date:20100603



- Original Message -
From: NG HUI WEN 
Date: Thursday, June 3, 2010 18:08
Subject: [gmx-users] pdb2gmx renumbers the residues in my pdb file
To: gmx-users@gromacs.org


 
---
| 

  
  > Hi,
  >  
  > I’m a new gromacs user. I have encountered a problem with pdb2gmx where it 
automatically renumbers the residues in my pdb file. 
  >  
  > For instance, the first residue in my protein F8 has become F1 – this 
affects all the residues in the protein, something I find rather inconvenient.
  >  
  > I’ve been searching the archive for previous posts which might have a 
solution to this but no luck so far. I might have been wrong. Many thanks for 
your help.
 |
---

I think you're out of luck. IIRC the facility you want is implemented in the 
development version, but not yet released. If you re-renumber by hand, then I 
suspect everything will be fine after that. grompp just needs something whose 
atom and residue naming and ordering matches the .top... how you produce that 
doesn't matter to it.

Mark



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RE: [gmx-users] pdb2gmx renumbers the residues in my pdb file

2010-06-03 Thread NG HUI WEN

Looks like I've got some work to do. Thanks Mark!

 

From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham
Sent: Thursday, June 03, 2010 4:27 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] pdb2gmx renumbers the residues in my pdb file

 



- Original Message -
From: NG HUI WEN 
Date: Thursday, June 3, 2010 18:08
Subject: [gmx-users] pdb2gmx renumbers the residues in my pdb file
To: gmx-users@gromacs.org

> Hi,

>  

> I'm a new gromacs user. I have encountered a problem with pdb2gmx
where it automatically renumbers the residues in my pdb file. 

>  

> For instance, the first residue in my protein F8 has become F1 - this
affects all the residues in the protein, something I find rather
inconvenient.

>  

> I've been searching the archive for previous posts which might have a
solution to this but no luck so far. I might have been wrong. Many
thanks for your help.


I think you're out of luck. IIRC the facility you want is implemented in
the development version, but not yet released. If you re-renumber by
hand, then I suspect everything will be fine after that. grompp just
needs something whose atom and residue naming and ordering matches the
.top... how you produce that doesn't matter to it.

Mark << 

Email has been scanned for viruses by UNMC email management service
 

>> 

<< Email has been scanned for viruses by UNMC email management service >>
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Re: [gmx-users] pdb2gmx renumbers the residues in my pdb file

2010-06-03 Thread Oliver Grant

1. pdb2gmx, editconf and then solvate.
2. use trjconv and make a pdb.
3. Take 7 water molecules and put them in the top of your original pdb and
start again from there.



On 3 June 2010 09:34, NG HUI WEN  wrote:

>  Looks like I’ve got some work to do. Thanks Mark!
>
>
>
> *From:* gmx-users-boun...@gromacs.org [mailto:
> gmx-users-boun...@gromacs.org] *On Behalf Of *Mark Abraham
> *Sent:* Thursday, June 03, 2010 4:27 PM
> *To:* Discussion list for GROMACS users
> *Subject:* Re: [gmx-users] pdb2gmx renumbers the residues in my pdb file
>
>
>
>
>
> - Original Message -
> From: NG HUI WEN 
> Date: Thursday, June 3, 2010 18:08
> Subject: [gmx-users] pdb2gmx renumbers the residues in my pdb file
> To: gmx-users@gromacs.org
>
> > Hi,
>
> >
>
> > I’m a new gromacs user. I have encountered a problem with pdb2gmx where
> it automatically renumbers the residues in my pdb file.
>
> >
>
> > For instance, the first residue in my protein F8 has become F1 – this
> affects all the residues in the protein, something I find rather
> inconvenient.
>
> >
>
> > I’ve been searching the archive for previous posts which might have a
> solution to this but no luck so far. I might have been wrong. Many thanks
> for your help.
>
>
> I think you're out of luck. IIRC the facility you want is implemented in
> the development version, but not yet released. If you re-renumber by hand,
> then I suspect everything will be fine after that. grompp just needs
> something whose atom and residue naming and ordering matches the .top... how
> you produce that doesn't matter to it.
>
> Mark <<
>
> Email has been scanned for viruses by UNMC email management 
> service
>
> >>
>  <<
>
> Email has been scanned for viruses by UNMC email management 
> service
> >>
>
> --
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[gmx-users] gromacs installation and test set

2010-06-03 Thread Gu, Xiang


Hi, all,

I'm trying to install a parallel version of gromacs-4.0.7 under my own 
account (on our campus supercomputing center, configured with 
--enable-threads, --enable-float, --enable-mpi, and prefixed with 
specified directory), because I need to develop some new extensions for 
our research and will have to do code modification and debugging from 
time to time.


Now the installation went through (I felt there was no severe error 
information shown). But when I started running it parallely, the mdrun 
program seemed to crash at the first MPI command it encountered (the 
MPI_Bcast in line 372 of gmxlib/network.c). It is not yet addressed what 
has gone wrong in the installation and I was trying to run the test set 
to get some information. I wonder if I had put the gmxtest directory at 
proper place, since after I sourced GMXRC and ran gmxtest.pl, for all 
the cases I was told "No topol.tpr file in kernel ...".


It would be quite appreciated if someone could guess what might have 
been wrong with the installation; also is it worth running the test set 
for locating the problem? and what does the error information "No 
topol.tpr file in kernel ..." imply?


Thank you!

Xiang Gu

--
_
Xiang Gu, PhD, Postdoctoral Research Fellow
Department of Applied Physics
Helsinki University of Technology (TKK), Finland
Tel: +358-9-470 23137
Email: x...@cc.hut.fi
http://tfy.tkk.fi/soft/ 


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[gmx-users] position restraints


Hello, 

I would like to restrain my molecule to a specific position in space. I would 
like for certain atoms to lie on the y-axis. To do this I used  the following 
code/lines in my .top file: 

[ position restraints ]
2 1 1000 0 1000 ; 
3 1 1000 0 1000 ;
4 1 1000 0 1000 ;
5 1 1000 0 1000 ;
6 1 1000 0 1000 ;
7 1 1000 0 1000 ;
8 1 1000 0 1000 ;
9 1 1000 0 1000 ;

Unfortunately, after minimization my file contained the molecule in the same 
position as when the restraints were not applied. 

Does anyone know what I am doing wrong? 

Thanks in advance,
Abdullah
  
_
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Re: [gmx-users] position restraints




abdullah ahmed wrote:

Hello,

I would like to restrain my molecule to a specific position in space. I 
would like for certain atoms to lie on the y-axis. To do this I used  
the following code/lines in my .top file:


[ position restraints ]


This is an incorrect directive.  It should be position_restraints.


2 1 1000 0 1000 ;
3 1 1000 0 1000 ;
4 1 1000 0 1000 ;
5 1 1000 0 1000 ;
6 1 1000 0 1000 ;
7 1 1000 0 1000 ;
8 1 1000 0 1000 ;
9 1 1000 0 1000 ;

Unfortunately, after minimization my file contained the molecule in the 
same position as when the restraints were not applied.


Does anyone know what I am doing wrong?



Perhaps the directive name is an issue, although I think grompp should have 
raised a warning of some sort.  Otherwise, is this block within the appropriate 
[moleculetype] in the topology?  Is it under control of an #ifdef block that you 
haven't invoked in the .mdp file?


-Justin


Thanks in advance,
Abdullah


Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign up 
now. 




--


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] gromacs installation and test set




Gu, Xiang wrote:

Hi, all,

I'm trying to install a parallel version of gromacs-4.0.7 under my own 
account (on our campus supercomputing center, configured with 
--enable-threads, --enable-float, --enable-mpi, and prefixed with 
specified directory), because I need to develop some new extensions for 
our research and will have to do code modification and debugging from 
time to time.




There is no point to using --enable-threads in version 4.0.7 - there's no thread 
support yet.


