Re: [gmx-users] soft-core and coulomb transformation

[bharat v. adkar]

Hi,
  I can see the curves getting overlapped after the code-modification 
suggested by Berk for ethane to methane coulomb transformations in forward 
and reverse directions.


Thanks Berk and David.

bharat


On Wed, 14 Nov 2007, bharat v. adkar wrote:



hi,
even i am also checking the ethane->methane case with the fix you suggested. 
equilibration values appear to be okay. will let you know by tommorrow the 
final results..


thanks

bharat


On Wed, 14 Nov 2007, Berk Hess wrote:


 Hi,

 The bug was indeed was I expected.
 I have fixed it for version 3.3.3.

 You might not notice it easily, since the direct space contribution is
 usually
 larger than the mesh part.
 But for a two particle system I got nan's.

 Berk.


>  From: "David Mobley" <[EMAIL PROTECTED]>
>  Reply-To: Discussion list for GROMACS users 
>  To: "Discussion list for GROMACS users" 
>  Subject: Re: [gmx-users] soft-core and coulomb transformation
>  Date: Mon, 12 Nov 2007 16:17:36 -0800
> 
>  Berk,
> 
> >   But what do you mean with charging and discharging?
> > 
> >   Going one way or the other in lambda does not matter.

> >   What matters is if there are particles that have zero charge
> >   in the A-state topology, while they have a non-zero charge
> >   in the B-state topology.
> 
>  Sorry, what I mean by "charging" versus "discharging" is that

>  "charging" is where the A state has zero charges and the B state has
>  normal charges, and discharging is the reverse. So "charging" is the
>  scenario you describe, and "discharging" is the reverse.
> 
>  David
> 
> >   Berk.
> > 
> > 
> > >  From: "David Mobley" <[EMAIL PROTECTED]>

> > >  Reply-To: Discussion list for GROMACS users 
> > >  To: "bharat v. adkar" <[EMAIL PROTECTED]>
> > >  CC: Discussion list for GROMACS users 
> > >  Subject: Re: [gmx-users] soft-core and coulomb transformation
> > >  Date: Mon, 12 Nov 2007 10:26:37 -0800
> > > 
> > >  Following up on this issue, discharging phenol in water appears to
> > >  give the same results as charging phenol in water. In other words, 
> > >  so

> > >  far the only cases for which there seem to be a problem are relative
> > >  calculations (and so far I haven't looked at this for any other than
> > >  Bharat's test cases).
> > > 
> > >  Bharat, be sure you submit a bugzilla and we'll see how things go 
> > >  from
> > >  there. I may at some point try setting up some of my own relative 
> > >  free

> > >  energy topologies and see if I see the same effects, but I'm not
> > >  likely to have time for that for a couple days.
> > > 
> > >  Thanks,

> > >  David
> > > 
> > > 
> > > 
> > 
> > 
> >   _

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RE: [gmx-users] tabulated bonded interactions

[Berk Hess]

Tabulated bonded interactions will be only in Gromacs 4.0.

We should indeed really try to keep the update lists up to date.

Berk.


From: Ran Friedman <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users 
To: Discussion list for GROMACS users 
Subject: [gmx-users] tabulated bonded interactions
Date: Wed, 14 Nov 2007 16:33:44 +0100

Dear all,

Tabulated bonded interactions have been implemented in December 2006. I
wanted to know if they can be used in GMX 3.3.2 or 3.3.3 (and how).
I couldn't find a list of changes between 3.3.1 and 3.3.2 online, and
even the updates from 3.2 to 3.3 are still "under construction"
according to the web site:
http://www.gromacs.org/index.php?option=com_content&task=category§ionid=4&id=58&Itemid=132

Thanks,
Ran.
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[gmx-users] make gives error in futil.c with mpi and ccc-6.5.6.002-1

[chris . neale]

I have had some success reproducing the event with a simple c program  
and the issue appears to be with the in-house mpicc wrapper script.  
The difference between gcc and mpicc appears limited to strings  
(-D=\"string\") and does not show up in numerical form (e.g. -D=4)


I'll post another update when the issue is resolved.

Chris.

In the following examples cc is the same as mpicc (they both point to  
a script called 'compile') but mpicc invokes slightly different  
linking options than cc


$ cat prog.c
#include 
#include 

int main(int argn,char *args[]){
printf("The value of MYDEF is %s\n",MYDEF);
}

$ gcc prog.c -DMYDEF=\"aaa\" -o prog
$ prog
The value of MYDEF is aaa
$ cc prog.c -DMYDEF=\"aaa\" -o prog
cc: Error: prog.c, line 5: In this statement, "aaa" is not declared.  
(undeclared)

printf("The value of MYDEF is %s\n",MYDEF);
--^

###
However, when the defined value is a number, the problem dissapears:

$ cat prog_num.c
#include 
#include 

int main(int argn,char *args[]){
printf("The value of MYDEF is %d\n",MYDEF);
}

$ gcc prog_num.c -DMYDEF=4 -o prog_num
$ prog_num
The value of MYDEF is 4
$ cc prog_num.c -DMYDEF=4 -o prog_num
$ prog_num
The value of MYDEF is 4

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Re: [gmx-users] problems about energy minimization

[Mark Abraham]

renying wrote:
> Hello, everyone.
> I have loaded a pdb file of protein complex from Protein Data Bank and put it 
> into water soltion with pdb2gmx, editconf and genbox.
> After 400 steps of energy minimization when the potential energy seems to be 
> more or less stable, I want to do position restraints. However, it always 
> failed. 
> 
> The error info is as follows:
> Step 1, time 0.002 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 0.000645 (between atoms 13241 and 13242) rms 0.43
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>   13241  13242   31.20.1000   0.0999  0.1000
> 
> t = 0.002 ps: Water molecule starting at atom 73326 can not be settled.
> Check for bad contacts and/or reduce the timestep.Wrote pdb files with 
> previous and current coordinates
> Large VCM(group System):  0.03330, -0.01095, -0.00024, ekin-cm:  
> 2.20013e+03

Check out http://wiki.gromacs.org/index.php/Errors#LINCS_warnings for
some ideas. Looking at this water molecule's environment can help.

