pdb -f traj_fit.trr -rms

But the programs stop with the following error:
Program g_rmsdist, VERSION 4.5.4
Source code file: matio.c, line: 953

Fatal error:
hi (-1000.00) <= lo (0.00)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Could you please help me?
Thanks
Andrea




all your rmsd have the same value. probably broken pdb or trr.

--
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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[gmx-users] unexpected results with stochastic dynamics

[Michael Brunsteiner]

Hi everybody,

I just ran a number of simulations with two large and roughly spherical 
molecules
in a primitive model electrolyte (epsilon=80), they are constrained to the 
z-axes and
i calculate the PMF using the pull code restraining the distance between the
two molecules. integration is done with langevin dynamcs (gmx-4.5.3)

what i see is this: I start several runs all with the same initial orientations 
of the two
molecules only the distance varies, the dynamics seems to go well, but when i 
compare

the FINAL ORIENTATIONS of the two molecules after multiple runs at different
distances they are NEARLY THE SAME not matter which distance i choose.

below is the relevant part of my mdp file:


integrator   = sd
tau_t    = 2.0
ref_t    = 300
gen_vel  = yes
gen_temp = 240.0
gen_seed = xxx ; this varies
tc_grps  = System
nsteps   = 20
dt   = 0.001

The forces depend on the distance of course (the molecules have
a heterogeneous charge distribution) and this is a highly chaotic system
therefore the probability that the conformations (basically the
rotational DOFs of the two molecules) are the same or very similar after
200 ps at 300K should basically be ZERO ... but this is what i see, 

its re-producible and happens at different distances AND with different
molecular topologies (charge distributions).


a possible explanation for this behaviour might be that of the terms 

in eqn. 3.108 only the velocity dependent and the random term are actually
considered but not force term AND gen_seed doesn't make any difference for 
SD ... then the small differences i see would be only from round-off errors ... 
???

has anybody seen something similar ?

i'd appreciate any suggestions!

thanks
Michael
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Re: [gmx-users] rigid tetrahedral molecule

[gyorgy . hantal]

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 :


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 
To: Discussion list for GROMACS users 
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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Re: [gmx-users] rigid tetrahedral molecule

[David van der Spoel]

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 :


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 
To: Discussion list for GROMACS users 
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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--
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

[gyorgy . hantal]

Citando David van der Spoel :


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 :


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 
To: Discussion list for GROMACS users 
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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--
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] MG-ATP

[Sajad Ahrari]

thanks felix
you are right.both exist.but how can i tell gromacs to put MG ions in the 
standard vicinity of ATP? or maybe gromacs knows it already and i have to just 
type "MG-ATP" instead of "ADP"?





From: "Rausch, Felix" 
To: Discussion list for GROMACS users 
Sent: Wed, April 27, 2011 1:33:52 PM
Subject: [gmx-users] MG-ATP


Hi.
 
Looking at the list of building blocks available in GROMACS 
(http://www.gromacs.org/Documentation/File_Formats/Gromacs_Building_Blocks?highlight=building+blocks)
 you can find ATP as well as MG. So having a ATP-MG-complex in your simulation 
shouldn't be a problem.
 
Regards,
Felix


 Von: gmx-users-boun...@gromacs.org im Auftrag von Sajad Ahrari
Gesendet: Mi 27.04.2011 10:52
An: gromacs user forum
Betreff: [gmx-users] MG-ATP


dear users
is "MG-ATP" known to gromacs ? in my pdb structure I have ADP and MG, apart 
from 
each other and not being crystallized in the right place. can i omit them and 
replace ADP's with MG-ATP? or I should introduce this topology to gromacs?
regards
sajad -- 
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Re: [gmx-users] MG-ATP

[Justin A. Lemkul]

Sajad Ahrari wrote:

thanks felix
you are right.both exist.but how can i tell gromacs to put MG ions in 
the standard vicinity of ATP? or maybe gromacs knows it already and i 
have to just type "MG-ATP" instead of "ADP"?




If all residues, including ligands and cofactors, exist in the .rtp database, 
all you need to do is run the structure through pdb2gmx and it will produce a 
topology.  Note that the presence of .rtp entries is a key caveat; pdb2gmx isn't 
magic and won't work for anything you provide as input.  But in the case that 
everything is in place for a given force field, then there should be no problem.


Try it and report back with specific errors if they arise.  Spending too much 
time on the hypothetical gets nothing accomplished :)


-Justin



*From:* "Rausch, Felix" 
*To:* Discussion list for GROMACS users 
*Sent:* Wed, April 27, 2011 1:33:52 PM
*Subject:* [gmx-users] MG-ATP

Hi.
 