Now the installation went through (I felt there was no severe error 
information shown). But when I started running it parallely, the mdrun 
program seemed to crash at the first MPI command it encountered (the 
MPI_Bcast in line 372 of gmxlib/network.c). It is not yet addressed what 
has gone wrong in the installation and I was trying to run the test set 
to get some information. I wonder if I had put the gmxtest directory at 
proper place, since after I sourced GMXRC and ran gmxtest.pl, for all 
the cases I was told "No topol.tpr file in kernel ...".




What is your MPI implementation?  OpenMPI, MPICH, etc?

It would be quite appreciated if someone could guess what might have 
been wrong with the installation; also is it worth running the test set 
for locating the problem? and what does the error information "No 
topol.tpr file in kernel ..." imply?




The test set is not terribly useful, and certainly won't diagnose this issue for 
you.  If you've failed to generate the necessary .tpr file, then errors occurred 
in grompp that prevented the .tpr file from being generated.


-Justin


Thank you!

Xiang Gu



--


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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FW: [gmx-users] position restraints


Thank you for your reply, 

I have been using [ position_restraints ], I do not know why it came out that 
way in the mail. 
I agree with you, the problem probably comes from the position the code lies in 
inside the .top file. I put it at the end of the file because I thought that 
was the way it was supposed to be done. Perhaps this is incorrect. 

The final lines of the .top file are: 

Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
Protein

[ molecules ]
; Compound#mols
Protein_A   1

[ position_restraints ]
2 1 1000 0 1000 ;
3 1 1000 0 1000 ;
4 1 1000 0 1000 ;
5 1 1000 0 1000 ;
6 1 1000 0 1000 ;
7 1 1000 0 1000 ;
8 1 1000 0 1000 ;
9 1 1000 0 1000 ;

 

> Date: Thu, 3 Jun 2010 09:00:36 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] position restraints
> 
> 
> 
> abdullah ahmed wrote:
> > Hello,
> > 
> > I would like to restrain my molecule to a specific position in space. I 
> > would like for certain atoms to lie on the y-axis. To do this I used  
> > the following code/lines in my .top file:
> > 
> > [ position restraints ]
> 
> This is an incorrect directive.  It should be position_restraints.
> 
> > 2 1 1000 0 1000 ;
> > 3 1 1000 0 1000 ;
> > 4 1 1000 0 1000 ;
> > 5 1 1000 0 1000 ;
> > 6 1 1000 0 1000 ;
> > 7 1 1000 0 1000 ;
> > 8 1 1000 0 1000 ;
> > 9 1 1000 0 1000 ;
> > 
> > Unfortunately, after minimization my file contained the molecule in the 
> > same position as when the restraints were not applied.
> > 
> > Does anyone know what I am doing wrong?
> > 
> 
> Perhaps the directive name is an issue, although I think grompp should have 
> raised a warning of some sort.  Otherwise, is this block within the 
> appropriate 
> [moleculetype] in the topology?  Is it under control of an #ifdef block that 
> you 
> haven't invoked in the .mdp file?
> 
> -Justin
> 
> > Thanks in advance,
> > Abdullah
> > 
> > 
> > Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign up 
> > now. 
> > 
> 
> -- 
> 
> 
> 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/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/mailing_lists/users.php
  
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_
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Re: [gmx-users] gromacs installation and test set

2010-06-03 Thread Gu, Xiang


Dear Justin,

(1) sorry, my ignorance; threads was enabled when installing FFTW 
instead of Gromacs, I should have said "configured with --enable-float 
and --enable-mpi" (and actually this is what I did).


(2) I think I used OpenMPI.

(3) Thank you. Is there anyway to fix the grompp?

Xiang

Justin A. Lemkul wrote:



Gu, Xiang wrote:

Hi, all,

I'm trying to install a parallel version of gromacs-4.0.7 under my 
own account (on our campus supercomputing center, configured with 
--enable-threads, --enable-float, --enable-mpi, and prefixed with 
specified directory), because I need to develop some new extensions 
for our research and will have to do code modification and debugging 
from time to time.




There is no point to using --enable-threads in version 4.0.7 - there's 
no thread support yet.


Now the installation went through (I felt there was no severe error 
information shown). But when I started running it parallely, the 
mdrun program seemed to crash at the first MPI command it encountered 
(the MPI_Bcast in line 372 of gmxlib/network.c). It is not yet 
addressed what has gone wrong in the installation and I was trying to 
run the test set to get some information. I wonder if I had put the 
gmxtest directory at proper place, since after I sourced GMXRC and 
ran gmxtest.pl, for all the cases I was told "No topol.tpr file in 
kernel ...".




What is your MPI implementation?  OpenMPI, MPICH, etc?

It would be quite appreciated if someone could guess what might have 
been wrong with the installation; also is it worth running the test 
set for locating the problem? and what does the error information "No 
topol.tpr file in kernel ..." imply?




The test set is not terribly useful, and certainly won't diagnose this 
issue for you.  If you've failed to generate the necessary .tpr file, 
then errors occurred in grompp that prevented the .tpr file from being 
generated.


-Justin


Thank you!

Xiang Gu






--
_
Xiang Gu, PhD, Postdoctoral Research Fellow
Department of Applied Physics
Helsinki University of Technology (TKK), Finland
Tel: +358-9-470 23137
Email: x...@cc.hut.fi
http://tfy.tkk.fi/soft/ 


--
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Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] position restraints




abdullah ahmed wrote:

Thank you for your reply,

I have been using [ position_restraints ], I do not know why it came out 
that way in the mail.
I agree with you, the problem probably comes from the position the code 
lies in inside the .top file. I put it at the end of the file because I 
thought that was the way it was supposed to be done. Perhaps this is 
incorrect.




That is incorrect.  The position restraints must belong to the [moleculetype] of 
the species to be restrained.  Once you #include a new molecule, you start a new 
[moleculetype] entry and the position restraints belong to it.  Putting it at 
the very end of a file probably has no effect whatsoever on any of the species 
in your system.


-Justin


The final lines of the .top file are:

Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
Protein

[ molecules ]
; Compound#mols
Protein_A   1

[ position_restraints ]
2 1 1000 0 1000 ;
3 1 1000 0 1000 ;
4 1 1000 0 1000 ;
5 1 1000 0 1000 ;
6 1 1000 0 1000 ;
7 1 1000 0 1000 ;
8 1 1000 0 1000 ;
9 1 1000 0 1000 ;

 


 > Date: Thu, 3 Jun 2010 09:00:36 -0400
 > From: jalem...@vt.edu
 > To: gmx-users@gromacs.org
 > Subject: Re: [gmx-users] position restraints
 >
 >
 >
 > abdullah ahmed wrote:
 > > Hello,
 > >
 > > I would like to restrain my molecule to a specific position in 
space. I

 > > would like for certain atoms to lie on the y-axis. To do this I used
 > > the following code/lines in my .top file:
 > >
 > > [ position restraints ]
 >
 > This is an incorrect directive. It should be position_restraints.
 >
 > > 2 1 1000 0 1000 ;
 > > 3 1 1000 0 1000 ;
 > > 4 1 1000 0 1000 ;
 > > 5 1 1000 0 1000 ;
 > > 6 1 1000 0 1000 ;
 > > 7 1 1000 0 1000 ;
 > > 8 1 1000 0 1000 ;
 > > 9 1 1000 0 1000 ;
 > >
 > > Unfortunately, after minimization my file contained the molecule in 
the

 > > same position as when the restraints were not applied.
 > >
 > > Does anyone know what I am doing wrong?
 > >
 >
 > Perhaps the directive name is an issue, although I think grompp 
should have
 > raised a warning of some sort. Otherwise, is this block within the 
appropriate
 > [moleculetype] in the topology? Is it under control of an #ifdef 
block that you

 > haven't invoked in the .mdp file?
 >
 > -Justin
 >
 > > Thanks in advance,
 > > Abdullah
 > >
 > > 


 > > Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign up
 > > now. 
 > >
 >
 > --
 > 
 >
 > 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/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/mailing_lists/users.php


Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign up 
now. 