> The system seems to be exploding. I have tried the follwing parameters and 
> sadly, none of them works.
> nsteps  =  200/400/800/1000 steps  in em.mdp
> dt  =  0.002/0.001/0.0002 ps  in pr.mdp
> tc-grps =  Protein  SOL  or
> tc-grps =  system in pr.mdp
> tau_t   =  0.0020.002  or longer time in pr.mdp

If you're sure the problem isn't a water trapped inside a protein or
suchlike, one thing you can try is a slow heating. You'll need to do a
series of .mdp files with an initial gen_vel to (e.g.) 50K, and then use
 ref_t to increase that in similar increments.

> The total charge of the system is  -273.000 e and I didn't neutralize it for 
> some reasons. Does this matter much?

It probably isn't breaking the numerical simulation, but it could well
mean you're not modelling reality. Nature abhors a vacuum, and an
isolated charge :-)

Mark
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Re: [gmx-users] REMD As A Function of Distance Between 2 Chains

[David van der Spoel]

Mark Abraham wrote:

Huey Ling Tan wrote:

Dear all ,
thank you for those comments, we are aware of the paper.  However, we 
are not sure how to implement the replica exchange in gromacs.  We 
would like to run a set of replicas in which each replica corresponds 
to a different set of umbrella parameters.  However, when setting up a 
replica exchange run, all .tpr files use the same .ppa file so that 
each replica will have the same umbrella potential parameters.   Do 
you know how to get around this problem.


You will have to change the code to implement this algorithm.'
But first check the pull code in the cvs version of gromacs, where all 
options have been moved to the mdp file.




Mark
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Husargatan 3, Box 596,  75124 Uppsala, Sweden
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Re: [gmx-users] make gives error in futil.c with mpi and ccc-6.5.6.002-1

[David van der Spoel]

[EMAIL PROTECTED] wrote:
I have had some success reproducing the event with a simple c program 
and the issue appears to be with the in-house mpicc wrapper script. The 
difference between gcc and mpicc appears limited to strings 
(-D=\"string\") and does not show up in numerical form (e.g. -D=4)


I'll post another update when the issue is resolved.

Chris.

In the following examples cc is the same as mpicc (they both point to a 
script called 'compile') but mpicc invokes slightly different linking 
options than cc


$ cat prog.c
#include 
#include 

int main(int argn,char *args[]){
printf("The value of MYDEF is %s\n",MYDEF);
}

$ gcc prog.c -DMYDEF=\"aaa\" -o prog
$ prog
The value of MYDEF is aaa
$ cc prog.c -DMYDEF=\"aaa\" -o prog
cc: Error: prog.c, line 5: In this statement, "aaa" is not declared. 
(undeclared)

printf("The value of MYDEF is %s\n",MYDEF);
--^


How about
cc prog.c '-DMYDEF="aaa"' -o prog




###
However, when the defined value is a number, the problem dissapears:

$ cat prog_num.c
#include 
#include 

int main(int argn,char *args[]){
printf("The value of MYDEF is %d\n",MYDEF);
}

$ gcc prog_num.c -DMYDEF=4 -o prog_num
$ prog_num
The value of MYDEF is 4
$ cc prog_num.c -DMYDEF=4 -o prog_num
$ prog_num
The value of MYDEF is 4

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--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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[gmx-users] make gives error in futil.c with mpi and ccc-6.5.6.002-1

[Chris Neale]

I am having difficulty installing the mpi version of gromacs 3.3.2 on  
a new computer. I have the same problems for 3.3.1. The serial version  
appears to have worked fine. The cluster uses elan for MPI 
I have parsed some values from config.log 


configure:3291: ccc -V >&5
Compaq C T6.5-002 on Linux 2.4.21-3.7qsnet alpha
Installed as ccc-6.5.6.002-1
Red Hat Linux release 7.2 (Enigma)
Using /usr/lib/gcc-lib/alpha-redhat-linux/2.96 (4).
Compiler Driver T6.5-001 (Linux) cc Driver

I believe my previous post was rejected since it was >2000 lines so I have put 
the
entire config.log here: http://www.pomeslab.com/CN_GromacsPost_111407.html
and reposted.

mpicc appears to link like this (although the script is complicated enough
that I am not sure if this variable gets modified later):
my %mpilibs ='-L/usr/lib/mpi/mpi_compaq/lib -lmpifarg -lmpi -lelan'

I think that I must have autoconf somewhere since the Makefile was created, 
however:
$automake --version
automake (GNU automake) 1.4-p5
$ autoconf --version
bash: autoconf: command not found

I have found some posts related to futil.c including the following  
potential fix

http://www.gromacs.org/pipermail/gmx-users/2005-January/013806.html
but I didn't understand where the quotes were intended to go and the  
next reply indicates that this is not a good idea in any event.


Another post indicates that I may be required to link it myself and  
avoid the mpicc wrapper. I have tried including the following lines in  
my compilation script before calling configure


export CC=gcc
export MPICC=gcc
export LIBS="-lmpi"

but configure ends very quickly with the error message:
checking for C compiler default output file name... configure: error:  
C compiler cannot create executables


Thanks for any assistance.
Chris.