Looking at the list of building blocks available in GROMACS 
(http://www.gromacs.org/Documentation/File_Formats/Gromacs_Building_Blocks?highlight=building+blocks) 
you can find ATP as well as MG. So having a ATP-MG-complex in your 
simulation shouldn't be a problem.
 
Regards,

Felix


*Von:* gmx-users-boun...@gromacs.org im Auftrag von Sajad Ahrari
*Gesendet:* Mi 27.04.2011 10:52
*An:* gromacs user forum
*Betreff:* [gmx-users] MG-ATP

dear users
is "MG-ATP" known to gromacs ? in my pdb structure I have ADP and MG, 
apart from each other and not being crystallized in the right place. can 
i omit them and replace ADP's with MG-ATP? or I should introduce this 
topology to gromacs?

regards
sajad 



--


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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[gmx-users] Re: Tcoupl default setting

[Charlie Forde]

Thank you Mark for your response,

In carrying out the test you recommended I realised that I had set the 
integrator to sd, in such a case the tcoupl parameter is ignored. This explains 
my well behave temperature in the absence of setting a tcoupl option. When I 
wrote the input file originally (months ago) I must have known what I was doing 
but then we live, we learn, we forget.

Regards

Charlie
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Re: [gmx-users] rigid tetrahedral molecule

[Sanku M]

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 
To: Discussion list for GROMACS users 
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 :
>
>> 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 
>> To: Discussion list for GROMACS users 
>> 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
>> 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
>>
>
>
>


-- 
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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http://lists.gromacs.org/ma

Re: [gmx-users] rigid tetrahedral molecule

[David van der Spoel]

On 2011-04-29 19.15, gyorgy.han...@fc.up.pt wrote:

Citando David van der Spoel :


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 :


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 
To: Discussion list for GROMACS users 
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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--
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.se http://folding.bmc.uu.se
--
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Please

[gmx-users] Modified Gromacs and OPENMM

[Chi-cheng Chiu]

Hi Gromacs users & developers,
If I modified gromacs, will my modification works if I complied it with
OPENMM and use GPU?
Thanks!

Regards,

Chi-cheng
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Re: [gmx-users] Modified Gromacs and OPENMM

[Justin A. Lemkul]

Chi-cheng Chiu wrote:

Hi Gromacs users & developers,
If I modified gromacs, will my modification works if I complied it with 
OPENMM and use GPU? 


Presumably, if you have written sound code that uses compatible functions that 
are actually implemented in the OpenMM library, then yes.  If you want a more 
specific answer, you'll have to be more specific about what "modified Gromacs" 
actually means.


-Justin


Thanks!

Regards,

Chi-cheng



--


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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Re: [gmx-users] Modified Gromacs and OPENMM

[Chi-cheng Chiu]

Hi Justin,
Thanks for the reply. The part I modified is the implicit solvent
part, particularly the Still model. Also I modified a part of nonbonded
kernel, not sse ones. So I assumed I have to link GROMACS with OPENMM
using customGBforce?

Is there a guide of how currently GROMACS is linked to OPENMM?

Thanks!

Chi-cheng


On Fri, Apr 29, 2011 at 3:08 PM, Justin A. Lemkul  wrote:

>
>
> Chi-cheng Chiu wrote:
>
>> Hi Gromacs users & developers,
>> If I modified gromacs, will my modification works if I complied it with
>> OPENMM and use GPU?
>>
>
> Presumably, if you have written sound code that uses compatible functions
> that are actually implemented in the OpenMM library, then yes.  If you want
> a more specific answer, you'll have to be more specific about what "modified
> Gromacs" actually means.
>
> -Justin
>
>  Thanks!
>>
>> Regards,
>>
>> Chi-cheng
>>
>>
> --
> 
>
> 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
>
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Re: [gmx-users] Modified Gromacs and OPENMM

[Justin A. Lemkul]

Chi-cheng Chiu wrote:

Hi Justin,
Thanks for the reply. The part I modified is the implicit solvent 
part, particularly the Still model. Also I modified a part of nonbonded 
kernel, not sse ones. So I assumed I have to link GROMACS with OPENMM 
using customGBforce? 



In order to use any of the OpenMM capabilities, yes, you have to link to the 
OpenMM library.  It doesn't sound like you've modified anything in such a way 
that such linking would be prevented.  I was thinking more along the lines of 
making sure you were only making use of supported features:


http://www.gromacs.org/Downloads/Installation_Instructions/GPUs#Supported_features


Is there a guide of how currently GROMACS is linked to OPENMM?



http://www.gromacs.org/Downloads/Installation_Instructions/GPUs

-Justin


Thanks!