--


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] extra non bonded interaction

2010-06-03 Thread Thanasis Koukoulas

hello 

I have a problem with C10O3H. The problem is that i use Trappe model and there 
you can add an extra repulsive interaction of molecule 10 (Oxygen) with 
molecule 14 (Hydrogen). The formula that TraPPE uses is 4E7/rij^12. with the 
transformation of 4E7in gromacs units (kJ*nm^12*mol-1) i take a numper 
3.325789e-7 witch until now i put it in [pairs] with the sexond function like 
this:

[Pairs]
10 14 2 0 0 0 03.325789e-7

the zeros i use is  for fudgeQQ because i dont want to have coulomb 14 in this 
pair and  charges of both of them for the same reason. it seem to work because 
at the end i have a coulombic energy 1-4 at a reasonable price but the total 
energy is not correct.

please if someone can think smth answer me. The prices i get i can compare them 
with another researcher who did the same work with the use of monte carlo. i am 
stucked for three months and i have read th manual over and and over again 
without result

thanks in advance

thanasis


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Re: [gmx-users] gromacs installation and test set




Gu, Xiang wrote:

Dear Justin,

(1) sorry, my ignorance; threads was enabled when installing FFTW 
instead of Gromacs, I should have said "configured with --enable-float 
and --enable-mpi" (and actually this is what I did).


(2) I think I used OpenMPI.



The use of "think" does not inspire confidence.  Knowing your implementation 
(including its version) will help decipher if this is a bug in MPI, since some 
versions have known issues.



(3) Thank you. Is there anyway to fix the grompp?



I doubt grompp is broken.  Did you compile the entire Gromacs suite with 
--enable-mpi?  If so, you might be getting weird behavior, since mdrun is the 
only program that is MPI-aware.  Otherwise, I'd suspect that the gmxtest 
directory is in the wrong place.  It should be a subdirectory of the "gromacs" 
directory of your installation.  If in the default /usr/local/gromacs, then you 
should have /usr/local/gromacs/gmxtest.


-Justin


Xiang

Justin A. Lemkul wrote:



Gu, Xiang wrote:

Hi, all,

I'm trying to install a parallel version of gromacs-4.0.7 under my 
own account (on our campus supercomputing center, configured with 
--enable-threads, --enable-float, --enable-mpi, and prefixed with 
specified directory), because I need to develop some new extensions 
for our research and will have to do code modification and debugging 
from time to time.




There is no point to using --enable-threads in version 4.0.7 - there's 
no thread support yet.


Now the installation went through (I felt there was no severe error 
information shown). But when I started running it parallely, the 
mdrun program seemed to crash at the first MPI command it encountered 
(the MPI_Bcast in line 372 of gmxlib/network.c). It is not yet 
addressed what has gone wrong in the installation and I was trying to 
run the test set to get some information. I wonder if I had put the 
gmxtest directory at proper place, since after I sourced GMXRC and 
ran gmxtest.pl, for all the cases I was told "No topol.tpr file in 
kernel ...".




What is your MPI implementation?  OpenMPI, MPICH, etc?

It would be quite appreciated if someone could guess what might have 
been wrong with the installation; also is it worth running the test 
set for locating the problem? and what does the error information "No 
topol.tpr file in kernel ..." imply?




The test set is not terribly useful, and certainly won't diagnose this 
issue for you.  If you've failed to generate the necessary .tpr file, 
then errors occurred in grompp that prevented the .tpr file from being 
generated.


-Justin


Thank you!

Xiang Gu








--


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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FW: [gmx-users] position restraints


Hi! 

In your previous mail you mentioned: 

The position restraints must belong to the [moleculetype] of 
the species to be restrained.  Once you #include a new molecule, you start a 
new 
[moleculetype] entry and the position restraints belong to it.  
 

So I rechecked my .top file and found that [moleculetype] only occurs once. 
Perhaps I have misunderstood you. So I added the top file below. I did not add 
the contents of [atoms] [bonds] etc because I felt the mail would become 
unnecessarily long. 

; Include forcefield parameters
#include "ffoplsaa.itp"

[ moleculetype ]
; Namenrexcl
Protein_A   3

[ atoms ]

[ bonds ]

[ pairs ]

[ angles ]

[ dihedrals ]

[ dihedrals ]

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Include water topology
#include "spc.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
Protein

[ molecules ]
; Compound#mols
Protein_A   1

Thanks again for your help,
Abdullah 

  
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Re: [gmx-users] position restraints




abdullah ahmed wrote:

Hi!

In your previous mail you mentioned:

The position restraints must belong to the [moleculetype] of
the species to be restrained. * Once you #include a new molecule, you 
start a new

[moleculetype] entry and the position restraints belong to it. *
 

So I rechecked my .top file and found that [moleculetype] only occurs 
once. Perhaps I have misunderstood you. So I added the top file below. I 


No it doesn't.  Each time you #include a new .itp file, you are telling grompp 
to copy and paste the contents of that .itp file in that location.  Have a look 
at spc.itp - it starts a new moleculetype.


http://www.gromacs.org/Documentation/Include_File_Mechanism

Note how the automatically-generated "posre.itp" file is #included at the end of 
the Protein_A moleculetype, *before* any other molecules are introduced.  You 
have to do the same with any new #include statements or directives you add.


-Justin

did not add the contents of [atoms] [bonds] etc because I felt the mail 
would become unnecessarily long.


; Include forcefield parameters
#include "ffoplsaa.itp"

[ moleculetype ]
; Namenrexcl
Protein_A   3

[ atoms ]

[ bonds ]

[ pairs ]

[ angles ]

[ dihedrals ]

[ dihedrals ]

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Include water topology
#include "spc.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
Protein

[ molecules ]
; Compound#mols
Protein_A   1

Thanks again for your help,
Abdullah



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up now. 


--


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] position restraints

Hi,

Sorry to bother you again, but I am new to gromacs and many theings don't make 
sense yet. 
I have tried reading the manual but I do not understand what you mean by "Note 
how the automatically-generated "posre.itp" file is #included at 
the end of the Protein_A moleculetype, *before* any other 
molecules are introduced. You have to do the same with any new #include 
statements or 
directives you add." 

I tried using #include in front of my code for [position_restraints] but that 
just gives an error. So I suppose that isn't what you mean. 
Furthermore, in section 5.7.1 of the manual pg110 an example topology file 
called urea.top is shown. there is no include there.

In this example .top file they just seem to have added the position restraints 
they want after the dihedrals. This approach does not seem to be working for me 
and I can not understand why. 