I ran it like this:

#!/bin/bash

MD=/scratch/cneale/exe/gromacs-3.3.2
cd $MD

mkdir exec
export FFTW_LOCATION=/home/cneale/exe/fftw-3.1.2/exec
export GROMACS_LOCATION=${MD}/exec
export CPPFLAGS="-I$FFTW_LOCATION/include"
export LDFLAGS="-L$FFTW_LOCATION/lib"

./configure --prefix=$GROMACS_LOCATION --enable-mpi  
--program-suffix="_mpi" --disable-nice > output.mpi_configure 2>&1

make mdrun > output.mpi_make_mdrun 2>&1
make install-mdrun > output.mpi_make_install_mdrun 2>&1
#make distclean



The first error in the 'make mdrun' output is:

source='futil.c' object='futil.lo' libtool=yes \
DEPDIR=.deps depmode=none /bin/sh ../../config/depcomp \
/bin/sh ../../libtool --tag=CC   --mode=compile mpicc -DHAVE_CONFIG_H  
-I. -I../../src  -I../../include  
-DGMXLIBDIR=\"/scratch/cneale/exe/gromacs-3.3.2/exec/share/top\"  
-I/home/cneale/exe/fftw-3.1.2/exec/include  -std1 -fast -O4 -no_ifo  
-arch ev6 -unroll 2 -fp_reorder -c -o futil.lo futil.c
 mpicc -DHAVE_CONFIG_H -I. -I../../src -I../../include  
-DGMXLIBDIR=\"/scratch/cneale/exe/gromacs-3.3.2/exec/share/top\"  
-I/home/cneale/exe/fftw-3.1.2/exec/include -std1 -fast -O4 -no_ifo  
-arch ev6 -unroll 2 -fp_reorder -c futil.c -o futil.o

cc: Error: futil.c, line 521: Invalid expression. (badexpr)
  strcpy(libpath,GMXLIBDIR);
-^
cc: Warning: futil.c, line 521: Invalid token discarded. (invaltoken)
  strcpy(libpath,GMXLIBDIR);
-^
make[2]: *** [futil.lo] Error 1
make[2]: Leaving directory `/mnt/scratch/cneale/exe/gromacs-3.3.2/src/gmxlib'
make[1]: *** [all-recursive] Error 1

make[1]: Leaving directory `/mnt/scratch/cneale/exe/gromacs-3.3.2/src/gmxlib'



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[gmx-users] Re: SGI Altix - mdrun_mpi

[Chris Neale]

Included with the things you recently tried did you use 'mpirun N mdrun -np 2' in place of 
'mpirun -np 2 mdrun -np 2'? I'm certainly no expert, but it is a difference between our scripts.

Otherwise I don't know. Perhaps recompile gromacs. Probably you have looked at 
this but did you check
to see that yout .tpr file was created properly? Also you may want to try a 
'sleep 10' between
grompp and mdrun in case you have NFS delay issues.

Good luck,
Chris.

### original message 


Hi Chris, again ;-)

I'm also running gromacs on another Cluster intel based ( using PBS), 
and my script submission procedure is similar to yours!


Now, this new machine I'm trying to use is a SGI 64-way, thus I think 
that the lam nodes file is correct: 64 cpu's in a single node, or 
something like that. And, as you can see, the "hello" program does work 
on this machine when called from mpirun.


As I told in my previous e-mail, there are people using the LAM-MPI on 
this machine, and in fact, the hostfile and part of the script 
submission file were written by my colleagues. Thus, I think that the 
hostfile is correct, and that probably something is not ok with the 
submission file,  the gmx compilation (though the compilation was 
successful) or even with the system configuration.


I tried also the suggestions in your script (exporting PATH, 
LD_LIBRARY_PATH, LAMRSH), but getting exactly the same error.

Oh well ...

Thanks for the reply,
Nuno


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[gmx-users] Re: SGI Altix - mdrun_mpi

[Nuno Loureiro Ferreira]

Hi Chris, again ;-)

I'm also running gromacs on another Cluster intel based ( using PBS), 
and my script submission procedure is similar to yours!


Now, this new machine I'm trying to use is a SGI 64-way, thus I think 
that the lam nodes file is correct: 64 cpu's in a single node, or 
something like that. And, as you can see, the "hello" program does work 
on this machine when called from mpirun.


As I told in my previous e-mail, there are people using the LAM-MPI on 
this machine, and in fact, the hostfile and part of the script 
submission file were written by my colleagues. Thus, I think that the 
hostfile is correct, and that probably something is not ok with the 
submission file,  the gmx compilation (though the compilation was 
successful) or even with the system configuration.


I tried also the suggestions in your script (exporting PATH, 
LD_LIBRARY_PATH, LAMRSH), but getting exactly the same error.

Oh well ...

Thanks for the reply,
Nuno



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[gmx-users] SGI Altix - mdrun_mpi

[Chris Neale]

I think that your host file is perhaps not correct. In any event, it is 
different than my usage. This is how I can run lam without a batch system:


ssh n1
./RunLam.sh &

###

$cat RunLam.sh
PATH=$PATH:/dir/to/lam/bin:.
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/dir/to/lam/lib
LAMRSH="ssh -x"
export LAMRSH PATH
lamboot -v lamhosts
/dir/to/lam/mpirun N /this/dir/mdrun.sh
lamhalt

###

$cat lamhosts
n1
n2
n3
n4


Chris.
##

Original message:

Hi guys

Just installed gmx on a SGI Altix system (64-way):

--> compiling mdrun with MPI support, single-precision
export CPPFLAGS=-I/home/nferreira/bin/fftw-3.0.1/include
export LDFLAGS=-L/home/nferreira/bin/fftw-3.0.1/lib
./configure --prefix=/home/nferreira/bin/gromacs-3.3.2 --enable-mpi 
--program-suffix=_mpi

make mdrun
make install-mdrun

--> compiling all gromacs package programs without MPI, single-precision
make distclean
./configure --prefix=/home/nferreira/bin/gromacs-3.3.2
make
make install



It runs fine on single nodes, but I can't put gmx running in parallel.
The jobs are submitted directly (see a sample script bellow), without 
any queuing handler, like PBS.