Chi-cheng


On Fri, Apr 29, 2011 at 3:08 PM, Justin A. Lemkul > wrote:




Chi-cheng Chiu wrote:

Hi Gromacs users & developers,
If I modified gromacs, will my modification works if I complied
it with OPENMM and use GPU?


Presumably, if you have written sound code that uses compatible
functions that are actually implemented in the OpenMM library, then
yes.  If you want a more specific answer, you'll have to be more
specific about what "modified Gromacs" actually means.

-Justin

Thanks!

Regards,

Chi-cheng


-- 



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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.
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--


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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Re: [gmx-users] rigid tetrahedral molecule

[Mark Abraham]

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 
*To:* Discussion list for GROMACS users 
*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 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 mailto:jalem...@vt.edu>>
>> To: Discussion list for GROMACS users >

>> 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

Re: [gmx-users] rigid tetrahedral molecule

[Mark Abraham]

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 
*To:* Discussion list for GROMACS users 
*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 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 mailto:jalem...@vt.edu>>
>> To: Discussion list for GROMACS users >

>> 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

[gmx-users] Gromacs 4.5.4 MPI

[Juliette N.]

Dear experts,

I have successfully installed a normal gromacs 4.5.4 installation on one of
my machines.

I have read the Installation Instructions that "As of GROMACS 4.5, threading
is supported, so for e.g multi-core workstations, MPI is no longer
required."

Does this mean that there is no longer the need to do a second configuration
with --enable-mpi?

Upon trying to configure using this command:

./configure --enable-mpi --program-suffix=_mpi

There is an error as below:

checking size of off_t... configure: error: in `/root/gromacs-4.5.4':
configure: error: cannot compute sizeof (off_t)
See `config.log' for more details.


-- 
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[gmx-users] LINCS error- 4.5.4 installation?

[Juliette N.]

Dear experts,

I just tried the command  mpirun -np 4 mdrun on 4.5.4 but after a few steps
I get LINCS error:

step 400, will finish Sat Apr 30 05:20:45 2011
Step 750, time 1.5 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 10.116560, max 72.359520 (between atoms 314 and 315)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
301302   61.00.1090   0.1841  0.1090


I tried to run using the same input files on 4.0.7 and simulation worked
fine. I mean the LINCS is not because of flawed topology or instability
issue. I am wondering this is happening because of MPI or installation
..Please help!

-- 
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[gmx-users] ionic liquids

[Prema Awati]

 Sir,

  I am trying to create an ionic-liquid system comprising of 
1-butyl-3-methyl-imidazolium(bmim) as cation and BF4-(bf4) as anion.  I have 
generated the system using following command:   
 genbox_d -cp bmim.gro -ci  bf4.gro  -nmol 125 -try 200 -o .pdb , well 
it created system of total 250 molecules 125 each but after equilibration the 
density is not matching with the reported.I tried  "simulated annealing" 
procedure still no much difference. I wonder if there is any other way to 
generate an ionic liquid system or how the people do it tp reproduce the 
results , I urge for any quick suggestion.


  thanx,

  student.

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[gmx-users] Fwd: gmx-users Digest, Vol 84, Issue 217

[saly jackson]

Hi Ivan

If in my system there are some of the other components such
SDS surfactant and one of these polarizable models can I use forcefield
parameters from PRODRG or not.
If no, would you please tell me about the references that I can find some
other components in polarizable water model
 force fields.

Thanks alot for your help

Regards

Saly
On Wed, Apr 27, 2011 at 5:29 PM,  wrote:

> Send gmx-users mailing list submissions to
>gmx-users@gromacs.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
>http://lists.gromacs.org/mailman/listinfo/gmx-users
> or, via email, send a message with subject or body 'help' to
>gmx-users-requ...@gromacs.org
>
> You can reach the person managing the list at
>gmx-users-ow...@gromacs.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gmx-users digest..."
>
>
> Today's Topics:
>
>   1. Re: polarizable water models (Mark Abraham)
>   2. Re: polarizable water models (Ivan Gladich)
>
>
> --
>
> Message: 1
> Date: Wed, 27 Apr 2011 22:39:56 +1000
> From: Mark Abraham 
> Subject: Re: [gmx-users] polarizable water models
> To: Discussion list for GROMACS users 
> Message-ID: <4db80e9c.7010...@anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 4/27/2011 10:08 PM, saly jackson wrote:
> > Hi Ivan
> >
>
> Please do not reply to whole digests with non-descriptive subject lines.
> It confuses the archives, and alienates people from finding out the
> topic of your interest, and thus being bothered to give you free help.
> Please leave only the relevant discussion, and use a useful subject line.
>
> > In which force field can I find the polarizable water models you said
> > in section "b" of your reply
>
> Have you done your own literature searching first? Then you'd already
> know what force fields they might have been used with...
>
> Mark
>
>
>
>
>
> --
>
> Message: 2
> Date: Wed, 27 Apr 2011 15:43:27 +0200
> From: Ivan Gladich 
> Subject: Re: [gmx-users] polarizable water models
> To: Discussion list for GROMACS users 
> Message-ID: <4db81d7f.70...@marge.uochb.cas.cz>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Skipped content of type multipart/alternative-- next part
> --
> ;
> ; Topology file for SW
> ;
> ; Paul van Maaren and David van der Spoel
> ; Molecular Dynamics Simulations of Water with Novel Shell Model Potentials
> ; J. Phys. Chem. B. 105 (2618-2626), 2001
> ;
> ; Force constants for the shell are given by:
> ;
> ; k = qs^2/(4 pi eps0 alpha)
> ; However, in the current version of the itp file and software (3.2+)
> ; force constants are computed in mdrun, and the input is the
> ; polarizability in nm^3.
> ;
> ; Some data: mu (water) = 1.8546 D ( 0.0386116 e nm)
> ;1/(4 pi eps0 alpha) = 94513.94
> ;
> ; Alpha-X = 1.415   kx = 608069
> ; Alpha-Y = 1.528   ky = 563101
> ; Alpha-Z = 1.468   kz = 586116
> ;
> ; Alpha   = 1.470   k  = 585318
> ;
> ; Bonding parameters from (but without cubic term):
> ; D. M. Ferguson:
> ; Parametrization and Evaluation of a Flexible Water Model
> ; J. Comp. Chem. 16(4), 501-511 (1995)
> ;
> ; Possible defines that you can put in your topol.top:
> ; -DANISOTROPIC Select anisotropic polarizibility (isotropic is default).
> ; -DRIGID   Rigid model (flexible is default)
> ; -DPOSRES  Position restrain oxygen atoms
> ;
>
> [ defaults ]
> LJ  Geometric
>
> [ atomtypes ]
> ;namemass  charge   ptype   c6  c12
>   WO15.99940   0.0 A   0.0 0.0
>   WH 1.00800   0.0 A   0.0 0.0
>   WS 0.0   0.0 S   0.0 0.0
>   WD 0.0   0.0 D   0.0 0.0
>
> [ nonbond_params ]
> #ifdef RIGID
> #ifdef ANISOTROPIC
> WH  WH  1   4.0e-5  4.0e-8
> WS  WO  1   1.0e-6  1.0e-12
> WS  WH  1   4.0e-5  2.766e-08
> WO  WO  1   2.0e-3  1.174e-06
> #else
> WH  WH  1   4.0e-5  4.0e-8
> WS  WO  1   1.0e-6  1.0e-12
> WS  WH  1   4.0e-5  2.769e-08
> WO  WO  1   2.0e-3  1.176e-06
> #endif
> #else
> #ifdef ANISOTROPIC
> WH  WH  1   4.0e-5  4.0e-8
> WS  WO  1   1.0e-6  1.0e-12
> WS  WH  1   4.0e-5  2.910e-08
> WO  WO  1   2.0e-3  1.189e-06
> #else
> WH  WH  1   4.0e-5  4.0e-8
> WS  WO  1   1.0e-6  1.0e-12
> WS  WH  1   4.0e-5  2.937e-08
> WO  WO  1   2.0e-3  1.187e-06
> #endif
> #endif
>
>
> 
> ;; This is a the 'classical YAW' model, in which we do have the dummy.
> ;; The shell is attached to the dummy, in this case the gas-phase
> ;;

[gmx-users] Fwd: gmx-users Digest, Vol 84, Issue 213

[saly jackson]

Hi Ivan

In which force field can I find the polarizable water models you said in
section "b" of your reply

Thanks alot

Regards

Saly


On Wed, Apr 27, 2011 at 2:30 PM,  wrote:

> Send gmx-users mailing list submissions to
>gmx-users@gromacs.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
>http://lists.gromacs.org/mailman/listinfo/gmx-users
> or, via email, send a message with subject or body 'help' to
>gmx-users-requ...@gromacs.org
>
> You can reach the person managing the list at
>gmx-users-ow...@gromacs.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gmx-users digest..."
>
>
> Today's Topics:
>
>   1. Re: MG-ATP (Mark Abraham)
>   2. Re: Docking (Mark Abraham)
>   3. Re: POL3 water model (Ivan Gladich)
>   4. Re: Docking (mohsen ramezanpour)
>
>
> --
>
> Message: 1
> Date: Wed, 27 Apr 2011 19:09:59 +1000
> From: Mark Abraham 
> Subject: Re: [gmx-users] MG-ATP
> To: Discussion list for GROMACS users 
> Message-ID: <4db7dd67.2050...@anu.edu.au>
> Content-Type: text/plain; charset="iso-8859-1"
>
> On 4/27/2011 6:52 PM, Sajad Ahrari wrote:
> > dear users
> > is "MG-ATP" known to gromacs ? in my pdb structure I have ADP and MG,
> > apart from each other and not being crystallized in the right place.
> > can i omit them and replace ADP's with MG-ATP? or I should introduce
> > this topology to gromacs?
>
> You'll have to do your own literature searching about previous
> treatments of ADP and ATP, I'm afraid :-) Pretty much anything that has
> been done can be made to work in GROMACS, however.
>
> See also http://www.gromacs.org/Documentation/How-tos/Parameterization
>
> Mark
>
>
>
> -- next part --
> An HTML attachment was scrubbed...
> URL:
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20110427/5a9bd821/attachment-0001.html
>
> --
>
> Message: 2
> Date: Wed, 27 Apr 2011 19:18:08 +1000
> From: Mark Abraham 
> Subject: Re: [gmx-users] Docking
> To: Discussion list for GROMACS users 
> Message-ID: <4db7df50.40...@anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 4/27/2011 7:05 PM, mohsen ramezanpour wrote:
> > Dear Users
> >
> > I read so many emails to mailing list, there were important notes
> > about docking but I couldn't extract a general result.
> > Please let me know:
> >
> > 1-Can we dock a ligand to it's protein's binding pocket with Pymol and
> > Gromacs as following?
> >
> > first:locating ligand outside and close to binding site  manually in
> > pymol and saving complex.pdb
> > second:doing all steps for generating complex.top and complex.gro as
> > Enzyme-Drug tutorial
> > third:running md (with out any pull code and constraint),in the other
> > words,full flexible system.
> >
> > I think drug can move freely and according to it's interaction with
> > binding site can be attracted by binding site.
> > reside for a distance time and then will come out of pocket.
> >
> > Am I right?
>
> In principle, yes, but it is wildly unlikely that you have a system that
> can bind and unbind reliably in the 100ns simulation range that you
> might be able to afford to run, and if you did happen to have one, what
> would you have learned?
>
> > I know what discussed in mainling list about deffinition of "Docking".
> >
> >
> > 2-I have some docked files by "Docking Server " for some of my
> > drug-protein's complexes.
> > now,I want to obtain them by doing MD in the above proccess.if I was
> > successful then try to do that for other drugs which I don't have any
> > docked pdb for them.
> >
> > How can I fit a trajectory with a typical pdb file?
>
> I don't understand what you are asking.
>
> Mark
>
>
>
>
>
> --
>
> Message: 3
> Date: Wed, 27 Apr 2011 12:14:42 +0200
> From: Ivan Gladich 
> Subject: Re: [gmx-users] POL3 water model
> To: Discussion list for GROMACS users 
> Message-ID: <4db7ec92.7080...@marge.uochb.cas.cz>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Saly
>  from my little experience, POL3 water model is a point polarizable
> water model.
> Point polarizable water models are not available in gromacs.
> Gromacs uses shell model, i.e. charge attached on a spring to mimic the
> stretching of the electronic cloud.
>
> So you have 3 solutions
> a) You can take the POL3 model, look the polarizability of oxygen and
> hydrogen atom  and attach shells on oxygen and hydrogens atoms in order
> to reproduce the model for gromacs.
> b) In Gromacs there are other polarizable water models using shell (e.g.
> SWM4-DP,  SWM4-NDP,  SW ), you could try with one of this...in my
> opinion this is the best solution..;)
> c) If you really need POL3 model, try with other molecular package that
> have point polarizable POL3 water (e.g. AMBER)
>
> I hope this help
> Ivan
>
>
>
>
> On 04/27/2011 11:04 AM, saly jackson w

[gmx-users] sulfate ion

[saly jackson]

Hi all

I want to know about the ability of GROMACS to simulate sulfate in(SO4
(2-)),

Do we can have the ion in our simulation using GROMACS?

Thanks alot

Saly
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