Thank you again for your help, 
Abdullah

> Date: Thu, 3 Jun 2010 09:43:18 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] position restraints
> 
> 
> 
> abdullah ahmed wrote:
> > Hi!
> > 
> > In your previous mail you mentioned:
> > 
> > The position restraints must belong to the [moleculetype] of
> > the species to be restrained. * Once you #include a new molecule, you 
> > start a new
> > [moleculetype] entry and the position restraints belong to it. *
> >  
> > 
> > So I rechecked my .top file and found that [moleculetype] only occurs 
> > once. Perhaps I have misunderstood you. So I added the top file below. I 
> 
> No it doesn't.  Each time you #include a new .itp file, you are telling 
> grompp 
> to copy and paste the contents of that .itp file in that location.  Have a 
> look 
> at spc.itp - it starts a new moleculetype.
> 
> http://www.gromacs.org/Documentation/Include_File_Mechanism
> 
> Note how the automatically-generated "posre.itp" file is #included at the end 
> of 
> the Protein_A moleculetype, *before* any other molecules are introduced.  You 
> have to do the same with any new #include statements or directives you add.
> 
> -Justin
> 
> > did not add the contents of [atoms] [bonds] etc because I felt the mail 
> > would become unnecessarily long.
> > 
> > ; Include forcefield parameters
> > #include "ffoplsaa.itp"
> > 
> > [ moleculetype ]
> > ; Namenrexcl
> > Protein_A   3
> > 
> > [ atoms ]
> > 
> > [ bonds ]
> > 
> > [ pairs ]
> > 
> > [ angles ]
> > 
> > [ dihedrals ]
> > 
> > [ dihedrals ]
> > 
> > ; Include Position restraint file
> > #ifdef POSRES
> > #include "posre.itp"
> > #endif
> > 
> > ; Include water topology
> > #include "spc.itp"
> > 
> > #ifdef POSRES_WATER
> > ; Position restraint for each water oxygen
> > [ position_restraints ]
> > ;  i funct   fcxfcyfcz
> >11   1000   1000   1000
> > #endif
> > 
> > ; Include generic topology for ions
> > #include "ions.itp"
> > 
> > [ system ]
> > ; Name
> > Protein
> > 
> > [ molecules ]
> > ; Compound#mols
> > Protein_A   1
> > 
> > Thanks again for your help,
> > Abdullah
> > 
> > 
> > 
> > Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign 
> > up now. 
> 
> -- 
> 
> 
> 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/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.
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Re: [gmx-users] position restraints

Have you seen the example here?

http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_defaults

What you need to do is place your [position_restraints] directive after the 
moleculetype to which it belongs, but before any other moleculetype has been 
introduced (usually by #including another topology, which introduces a new 
molecule, and hence, moleculetype).

The example I mentioned regarding posre.itp is to demonstrate exactly how this 
is done.  The posre.itp file is produced by pdb2gmx and is used to restrain the 
heavy atoms of the protein.  It is #included (basically inserting the relevant 
[position_restraints] directive) at the end of the Protein_A moleculetype 
definition, but prior to the #include "spc.itp" statement, which starts the SPC 
water moleculetype definition.

So the topology is like this:

[ moleculetype ]
Protein

(atoms, bonds, other stuff...)

[ position_restraints ] <- Note how it is placed before the next moleculetype.

[ moleculetype ] <- This part comes from the #include "spc.itp" statement.
SOL

etc.

-Justin

abdullah ahmed wrote:

Hi,

Sorry to bother you again, but I am new to gromacs and many theings 
don't make sense yet.
I have tried reading the manual but I do not understand what you mean by 
"Note how the automatically-generated "posre.itp" file is #included at 
the end of the Protein_A moleculetype, *before* any other molecules are 
introduced. You have to do the same with any new #include statements or 
directives you add."

I tried using #include in front of my code for [position_restraints] but 
that just gives an error. So I suppose that isn't what you mean.
Furthermore, in section 5.7.1 of the manual pg110 an example topology 
file called urea.top is shown. there is no include there.

In this example .top file they just seem to have added the position 
restraints they want after the dihedrals. This approach does not seem to 
be working for me and I can not understand why.

Thank you again for your help,
Abdullah

 > Date: Thu, 3 Jun 2010 09:43:18 -0400
 > From: jalem...@vt.edu
 > To: gmx-users@gromacs.org
 > Subject: Re: [gmx-users] position restraints
 >
 >
 >
 > abdullah ahmed wrote:
 > > Hi!
 > >
 > > In your previous mail you mentioned:
 > >
 > > The position restraints must belong to the [moleculetype] of
 > > the species to be restrained. * Once you #include a new molecule, you
 > > start a new
 > > [moleculetype] entry and the position restraints belong to it. *
 > >
 > >
 > > So I rechecked my .top file and found that [moleculetype] only occurs
 > > once. Perhaps I have misunderstood you. So I added the top file 
below. I

 >
 > No it doesn't. Each time you #include a new .itp file, you are 
telling grompp
 > to copy and paste the contents of that .itp file in that location. 
Have a look

 > at spc.itp - it starts a new moleculetype.
 >
 > http://www.gromacs.org/Documentation/Include_File_Mechanism
 >
 > Note how the automatically-generated "posre.itp" file is #included at 
the end of
 > the Protein_A moleculetype, *before* any other molecules are 
introduced. You
 > have to do the same with any new #include statements or directives 
you add.

 >
 > -Justin
 >
 > > did not add the contents of [atoms] [bonds] etc because I felt the 
mail

 > > would become unnecessarily long.
 > >
 > > ; Include forcefield parameters
 > > #include "ffoplsaa.itp"
 > >
 > > [ moleculetype ]
 > > ; Name nrexcl
 > > Protein_A 3
 > >
 > > [ atoms ]
 > >
 > > [ bonds ]
 > >
 > > [ pairs ]
 > >
 > > [ angles ]
 > >
 > > [ dihedrals ]
 > >
 > > [ dihedrals ]
 > >
 > > ; Include Position restraint file
 > > #ifdef POSRES
 > > #include "posre.itp"
 > > #endif
 > >
 > > ; Include water topology
 > > #include "spc.itp"
 > >
 > > #ifdef POSRES_WATER
 > > ; Position restraint for each water oxygen
 > > [ position_restraints ]
 > > ; i funct fcx fcy fcz
 > > 1 1 1000 1000 1000
 > > #endif
 > >
 > > ; Include generic topology for ions
 > > #include "ions.itp"
 > >
 > > [ system ]
 > > ; Name
 > > Protein
 > >
 > > [ molecules ]
 > > ; Compound #mols
 > > Protein_A 1
 > >
 > > Thanks again for your help,
 > > Abdullah
 > >
 > >
 > > 

 > > Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign
 > > up now. 
 >
 > --
 > 
 >
 > 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/search before 
posting!

 > Please don't post (un)subscribe requests to the list. Use the
 > www interface or send i

[gmx-users] 1-4 interaction not within cut-off

2010-06-03 Thread Rabab Toubar

Hi,

I set my .mdp file to minimize the system for 1000 steps, but it stopped at 
~200 saying: "Stepsize too small, or no change in energy.
Converged to machine precision, but not to the requested precision Fmax < 10" 
but the molecule is now outside the box

I did position restraint for 2ns using LINCS, and things went well

running md, it ran for only 0.3 ns out of 30, and I got an error message that 
1-4 interaction between 2 atoms are at a distance > table-size (1nm) with a 
suggestion to increase the table-extension in mdp file.
I checked  
http://www.gromacs.org/Documentation/Errors#1-4_interaction_not_within_cut-off 
suggesting reminimizing. 

My question is: is it OK that the system doesn't minimize till the end of the 
specified number of steps? is it OK to be outside the box as long as you assign 
boundary conditions as in case of NAMD? and what is the best option - you think 
- I have to solve the md problem

Any suggestions are highly apprecitaed
Rabab



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[gmx-users] Creation of a Non-Standard Residue

2010-06-03 Thread Mark Zottola

I am trying to to create a non-standard residue - HCN.  This cannot be done
by the Dundee PRODRG server as it subsumes the polar hydrogen into the
carbon.  This results in a diatomic molecule that the program cannot handle.

I do mind creating a new drug by hand, but a search through the email list
has been less than fruitful.  I have done parameter/non-standard residue
formation in AMBER, I believe I understand the process.  Yet, there is no
clear delineation of how one does charges.  The best I found was the proper
suggestion that CHELPG charges from a QM calculation should be
employed.  This is to be expected, but WHICH method should one use:
hf/6-31g*, MNDO, something else?

I know I will have to augment my parameter file to include the new atom
types and parameters.  But as HCN has a polar hydrogen "on a carbon" how do
I ensure that this is explicitly maintained?  If I lie and call the hydrogen
on carbon "H", the designation for an atom bonded to Nitrogen, is this
enough to keep that hydrogen explicit?  I also want to make a solvent box of
HCN (cheaper and safer than trying this experimentally!!).  I am assuming
that simple electrostatics balanced against Van der Waals interactions will
dictate the proximity of hydrogen bond donor to acceptor in this
forcefield.