# This is my submission script
###
lamboot -v hostfile
lamnodes
# Testing mpi
mpirun -np 2 hello
# GMX run
grompp -np 2  -f equil -po equil_out -c after_em -p topology -o equil
mpirun -np 2 mdrun_mpi -np 2 -deffnm equil -c after_equil
lamhalt



# This is hostfile file
###
# My boot schema
localhost cpu=64


I tryed several stuff (full paths for mpirun, mdrun_mpi, etc), but I'm 
always getting the same error. I also tested a hello program (from 
LAM-MPI user guide) and it gives no problems. Bellow is the output of 
the submission script:


nferreira at behemoth 
:~/gmxbench> ./script

LAM 7.1.3/MPI 2 C++/ROMIO - Indiana University

n-1<16608> ssi:boot:base:linear: booting n0 (localhost)
n-1<16608> ssi:boot:base:linear: finished
n0  localhost:64:origin,this_node
Hello, world! I am 0 of 2
Hello, world! I am 1 of 2
NNODES=2, MYRANK=1, HOSTNAME=behemoth
NNODES=2, MYRANK=0, HOSTNAME=behemoth
NODEID=0 argc=8
NODEID=1 argc=8
:-)  G  R  O  M  A  C  S  (-:

  GRoups of Organic Molecules in ACtion for Science

   :-)  VERSION 3.3.2  (-:
[ ... snipped ...]

Getting Loaded...
Reading file equil.tpr, VERSION 3.3.2 (single precision)
-
One of the processes started by mpirun has exited with a nonzero exit
code.  This typically indicates that the process finished in error.
If your process did not finish in error, be sure to include a "return
0" or "exit(0)" in your C code before exiting the application.

PID 16623 failed on node n0 (127.0.0.1) due to signal 11.
-

LAM 7.1.3/MPI 2 C++/ROMIO - Indiana University



Any ideas? Searching the mailing list, seems that this is a recurrent  
issue, but I was not able to find and answer.

And, the machine admin is not proficient in MPI.

Cheers,
Nuno

P.S. Other programs are running fine on this machine using the same LAM-MPI.








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[gmx-users] SGI Altix - mdrun_mpi

[Nuno Loureiro Ferreira]

Hi guys

Just installed gmx on a SGI Altix system (64-way):

--> compiling mdrun with MPI support, single-precision
export CPPFLAGS=-I/home/nferreira/bin/fftw-3.0.1/include
export LDFLAGS=-L/home/nferreira/bin/fftw-3.0.1/lib
./configure --prefix=/home/nferreira/bin/gromacs-3.3.2 --enable-mpi 
--program-suffix=_mpi

make mdrun
make install-mdrun

--> compiling all gromacs package programs without MPI, single-precision
make distclean
./configure --prefix=/home/nferreira/bin/gromacs-3.3.2
make
make install



It runs fine on single nodes, but I can't put gmx running in parallel.
The jobs are submitted directly (see a sample script bellow), without 
any queuing handler, like PBS.




# This is my submission script
###
lamboot -v hostfile
lamnodes
# Testing mpi
mpirun -np 2 hello
# GMX run
grompp -np 2  -f equil -po equil_out -c after_em -p topology -o equil
mpirun -np 2 mdrun_mpi -np 2 -deffnm equil -c after_equil
lamhalt



# This is hostfile file
###
# My boot schema
localhost cpu=64


I tryed several stuff (full paths for mpirun, mdrun_mpi, etc), but I'm 
always getting the same error. I also tested a hello program (from 
LAM-MPI user guide) and it gives no problems. Bellow is the output of 
the submission script:


[EMAIL PROTECTED]:~/gmxbench> ./script

LAM 7.1.3/MPI 2 C++/ROMIO - Indiana University

n-1<16608> ssi:boot:base:linear: booting n0 (localhost)
n-1<16608> ssi:boot:base:linear: finished
n0  localhost:64:origin,this_node
Hello, world! I am 0 of 2
Hello, world! I am 1 of 2
NNODES=2, MYRANK=1, HOSTNAME=behemoth
NNODES=2, MYRANK=0, HOSTNAME=behemoth
NODEID=0 argc=8
NODEID=1 argc=8
:-)  G  R  O  M  A  C  S  (-:

  GRoups of Organic Molecules in ACtion for Science

   :-)  VERSION 3.3.2  (-:
[ ... snipped ...]

Getting Loaded...
Reading file equil.tpr, VERSION 3.3.2 (single precision)
-
One of the processes started by mpirun has exited with a nonzero exit
code.  This typically indicates that the process finished in error.
If your process did not finish in error, be sure to include a "return
0" or "exit(0)" in your C code before exiting the application.

PID 16623 failed on node n0 (127.0.0.1) due to signal 11.
-

LAM 7.1.3/MPI 2 C++/ROMIO - Indiana University



Any ideas? Searching the mailing list, seems that this is a recurrent  
issue, but I was not able to find and answer.

And, the machine admin is not proficient in MPI.