Finally, I assume a kluge of non-bonded parameters (van derWaals) is
reasonable or is there a preferred way of determining an L-J potential?

If I totally missed the answers to these questions, a hint on better
keywords or a good reference encompassing these issues would be welcome.

Thanks.


Mark
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[gmx-users] Re: Creation of a Non-Standard Residue

2010-06-03 Thread Mark Zottola

I just realized a damning typo...

I do NOT mind creating a new drug file by hand... is what I meant to write


On Thu, Jun 3, 2010 at 11:53 AM, Mark Zottola  wrote:

>
> I do mind creating a new drug by hand, but a search through the email list
> has been less than fruitful.  I have done parameter/non-standard residue
> formation in AMBER, I believe I understand the process.  Yet, there is no
> clear delineation of how one does charges.  The best I found was the proper
> suggestion that CHELPG charges from a QM calculation should be
> employed.  This is to be expected, but WHICH method should one use:
> hf/6-31g*, MNDO, something else?
>
>
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[gmx-users] intermolecular contributions/building up a long polymer chain

2010-06-03 Thread Moeed

Dear gmx users,

Please kindly help me with the following issues:

I am trying to extract interaction energies (non bonded) between hexane
molecules (vdw and electrostatics). I have used rerun program to exclude
intramolecular non bonded terms and here is the breakdown of energy from
g_energy. However, in the manual I read about dispersion correction and long
range interactions.

Actually, I do not know for a hydrocarbon (hexane) system I should look at
which contributions to get intermolecular interaction energies (long range,
short range, dispersion correction) mainly because I can not distinguish
them even after reding the maual

1- Can you please explain the difference between longe range and short range
interactions. What this breakdown shows for intermolecular contributions is
just short range LJ and coulomb (SR). Is there any other program (other than
g_energy) to list other energy terms?

Energy  Average   RMSD Fluct.  Drift
Tot-Drift

---

Angle   4400.09284.259237.26854.2184
542.293

Ryckaert-Bell.  1009.62124.46894.037928.2417
282.474

LJ-14   648.41140.6844 39.9262.70793
27.0848

Coulomb-14 -278.65434.422711.807111.1987
112.01

LJ (SR)-3010.16 47.96842.53887.67736
76.789

Coulomb (SR)74.7846 2.51862.47007   0.170417
1.70451

Coul. recip.   -78.04362.586061.54725  -0.717662
-7.17805

Potential   2766.05454.268342.141103.497
1035.18


2- In the manual I see the unit for energy is :KJ/mol but the unit for heat
capacity obtained form g energy is in J/mol K. For this reason, I doubt the
unit of energy in this list. Is it KJ/mol or J/mol?

3- I am trying to generate the top file for polyethylene chain using the
information from the archive:
http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html

What I intend to do is investigating the conformations of a much longer
chain. Could you please tell me how to generate a longer chain with the
given residue types proposed in the above post.


thank you,
moeed
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Re: [gmx-users] 1-4 interaction not within cut-off

Rabab Toubar wrote:

Hi,

I set my .mdp file to minimize the system for 1000 steps, but it stopped
at ~200 saying: "Stepsize too small, or no change in energy.
Converged to machine precision, but not to the requested precision Fmax
< 10" but the molecule is now outside the box

This is not really a problem, provided that both the potential energy and Fmax
that resulted are
reasonable.http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision

I did position restraint for 2ns using LINCS, and things went well

running md, it ran for only 0.3 ns out of 30, and I got an error message
that 1-4 interaction between 2 atoms are at a distance > table-size
(1nm) with a suggestion to increase the table-extension in mdp file.
I checked
http://www.gromacs.org/Documentation/Errors#1-4_interaction_not_within_cut-off
suggesting reminimizing.

The other possibility is that your .mdp settings are inappropriate, but you
haven't provided that information.

My question is: is it OK that the system doesn't minimize till the end
of the specified number of steps? is it OK to be outside the box as long
as you assign boundary conditions as in case of NAMD? and what is the
best option - you think - I have to solve the md problem

Whether or not you need to revisit the EM procedure depends on how well it
actually did (see comment above). The periodicity effect is a non-issue, since
there is no "outside" of a periodic box.

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

-Justin

Any suggestions are highly apprecitaed
Rabab

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] intermolecular contributions/building up a long polymer chain




Moeed wrote:

Dear gmx users,

Please kindly help me with the following issues:

I am trying to extract interaction energies (non bonded) between hexane 
molecules (vdw and electrostatics). I have used rerun program to exclude 
intramolecular non bonded terms and here is the breakdown of energy from 
g_energy. However, in the manual I read about dispersion correction and 
long range interactions.


Actually, I do not know for a hydrocarbon (hexane) system I should look 
at which contributions to get intermolecular interaction energies (long 
range, short range, dispersion correction) mainly because I can not 
distinguish them even after reding the maual


1- Can you please explain the difference between longe range and short 
range interactions. What this breakdown shows for intermolecular 
contributions is just short range LJ and coulomb (SR). Is there any 
other program (other than g_energy) to list other energy terms?




Long range interactions fall outside the short-range cutoff.  You will not have 
an explicit "LR" term unless you are using a twin-range cutoff, which presumably 
you are not.


Energy  Average   RMSD Fluct.  Drift  
Tot-Drift


---

Angle   4400.09284.259237.26854.2184
542.293


Ryckaert-Bell.  1009.62124.46894.037928.2417
282.474


LJ-14   648.41140.6844 39.9262.70793
27.0848


Coulomb-14 -278.65434.422711.807111.1987 
112.01


LJ (SR)-3010.16 47.96842.53887.67736 
76.789


Coulomb (SR)74.7846 2.51862.47007   0.170417
1.70451


Coul. recip.   -78.04362.586061.54725  -0.717662   
-7.17805


Potential   2766.05454.268342.141103.497
1035.18


 

2- In the manual I see the unit for energy is :KJ/mol but the unit for 
heat capacity obtained form g energy is in J/mol K. For this reason, I 
doubt the unit of energy in this list. Is it KJ/mol or J/mol?




Energies are kJ/mol.  Believe the manual.

3- I am trying to generate the top file for polyethylene chain using the 
information from the archive: 
http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html


What I intend to do is investigating the conformations of a much longer 
chain. Could you please tell me how to generate a longer chain with the 
given residue types proposed in the above post.




The length of the chain is dependent solely upon what you have in your 
coordinate file.  The use of pdb2gmx with .rtp entries implies only that you 
have some sort of repeating building blocks.  Do confirm that the parameters in 
the post you quote are appropriate; I created those entries as an example only, 
and have had no reason to confirm their usefulness or validity.


-Justin



thank you,
moeed

 



--


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] Extracting enthalpies during or after MD

2010-06-03 Thread lists

Hello,

I am wondering if it is possible to output interaction energies/enthalpies
during an MD simulation between specific groups of atoms.

The energies are all calculated anyways before the forces are calculated,
so I am wondering if there is an option to output those energies to a
file?

I saw someone on the list who had re-coded gromacs to output these
energies, but this resulted in a significant slowdown of the simulation
because he made the code perform output in an inner-loop.

If this is not an option, is there a clever way to get these numbers out
after having run the simulation. Essentially, what I want is to get the
enthalpy, between e.g. a PO4 head-group bead and a C1A tail-bead using the
Martini FF.

Any and all suggestions are welcome!
Best regards,
Jesper

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Re: [gmx-users] Extracting enthalpies during or after MD

- Original Message -
From: li...@jsx.dk
Date: Friday, June 4, 2010 8:47
Subject: [gmx-users] Extracting enthalpies during or after MD
To: gmx-users@gromacs.org

> Hello,
> 
> I am wondering if it is possible to output interaction 
> energies/enthalpiesduring an MD simulation between specific 
> groups of atoms.

Yes. Look up "energy groups" in the manual.
 
> The energies are all calculated anyways before the forces are 
> calculated,so I am wondering if there is an option to output 
> those energies to a
> file?

They'll go to the .edr file and be accessible with (e.g.) g_energy

> I saw someone on the list who had re-coded gromacs to output these
> energies, but this resulted in a significant slowdown of the 
> simulationbecause he made the code perform output in an inner-loop.

Yep, don't do that.

> If this is not an option, is there a clever way to get these 
> numbers out
> after having run the simulation. Essentially, what I want is to 
> get the
> enthalpy, between e.g. a PO4 head-group bead and a C1A tail-bead 
> using the
> Martini FF.

You can implement the above to happen during your simulation, or use the 
facility of mdrun -rerun on a previously computed trajectory with a suitable 
.tpr to recompute only the energies of the groups of interest .

Mark

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Re: [gmx-users] Creation of a Non-Standard Residue



- Original Message -
From: Mark Zottola 
Date: Friday, June 4, 2010 1:55
Subject: [gmx-users] Creation of a Non-Standard Residue
To: Discussion list for GROMACS users 

> I am trying to to create a non-standard residue - HCN.  This cannot be done 
> by the Dundee PRODRG server as it subsumes the polar hydrogen into the 
> carbon.  This results in a diatomic molecule that the program cannot handle.  
> >   > I do mind creating a new drug by hand, but a search through the email 
> list has been less than fruitful.  I have done parameter/non-standard residue 
> formation in AMBER, I believe I understand the process.  Yet, there is no 
> clear delineation of how one does charges.  The best I found was the proper 
> suggestion that CHELPG charges from a QM calculation should be employed.  
> This is to be expected, but WHICH method should one use:  hf/6-31g*, MNDO, 
> something else?

The standard advice is here 
http://www.gromacs.org/Documentation/How-tos/Parameterization. For starters, 
choose a force field you want to parameterize HCN to work *with*.

 > I know I will have to augment my parameter file to include the new atom 
 > types and parameters.  But as HCN has a polar hydrogen "on a carbon" how do 
 > I ensure that this is explicitly maintained?  If I lie and call the hydrogen 
 > on carbon "H", the designation for an atom bonded to Nitrogen, is this 
 > enough to keep that hydrogen explicit?  I also want to make a solvent box of 
 > HCN (cheaper and safer than trying this experimentally!!).  I am assuming 
 > that simple electrostatics balanced against Van der Waals interactions will 
 > dictate the proximity of hydrogen bond donor to acceptor in this forcefield. 
 >  

You seem to be creating problems for yourself by not having a clear objective - 
or at least not expressing it here!
   
 > Finally, I assume a kluge of non-bonded parameters (van derWaals) is 
 > reasonable or is there a preferred way of determining an L-J potential?

Guessing values randomly is likely to get random results. Parameterization and 
validation of parameters are difficult topics to work on, and not encouraged 
for newcomers.
  
 > If I totally missed the answers to these questions, a hint on better 
 > keywords or a good reference encompassing these issues would be welcome.
Mark

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Re: [gmx-users] extra non bonded interaction

- Original Message -
From: Thanasis Koukoulas 
Date: Thursday, June 3, 2010 23:26
Subject: [gmx-users] extra non bonded interaction
To: gmx-users@gromacs.org

---
| > hello 
> 
> I have a problem with C10O3H. The problem is that i use Trappe model and 
> there you can add an extra repulsive interaction of molecule 10 (Oxygen) with 
> molecule 14 (Hydrogen). The formula that TraPPE uses is 4E7/rij^12. with the 
> transformation of 4E7in gromacs units (kJ*nm^12*mol-1) i take a numper 
> 3.325789e-7 witch until now i put it in [pairs] with the sexond function like 
> this:
> 
> [Pairs]
> 10 14 2 0 0 0 03.325789e-7

This line doesn't seem to have enough fields (See table 5.4 of manual)

> the zeros i use is  for fudgeQQ because i dont want to have coulomb 14 in 
> this pair and  charges of both of them for the same reason. it seem to work 
> because at the end i have a coulombic energy 1-4 at a reasonable price but 
> the total energy is not correct.

Construct a toy example (minimal single molecule in vacuo?) that will let you 
trouble-shoot what you are doing by computing by hand what the energy should 
be. Compare with GROMACS with and without this extra [pairs].

Be sure your combination rule paradigm is what you want it to be.

Mark

> please if someone can think smth answer me. The prices i get i can compare 
> them with another researcher who did the same work with the use of monte  
> carlo. i am stucked for three months and i have read th manual over and and 
> over again without result
 |
---


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Re: [gmx-users] Extracting enthalpies during or after MD

2010-06-03 Thread lists

Hi Mark,

Thanks for the quick reply.

The thing with the energy groups makes sense now. But I have run into
another problem with the method...

The same atom cannot be in multiple energy groups during a simulation.

Let say that I want the interaction energy between water and lipid
head-group and also water and protein. Will I then have to do "mdrun
-rerun" to get all the energy group I want out of this?
And does mdrun -rerun work on a parallel cluster?

Best regards,
Jesper




> - Original Message -
> From: li...@jsx.dk
> Date: Friday, June 4, 2010 8:47
> Subject: [gmx-users] Extracting enthalpies during or after MD
> To: gmx-users@gromacs.org
>
>> Hello,
>>
>> I am wondering if it is possible to output interaction
>> energies/enthalpiesduring an MD simulation between specific
>> groups of atoms.
>
> Yes. Look up "energy groups" in the manual.
>
>> The energies are all calculated anyways before the forces are
>> calculated,so I am wondering if there is an option to output
>> those energies to a
>> file?
>
> They'll go to the .edr file and be accessible with (e.g.) g_energy
>
>> I saw someone on the list who had re-coded gromacs to output these
>> energies, but this resulted in a significant slowdown of the
>> simulationbecause he made the code perform output in an inner-loop.
>
> Yep, don't do that.
>
>> If this is not an option, is there a clever way to get these
>> numbers out
>> after having run the simulation. Essentially, what I want is to
>> get the
>> enthalpy, between e.g. a PO4 head-group bead and a C1A tail-bead
>> using the
>> Martini FF.
>
> You can implement the above to happen during your simulation, or use the
> facility of mdrun -rerun on a previously computed trajectory with a
> suitable .tpr to recompute only the energies of the groups of interest .
>
> 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/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.
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Re: [gmx-users] Creation of a Non-Standard Residue

2010-06-03 Thread Mark Zottola

Let me clarify.

I have no problem determining the bond stretching or angle bending
parameters for HCN.  This was a very straightforward task.  Unit conversion
to get those values in a gromacs force field was also a non-issue.

The problems I am having are:

1) How do I specify a POLAR hydrogen on a carbon atom?  There are polar
hydrogens (or so it seems) in the gromacs forcei field, but ostensibly they
are on heteroatoms such as nitrogen or oxyen.  Is there a way to force
gromacs to let a polar hydrogen on a carbon?

2) I AM looking for advice on the van der Waals parameters.  Yes, I can
guess and tweak until the cows come home, but obviously there are
recommendations which I do not know.  So... any suggestions on this.

3)  The problem is quite simple, I want to develop parameters for HCN so I
can use it as both ligand AND as a component n a solvent box.  I do have the
formula (4 or 5 steps from the web) to create my solvent box, but I need to
have HCN properly parameterized.

4)  I am asking for this as I cannot use the Dundee server to make the
appropriate topology file.

The warning blurb was good at saying "Parameter development is done by
professionals, so please do not try this at home."  I am asking for help in
the above issues as I am new to GROMACS but NOT other MD programs.

Thanks again for any help.