Cheers,
Nuno

P.S. Other programs are running fine on this machine using the same LAM-MPI.

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[gmx-users] tabulated bonded interactions

[Ran Friedman]

Dear all,

Tabulated bonded interactions have been implemented in December 2006. I
wanted to know if they can be used in GMX 3.3.2 or 3.3.3 (and how).
I couldn't find a list of changes between 3.3.1 and 3.3.2 online, and
even the updates from 3.2 to 3.3 are still "under construction"
according to the web site:
http://www.gromacs.org/index.php?option=com_content&task=category§ionid=4&id=58&Itemid=132

Thanks,
Ran.
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Re: [gmx-users] g_order in a micelle

[Jonathan Khao]

Problem solved, thanks !

> Jonathan Khao wrote:
> > Hello, 
> > 
> > I'm trying to get the order parameter of lipids in a micelle, so i've
> > decided to make a script that makes a trjconv of individual lipids, with
> > a fit to a structure that is aligned along the Z axis.
> > 
> > Now that I have the trajectories, i'm trying to launch g_order. The
> > problem is that it requiers a tpr file that I don't have. I have tried
> > to generate one using a modified mdp, top, and gro file , but i get a
> > semgentation error. 
> > 
> > Is it possible to get a Tpr from a Trr ?
> > Or even better , is it possible to make a g_order with a defined vector
> > instead of the three axis ? 
> > 
> > Thanks.
> > 
> >  
> you can use tpbconv with an index file to make a tpr for one lipid from 
> your original tpr file.
> 
-- 
Jonathan KHAO
LISM-IBSM-CNRS
31 Chemin Joseph Aiguier
13402 Marseille Cedex 20
France
[EMAIL PROTECTED]
tel : 0616738391

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Re: [gmx-users] REMD As A Function of Distance Between 2 Chains

[Huey Ling Tan]

Dear all ,
thank you for those comments, we are aware of the paper.  However, we are
not sure how to implement the replica exchange in gromacs.  We would like to
run a set of replicas in which each replica corresponds to a different set
of umbrella parameters.  However, when setting up a replica exchange run,
all .tpr files use the same .ppa file so that each replica will have the
same umbrella potential parameters.   Do you know how to get around this
problem.
Thank you in advance,
Huey Ling

On 13/11/2007, Marcus Kubitzki <[EMAIL PROTECTED]> wrote:
>
> Hi Huey Ling,
>
> have a look at Y.Sugita et al. J Chem Phys 113, 6042-6051 (2000) for
> details on Hamiltonian REMD, especially the correct exchange criterion.
> In their paper, they discuss in detail what you want to do, namely
> Replica Exchange Umbrella Sampling.
>
> Marcus
>
> Huey Ling Tan wrote:
> > Hi all,
> >
> > Is it feasible to do parallel tempering (replica exchange) as a function
> > of distance with umbrella sampling applied?
> >
> > I can do REMD for a system containing 2 peptide chains as a function as
> > temperatures, where I grompp each of the systems at different
> > temperatures, and then gather the fullmd.tpr files in one folder with
> > the script I want for full md run.
> >
> > But what if I want to do REMD as a function of distances (for example at
> > 0.4, 0.6, 0.8, 1.0 nm between the chains, defined in the pull.ppa file),
> > at a fixed temperature, with umbrella sampling applied? If this can be
> > done, how should I write the script for the full md run so that each of
> > the pull.ppa files can recognise the system that it suppose to pull?
> >
> > If anyone know how this can be done?
> >
> > Many thanks.
> >
> > --
> > Best regards,
> > Huey Ling
> >
> >
> > 
> >
> > ___
> > gmx-users mailing listgmx-users@gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> posting!
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> > www interface or send it to [EMAIL PROTECTED]
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>
> --
> Marcus Kubitzki
> Max Planck Institute for Biophysical Chemistry
> Computational Biomolecular Dynamics Group
> Am Fassberg 11
> D-37077 Göttingen
> Germany
> phone: ++49-551-2012312
> fax: ++49-551-2012302
> Email: mkubitz[at]gwdg.de
> www: http://www.mpibpc.mpg.de/groups/de_groot/
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>



-- 
Best regards,
Huey Ling
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Re: [gmx-users] g_order in a micelle

[David van der Spoel]

Jonathan Khao wrote:
Hello, 


I'm trying to get the order parameter of lipids in a micelle, so i've
decided to make a script that makes a trjconv of individual lipids, with
a fit to a structure that is aligned along the Z axis.

Now that I have the trajectories, i'm trying to launch g_order. The
problem is that it requiers a tpr file that I don't have. I have tried
to generate one using a modified mdp, top, and gro file , but i get a
semgentation error. 


Is it possible to get a Tpr from a Trr ?
Or even better , is it possible to make a g_order with a defined vector
instead of the three axis ? 


Thanks.

 
you can use tpbconv with an index file to make a tpr for one lipid from 
your original tpr file.


--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
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[gmx-users] g_order in a micelle

[Jonathan Khao]

Hello, 

I'm trying to get the order parameter of lipids in a micelle, so i've
decided to make a script that makes a trjconv of individual lipids, with
a fit to a structure that is aligned along the Z axis.

Now that I have the trajectories, i'm trying to launch g_order. The
problem is that it requiers a tpr file that I don't have. I have tried
to generate one using a modified mdp, top, and gro file , but i get a
semgentation error. 

Is it possible to get a Tpr from a Trr ?
Or even better , is it possible to make a g_order with a defined vector
instead of the three axis ? 

Thanks.