On Thu, Jun 3, 2010 at 7:30 PM, Mark Abraham wrote:

>
>
> - Original Message -
> From: Mark Zottola 
> Date: Friday, June 4, 2010 1:55
> Subject: [gmx-users] Creation of a Non-Standard Residue
> To: Discussion list for GROMACS users 
>
> > I am trying to to create a non-standard residue - HCN.  This cannot be
> done by the Dundee PRODRG server as it subsumes the polar hydrogen into the
> carbon.  This results in a diatomic molecule that the program cannot handle.
>
> >
>
>  > I do mind creating a new drug by hand, but a search through the email
> list has been less than fruitful.  I have done parameter/non-standard
> residue formation in AMBER, I believe I understand the process.  Yet, there
> is no clear delineation of how one does charges.  The best I found was the
> proper suggestion that CHELPG charges from a QM calculation should be
> employed.  This is to be expected, but WHICH method should one use:
> hf/6-31g*, MNDO, something else?
>
> The standard advice is here
> http://www.gromacs.org/Documentation/How-tos/Parameterization. For
> starters, choose a force field you want to parameterize HCN to work *with*.
>
>
>
> > I know I will have to augment my parameter file to include the new atom
> types and parameters.  But as HCN has a polar hydrogen "on a carbon" how do
> I ensure that this is explicitly maintained?  If I lie and call the hydrogen
> on carbon "H", the designation for an atom bonded to Nitrogen, is this
> enough to keep that hydrogen explicit?  I also want to make a solvent box of
> HCN (cheaper and safer than trying this experimentally!!).  I am assuming
> that simple electrostatics balanced against Van der Waals interactions will
> dictate the proximity of hydrogen bond donor to acceptor in this
> forcefield.
>
> You seem to be creating problems for yourself by not having a clear
> objective - or at least not expressing it here!
>
>
>
> > Finally, I assume a kluge of non-bonded parameters (van derWaals) is
> reasonable or is there a preferred way of determining an L-J potential?
>
> Guessing values randomly is likely to get random results. Parameterization
> and validation of parameters are difficult topics to work on, and not
> encouraged for newcomers.
>
>
>
> > If I totally missed the answers to these questions, a hint on better
> keywords or a good reference encompassing these issues would be welcome.
>
> 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/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
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>
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Re: [gmx-users] Extracting enthalpies during or after MD



- Original Message -
From: li...@jsx.dk
Date: Friday, June 4, 2010 10:35
Subject: Re: [gmx-users] Extracting enthalpies during or after MD
To: Discussion list for GROMACS users 

> Hi Mark,
> 
> Thanks for the quick reply.
> 
> The thing with the energy groups makes sense now. But I have run into
> another problem with the method...
> 
> The same atom cannot be in multiple energy groups during a simulation.

It doesn't want to be... see manual 3.3
 
> Let say that I want the interaction energy between water and lipid
> head-group and also water and protein. Will I then have to do "mdrun
> -rerun" to get all the energy group I want out of this?

One (re)run will suffice unless you have large numbers of groups. Consider 
whether g_enemat is useful for you.

> And does mdrun -rerun work on a parallel cluster?

Yes, it's exactly like mdrun, but derives the next positions from the 
trajectory, not from integration. If your groups are small, then use of energy 
group exclusions will make the problem small enough that you don't need 
parallelism, however.

Obviously these interaction energies won't mean anything if you're using PME, 
since the long-range term can't be decomposed.

Mark 

> > - Original Message -
> > From: li...@jsx.dk
> > Date: Friday, June 4, 2010 8:47
> > Subject: [gmx-users] Extracting enthalpies during or after MD
> > To: gmx-users@gromacs.org
> >
> >> Hello,
> >>
> >> I am wondering if it is possible to output interaction
> >> energies/enthalpiesduring an MD simulation between specific
> >> groups of atoms.
> >
> > Yes. Look up "energy groups" in the manual.
> >
> >> The energies are all calculated anyways before the forces are
> >> calculated,so I am wondering if there is an option to output
> >> those energies to a
> >> file?
> >
> > They'll go to the .edr file and be accessible with (e.g.) g_energy
> >
> >> I saw someone on the list who had re-coded gromacs to output these
> >> energies, but this resulted in a significant slowdown of the
> >> simulationbecause he made the code perform output in an inner-loop.
> >
> > Yep, don't do that.
> >
> >> If this is not an option, is there a clever way to get these
> >> numbers out
> >> after having run the simulation. Essentially, what I want is to
> >> get the
> >> enthalpy, between e.g. a PO4 head-group bead and a C1A tail-bead
> >> using the
> >> Martini FF.
> >
> > You can implement the above to happen during your simulation, 
> or use the
> > facility of mdrun -rerun on a previously computed trajectory 
> with a
> > suitable .tpr to recompute only the energies of the groups of 
> interest .
> >
> > 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/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/mailing_lists/users.php
> 
> 
> -- 
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Re: [gmx-users] Creation of a Non-Standard Residue



- Original Message -
From: Mark Zottola 
Date: Friday, June 4, 2010 10:40
Subject: Re: [gmx-users] Creation of a Non-Standard Residue
To: Discussion list for GROMACS users 

> Let me clarify. >   > I have no problem determining the bond stretching or 
> angle bending parameters for HCN.  This was a very straightforward task.  
> Unit conversion to get those values in a gromacs force field was also a 
> non-issue.  >   > The problems I am having are: >   > 1) How do I specify a 
> POLAR hydrogen on a carbon atom?  There are polar hydrogens (or so it seems) 
> in the gromacs forcei field, but ostensibly they are on heteroatoms such as 
> nitrogen or oxyen.  Is there a way to force gromacs to let a polar hydrogen 
> on a carbon?

ffgmx has been deprecated for years (as pdb2gmx tells users), so you'll find it 
hard to interest people with this problem. PRODRG beta works for one of the 
GROMOS forcefields, however. The general issue is that you're trying to develop 
an all-atom model, so you need to target an all-atom forcefield.
   
 > 2) I AM looking for advice on the van der Waals parameters.  Yes, I can 
 > guess and tweak until the cows come home, but obviously there are 
 > recommendations which I do not know.  So... any suggestions on this. >   > 
 > 3)  The problem is quite simple, I want to develop parameters for HCN so I 
 > can use it as both ligand AND as a component n a solvent box.  I do have the 
 > formula (4 or 5 steps from the web) to create my solvent box, but I need to 
 > have HCN properly parameterized.>   > 4)  I am asking for this as I 
 > cannot use the Dundee server to make the appropriate topology file. >   > 
 > The warning blurb was good at saying "Parameter development is done by 
 > professionals, so please do not try this at home."  I am asking for help in 
 > the above issues as I am new to GROMACS but NOT other MD programs.
Well, then you'll know how to follow up on the concrete advice there - start by 
reading the literature for the force field of interest to see how VDW 
parameters were derived. How best to follow up is strongly problem- and 
forcefield-dependent. You might decide the path of least resistance is to use 
an AMBER forcefield in GROMACS so that you can use AMBERTools automated 
parameterization tools.

Mark

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Re: [gmx-users] Creation of a Non-Standard Residue

Mark Zottola wrote:

Let me clarify.

I have no problem determining the bond stretching or angle bending 
parameters for HCN.  This was a very straightforward task.  Unit 
conversion to get those values in a gromacs force field was also a 
non-issue.

The problems I am having are:

1) How do I specify a POLAR hydrogen on a carbon atom?  There are polar 
hydrogens (or so it seems) in the gromacs forcei field, but ostensibly 
they are on heteroatoms such as nitrogen or oxyen.  Is there a way to 
force gromacs to let a polar hydrogen on a carbon?

You can specify whatever you want in the topology, as long as you can justify 
that it is consistent with the underlying force field model.  For instance, 
aromatic C-H pairs are represented by explicit hydrogens in the Gromos force fields.

2) I AM looking for advice on the van der Waals parameters.  Yes, I can 
guess and tweak until the cows come home, but obviously there are 
recommendations which I do not know.  So... any suggestions on this.