 
-- 
Jonathan KHAO
LISM-IBSM-CNRS
31 Chemin Joseph Aiguier
13402 Marseille Cedex 20
France
[EMAIL PROTECTED]
tel : 0616738391

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Re: [gmx-users] g-hbond and N acceptors

[David van der Spoel]

Michel Cuendet wrote:


David,

Thanks for your reply.

NH2 groups that are not aromatic (amines) one accept Hbonds of course. 
However there is not so much chemical knowledge in the program, and to 
make matters worse, you can not select acceptors or donors separately.


Of course amine groups with a lone electron pair can in principle accept 
H-bonds. But in the case of proteins, no such groups are found  (except 
on a deprotonated Lys). Peptide groups in the backbone as well as 
carboxyamide groups on Asn and Gln have hybrid orbitals which makes 
their structure planar and prevents to accept H-bonds. In proteins at 
reasonable pH, only deprotonated aromatic nitrogens on His should be 
considered acceptors. The GROMOS and HBPLUS manuals agree on this. In 
HBPLUS there is an option to accept other nitrogens as acceptors (see 
below) but only in cases where the protonation of His and orientation of 
Asn and Gln are not determined. These nitrogens are not considered 
acceptors by themselves.


I would like to hack a correction for this in the code.  I guess I would 
have to simply change line 400 of gmx_hbond.c (3.3.1) with something like :


(*top->atoms.atomtype[i])[0] == 'NR5')

Does this look right ? What is the difference between atomtype and 
atomtypeB ?


No, this is GROMOS specific. I would in that case prefer a solution like 
that from HBPLUS you are describing, where there is an (optional) list 
of atom names that are allowed. Problem is, that this is difficult to 
make general, but putting all possible atom names for proteins and 
DNA/RNA in there should be a good start.


The protonation state remains an issue though. We do quite a bit of 
vacuum simulations and there one might have deprotonated N-terminal, Lys 
and Arg, as well as protonated Asp, Glu and even Gln. Deprotonated 
N-term and Lys side chain given an NH2 moiety which can accept. This 
means it is not good enough to check atom names. Atomtypes are force 
field dependent however, and therefore not suitable.


One could have an auto-generated list (like index files for proteins) 
with the possibility of overriding this with an index file. Would that 
be a good solution?





Cheers,
Michel


FROM THE HBPLUS MANUAL

Acceptors :

1.  O (ie Main Chain COs of recognised amino - not imino - acid residues)

2.  CYH SG, CSS SG, ASP OD1, ASP OD2, GLU OE1, GLU OE2, HIS ND1, MET SD,
   ASN OD1, GLN OE1, SER OG, THR OG1, TYR OH
3.  Recognised acceptors of non-standard recognised molecules

4.  Oxygen atoms in HETATM molecules (including waters)

Atoms that may act as both donors and acceptors under the -X or -x 
options :


1.  HIS CD2, HIS CE1, ASN OD1, ASN ND2, GLN OE1, GLN NE2

-x  Exchange the side-chains of Histidine, Glutamine and Asparagnine.
These side-chains are difficult to resolve crystallographically with
certainty, which is why there is the option of adding potential hydrogen
bonds that would be formed if HIS CD2 was actually ND1, HIS CE1 was NE2 and
the nitrogens and oxygens of the ASN / GLN amide groups were actually the
other way round.  (Default is not to do this.)









--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
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Re: [gmx-users] soft-core and coulomb transformation

[bharat v. adkar]

hi,
even i am also checking the ethane->methane case with the fix you 
suggested. equilibration values appear to be okay. will let you know by 
tommorrow the final results..


thanks

bharat


On Wed, 14 Nov 2007, Berk Hess wrote:


Hi,

The bug was indeed was I expected.
I have fixed it for version 3.3.3.

You might not notice it easily, since the direct space contribution is 
usually

larger than the mesh part.
But for a two particle system I got nan's.

Berk.



From: "David Mobley" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users 
To: "Discussion list for GROMACS users" 
Subject: Re: [gmx-users] soft-core and coulomb transformation
Date: Mon, 12 Nov 2007 16:17:36 -0800

Berk,

>  But what do you mean with charging and discharging?
> 
>  Going one way or the other in lambda does not matter.

>  What matters is if there are particles that have zero charge
>  in the A-state topology, while they have a non-zero charge
>  in the B-state topology.

Sorry, what I mean by "charging" versus "discharging" is that
"charging" is where the A state has zero charges and the B state has
normal charges, and discharging is the reverse. So "charging" is the
scenario you describe, and "discharging" is the reverse.

David

>  Berk.
> 
> 
> > From: "David Mobley" <[EMAIL PROTECTED]>

> > Reply-To: Discussion list for GROMACS users 
> > To: "bharat v. adkar" <[EMAIL PROTECTED]>
> > CC: Discussion list for GROMACS users 
> > Subject: Re: [gmx-users] soft-core and coulomb transformation
> > Date: Mon, 12 Nov 2007 10:26:37 -0800
> > 
> > Following up on this issue, discharging phenol in water appears to

> > give the same results as charging phenol in water. In other words, so
> > far the only cases for which there seem to be a problem are relative
> > calculations (and so far I haven't looked at this for any other than
> > Bharat's test cases).
> > 
> > Bharat, be sure you submit a bugzilla and we'll see how things go from

> > there. I may at some point try setting up some of my own relative free
> > energy topologies and see if I see the same effects, but I'm not
> > likely to have time for that for a couple days.
> > 
> > Thanks,

> > David
> > 
> > 
> > 
> 
> 
>  _

>  Play online games with your friends with Messenger
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[gmx-users] problems about energy minimization

[renying]

Hello, everyone.
I have loaded a pdb file of protein complex from Protein Data Bank and put it 
into water soltion with pdb2gmx, editconf and genbox.
After 400 steps of energy minimization when the potential energy seems to be 
more or less stable, I want to do position restraints. However, it always 
failed. 