This is a tough task.  Much of the Gromos derivation relies on empirical fitting 
and tweaking to reproduce condensed-phase behavior.  You could start with a few 
existing atom types, simulating a box of HCN, and revising based on the results 
you get (densities, heat of vaporization, etc).  The primary literature on the 
derivation of these parameter sets is a bit sparse, but you should be able to 
get started.

3)  The problem is quite simple, I want to develop parameters for HCN so 
I can use it as both ligand AND as a component n a solvent box.  I do 
have the formula (4 or 5 steps from the web) to create my solvent box, 
but I need to have HCN properly parameterized. 

As is the case for any small molecule :)

4)  I am asking for this as I cannot use the Dundee server to make the 
appropriate topology file.

The warning blurb was good at saying "Parameter development is done by 
professionals, so please do not try this at home."  I am asking for help 
in the above issues as I am new to GROMACS but NOT other MD programs.

I would estimate that 95% of the parameterization questions asked on the list 
are posted by people in way over their heads, so it is good to know your 
experience level.  I would say that the best approach is (unfortunately) 
somewhat empirical, but such is the nature of the beast with Gromos force 
fields.  Some simple QM might give you a start for calculating charges, but as I 
understand it, QM was used in the Gromos derivations only to get relative 
electron densities around all of the atoms, after which charges were assigned 
(empirically) and revised to fit condensed-phase behavior.

-Justin

Thanks again for any help. 

On Thu, Jun 3, 2010 at 7:30 PM, Mark Abraham > wrote:

- Original Message -
From: Mark Zottola mailto:mzott...@gmail.com>>
Date: Friday, June 4, 2010 1:55
Subject: [gmx-users] Creation of a Non-Standard Residue
To: Discussion list for GROMACS users mailto:gmx-users@gromacs.org>>

 > I am trying to to create a non-standard residue - HCN.  This
cannot be done by the Dundee PRODRG server as it subsumes the polar
hydrogen into the carbon.  This results in a diatomic molecule that
the program cannot handle.

 >  

 > I do mind creating a new drug by hand, but a search through the

email list has been less than fruitful.  I have
done parameter/non-standard residue formation in AMBER, I believe I
understand the process.  Yet, there is no clear delineation of how
one does charges.  The best I found was the proper suggestion
that CHELPG charges from a QM calculation should be employed.  This
is to be expected, but WHICH method should one use:  hf/6-31g*,
MNDO, something else?

The standard advice is here
http://www.gromacs.org/Documentation/How-tos/Parameterization. For
starters, choose a force field you want to parameterize HCN to work
*with*.

 > I know I will have to augment my parameter file to include the

new atom types and parameters.  But as HCN has a polar hydrogen "on
a carbon" how do I ensure that this is explicitly maintained?  If I
lie and call the hydrogen on carbon "H", the designation for an atom
bonded to Nitrogen, is this enough to keep that hydrogen explicit?
 I also want to make a solvent box of HCN (cheaper and safer than
trying this experimentally!!).  I am assuming that simple
electrostatics balanced against Van der Waals interactions will
dictate the proximity of hydrogen bond donor to acceptor in this
forcefield. 

You seem to be creating problems for yourself by not having a clear
objective - or at least not expressing it here!

 > Finally, I assume a kluge of non-bonded parameters (van derWaals)

is reasonable or is there a preferred way of determining an L-J
potential?

Guessing values randomly is

Re: [gmx-users] Creation of a Non-Standard Residue



- Original Message -
From: Mark Abraham 
Date: Friday, June 4, 2010 11:51
Subject: Re: [gmx-users] Creation of a Non-Standard Residue
To: Discussion list for GROMACS users 

> 
> 
> - Original Message -
> From: Mark Zottola 
> Date: Friday, June 4, 2010 10:40
> Subject: Re: [gmx-users] Creation of a Non-Standard Residue
> To: Discussion list for GROMACS users 
> 
> > Let me clarify.>  >  >  > I have no problem determining the bond stretching 
> > or angle bending parameters for HCN.  This was a very straightforward task. 
> >  Unit conversion to get those values in a gromacs force field was also a 
> > non-issue.>   >  >  > The problems I am having are:>  >  >  > 1) How do I 
> > specify a POLAR hydrogen on a carbon atom?  There are polar hydrogens (or 
> > so it seems) in the gromacs forcei field, but ostensibly they are on 
> > heteroatoms such as nitrogen or oxyen.  Is there a way to force gromacs to 
> > let a polar hydrogen on a carbon?

Perhaps I misinterpreted this the first time. Of course all-atom forcefields 
have polar hydrogens. It seems your problem is that you can't make PRODRG 
produce an .itp suitable for ffgmx for HCN, because it assumes H bonded to C is 
non-polar. If so, then you have a potentially tricky problem and need to 
consult the documentation of that tool. Such a problem exists before GROMACS 
gets involved, so your second question seems misformed - GROMACS will do 
whatever you tell it, if that is consistent with the force field you're using.

Mark
 
> ffgmx has been deprecated for years (as pdb2gmx tells users), so you'll find 
> it hard to interest people with this problem. PRODRG beta works for one of 
> the GROMOS forcefields, however. The general issue is that you're trying to 
> develop an all-atom model, so you need to target an all-atom forcefield.
>
>  > 2) I AM looking for advice on the van der Waals parameters.  Yes, I can 
> guess and tweak until the cows come home, but obviously there are 
> recommendations which I do not know.  So... any suggestions on this.>  >  >  
> > 3)  The problem is quite simple, I want to develop parameters for HCN so I 
> can use it as both ligand AND as a component n a solvent box.  I do have the 
> formula (4 or 5 steps from the web) to create my solvent box, but I need to 
> have HCN properly parameterized.  >   >  >  > 4)  I am asking for this as I 
> cannot use the Dundee server to make the appropriate topology file.>  >  >  > 
> The warning blurb was good at saying "Parameter development is done by 
> professionals, so please do not try this at home."  I am asking for help in 
> the above issues as I am new to GROMACS but NOT other MD programs.> 
> Well, then you'll know how to follow up on the concrete advice there - start 
> by reading the literature for the force field of interest to see how VDW 
> parameters were derived. How best to follow up is strongly problem- and 
> forcefield-dependent. You might decide the path of least resistance is to use 
> an AMBER forcefield in GROMACS so that you can use AMBERTools automated 
> parameterization tools.
> 
> Mark > -- 
> gmx-users mailing listgmx-users@gromacs.org
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[gmx-users] Is there a way to energy minimize only part of macromolecular structure?

2010-06-03 Thread Arthur Roberts


Hi, all,

Is there a way to energy minimize only part of the structure?  I have  
made the ndx file, but I am not sure what parameters to use with  
mdrun.  Your help is much appreciated.


Art

Dr. Arthur Roberts, Ph.D.
University of California, San Diego
Skaggs School of Pharmacy and Pharmaceutical Sciences
9500 Gilman Drive #0703
La Jolla, CA 92093-0703

email: aroberts99...@yahoo.com
cell: 206-850-7468
skype=aroberts92122



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[gmx-users] After simulated annealing and then energy minimizing, a docked molecule seems to still be distorted?

2010-06-03 Thread Arthur Roberts


Hi, All,

I am doing simulated annealing of a docked molecule.  Because of  
vibrational modes, the aromatic rings are somewhat distorted.  I tried  
energy minimization afterwords, but I can't seem to get the  
distortions out of the rings.  Is there a way to energy minimize, so  
that the geometry is correct for the docked molecule?  I tried  
reducing the emtol a lot (i.e. 0.0001), but this didn't improve things  
much.  Your help is much appreciated.


Art

Dr. Arthur Roberts, Ph.D.
University of California, San Diego
Skaggs School of Pharmacy and Pharmaceutical Sciences
9500 Gilman Drive #0703
La Jolla, CA 92093-0703

email: aroberts99...@yahoo.com
cell: 206-850-7468
skype=aroberts92122



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Re: [gmx-users] Is there a way to energy minimize only part of macromolecular structure?