The error info is as follows:
Step 1, time 0.002 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.000645 (between atoms 13241 and 13242) rms 0.43
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  13241  13242   31.20.1000   0.0999  0.1000

t = 0.002 ps: Water molecule starting at atom 73326 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous 
and current coordinates
Large VCM(group System):  0.03330, -0.01095, -0.00024, ekin-cm:  
2.20013e+03


The system seems to be exploding. I have tried the follwing parameters and 
sadly, none of them works.
nsteps  =  200/400/800/1000 steps  in em.mdp
dt  =  0.002/0.001/0.0002 ps  in pr.mdp
tc-grps =  Protein  SOL  or
tc-grps =  system in pr.mdp
tau_t   =  0.0020.002  or longer time in pr.mdp



The total charge of the system is  -273.000 e and I didn't neutralize it for 
some reasons. Does this matter much?


Some files are as follows:
=== *.top =
.
[ molecules ]
; Compound#mols
Protein_A   1
Protein_B   1
Protein_C   1
Protein_D   1
Protein_E   1
Protein_F   1
Protein_G   1
Protein_H   1
Protein_I   1
Protein_J   1
Protein_K   1
Protein_L   1
Protein_M   1
Protein_N   1
Protein_O   1
Protein_P   1
Protein_Q   1
Protein_R   1
Protein_S   1
Protein_T   1
Protein_U   1
SOL 151936





===  em.mdp 
cpp =  /usr/bin/cpp
define  =  -DFLEX_SPC
constraints =  none
integrator  =  steep
nsteps  =  1000;
emtol   =  1000
emstep  =  0.01

nstxout =  50
nstlist =  5
nstcomm =  1
ns_type =  grid
rlist   =  1.0
coulombtype =PME
rcoulomb=  1.0
vdwtype = cut-off
rvdw=  1.4
fourierspacing  =  0.12
pme_order   =  4
ewald_rtol  =  1e-5
optimize_fft=  yes

= pr.mdp ===
cpp =  /usr/bin/cpp
define  =  -DPOSRES
;constraints =  none
constraints =  all-bonds
integrator  =  md
dt  =  0.002; ps !
nsteps  =  5000 ; total 10 ps.
nstcomm =  1
comm_grps   =  system

nstxout =  100
nstvout =  1000
nstfout =  0
nstlog  =  10
nstenergy   =  10
nstlist =  1
ns_type =  grid
vdwtype  = Cut-off
rlist   =  1.0
rvdw=  1.4

;coulombtype=Cut-off
;rcoulomb=2.2
coulombtype = PME
rcoulomb= 1.0
fourierspacing  = 0.12
pme_order   = 4
ewald_rtol  = 1e-5
optimize_fft= yes

; Berendsen temperature coupling is on in two groups
Tcoupl  =  berendsen
tc-grps =  Protein  SOL
tau_t   =  0.0020.002
ref_t   =  300  300

; Generate velocites is on at 300 K.
gen_vel =  yes
gen_temp=  300.0
gen_seed=  173529
===




All the best

Ying Ren 
2007-11-14



　　
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Re: [gmx-users] stop mailing me

[Erik Lindahl]

On Nov 13, 2007, at 11:56 AM, Henry O Ify wrote:


please stop mailing me, i am tired of all this mail


First, it was you and not we who subscribed you to the list :-)

Second, you're more than welcome to unsubscribe. However, you would  
probably have had better luck if you had read the footer included in  
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Cheers,

Erik

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Re: [gmx-users] soft-core and coulomb transformation

[Berk Hess]

Hi,

The bug was indeed was I expected.
I have fixed it for version 3.3.3.

You might not notice it easily, since the direct space contribution is 
usually

larger than the mesh part.
But for a two particle system I got nan's.

Berk.



From: "David Mobley" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users 
To: "Discussion list for GROMACS users" 
Subject: Re: [gmx-users] soft-core and coulomb transformation
Date: Mon, 12 Nov 2007 16:17:36 -0800

Berk,

> But what do you mean with charging and discharging?
>
> Going one way or the other in lambda does not matter.
> What matters is if there are particles that have zero charge
> in the A-state topology, while they have a non-zero charge
> in the B-state topology.

Sorry, what I mean by "charging" versus "discharging" is that
"charging" is where the A state has zero charges and the B state has
normal charges, and discharging is the reverse. So "charging" is the
scenario you describe, and "discharging" is the reverse.

David

> Berk.
>
>
> >From: "David Mobley" <[EMAIL PROTECTED]>
> >Reply-To: Discussion list for GROMACS users 
> >To: "bharat v. adkar" <[EMAIL PROTECTED]>
> >CC: Discussion list for GROMACS users 
> >Subject: Re: [gmx-users] soft-core and coulomb transformation
> >Date: Mon, 12 Nov 2007 10:26:37 -0800
> >
> >Following up on this issue, discharging phenol in water appears to
> >give the same results as charging phenol in water. In other words, so
> >far the only cases for which there seem to be a problem are relative
> >calculations (and so far I haven't looked at this for any other than
> >Bharat's test cases).
> >
> >Bharat, be sure you submit a bugzilla and we'll see how things go from
> >there. I may at some point try setting up some of my own relative free
> >energy topologies and see if I see the same effects, but I'm not
> >likely to have time for that for a couple days.
> >
> >Thanks,
> >David
> >
> >
> >
>
>
> _
> Play online games with your friends with Messenger
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Re: [gmx-users] g-hbond and N acceptors

[Michel Cuendet]

David,

Thanks for your reply.

NH2 groups that are not aromatic (amines) 
one accept Hbonds of course. However there is not so much chemical 
knowledge in the program, and to make matters worse, you can not select 
acceptors or donors separately.


Of course amine groups with a lone electron pair can in principle accept 
H-bonds. But in the case of proteins, no such groups are found  (except 
on a deprotonated Lys). Peptide groups in the backbone as well as 
carboxyamide groups on Asn and Gln have hybrid orbitals which makes 
their structure planar and prevents to accept H-bonds. In proteins at 
reasonable pH, only deprotonated aromatic nitrogens on His should be 
considered acceptors. The GROMOS and HBPLUS manuals agree on this. In 
HBPLUS there is an option to accept other nitrogens as acceptors (see 
below) but only in cases where the protonation of His and orientation of 
Asn and Gln are not determined. These nitrogens are not considered 
acceptors by themselves.


I would like to hack a correction for this in the code.  I guess I would 
have to simply change line 400 of gmx_hbond.c (3.3.1) with something like :


(*top->atoms.atomtype[i])[0] == 'NR5')

Does this look right ? What is the difference between atomtype and 
atomtypeB ?


Cheers,
Michel


FROM THE HBPLUS MANUAL

Acceptors :

1.  O (ie Main Chain COs of recognised amino - not imino - acid residues)

2.  CYH SG, CSS SG, ASP OD1, ASP OD2, GLU OE1, GLU OE2, HIS ND1, MET SD,
   ASN OD1, GLN OE1, SER OG, THR OG1, TYR OH 


3.  Recognised acceptors of non-standard recognised molecules

4.  Oxygen atoms in HETATM molecules (including waters)

Atoms that may act as both donors and acceptors under the -X or -x options :

1.  HIS CD2, HIS CE1, ASN OD1, ASN ND2, GLN OE1, GLN NE2

-x  Exchange the side-chains of Histidine, Glutamine and Asparagnine.
These side-chains are difficult to resolve crystallographically with
certainty, which is why there is the option of adding potential hydrogen
bonds that would be formed if HIS CD2 was actually ND1, HIS CE1 was NE2 and
the nitrogens and oxygens of the ASN / GLN amide groups were actually the
other way round.  (Default is not to do this.)






--

==
Michel Cuendet, Ph.D
Molecular Modeling Group
Swiss Institute of Bioinformatics
CH-1015 Lausanne, Switzerland
www.isb-sib.ch/groups/Molecular_Modeling.htm
==


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Re: [gmx-users] Creating .top, .gro, .ndx, .itp files for TIP5Pwater

[David van der Spoel]

JMandumpal wrote:

  Friends,

  I would like to simulate a box of water  (TIP5P model), with 258 water 
molecules. When I tried to build up the .top, .gro and .ndx files using 
the command pdb2gmx -p -i -n -o -f tip5p_W.pdb,


I got an error message : input/ output error, program aborted.

MY input structure, ie, tip5p_W.pdb contains the co ordinates for the 
solvent box and therefore I dont need to solvate it again!!


Could you suggest the exact way to build up thes files ( .top, .gro, 
.ndx, .itp ) with a starting structure (.pdb files)?



there are starting structures and topology in your share/gromacs/top dir.




regards,
Jestin Mandumpal






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--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
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[gmx-users] Re: gmx-users Digest, Vol 43, Issue 49

[Gerrit Groenhof]

What you want to do, a dynamic updating of the QM atoms is not 
implemented yet.
The difficulty with such scheme is energy conservation and force 
conservation when translocating an atom from the MM into the QM region 
and vice versa.
This is a difficult problem. However, there soluitons, see for instance 
Heyden, Lin and Truhlar (J. Phys. Chem. B 2007, 111, 2231-2241).
Therefore, if such a dynamic partitioning is essential for your 
research, you could implement their ideas into gromacs. 


Gerrit




Message: 1
Date: Mon, 12 Nov 2007 15:10:08 -0500
From: "Tandia, Adama" <[EMAIL PROTECTED]>
Subject: [gmx-users] QMMM for element with "unknown" forcefield
To: gmx-users@gromacs.org
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset=US-ASCII

Dear GMX users,

I'm not very familiar with the QMMM implementation in Gromacs, but I
have two questions. 


1- I would like to run a MD simulation for glass materials that
contain B and Sb based oxides. Both elements are known to be multivalent
in the compositions that I'm interested. Is it possible to setup a QMMM
that assigns a sphere where QMMM is performed with a fixed radius around
Sb and B, and have the spheres to move with the assigned atoms during
the simulation? This would be a sort of Learn-On-The-Fly method.

2- Has anyone successfully compiled Gromacs 3.3.2 with QMMM set
to work with Gaussian or CPMD? If yes, can I request the details of the
compilation procedure?

Best wishes,

Adama

 
==

Adama Tandia
Modeling & Simulation
Corning INC
USA
 
Tel:  607 248 1036

Fax: 607 974 3405
www.corning.com

  


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[gmx-users] Creating .top, .gro, .ndx, .itp files for TIP5Pwater

[JMandumpal]

 Friends,

  I would like to simulate a box of water  (TIP5P model), with 258 water 
molecules. When I tried to build up the .top, .gro and .ndx files using the 
command pdb2gmx -p -i -n -o -f tip5p_W.pdb,

I got an error message : input/ output error, program aborted.

MY input structure, ie, tip5p_W.pdb contains the co ordinates for the solvent 
box and therefore I dont need to solvate it again!!

Could you suggest the exact way to build up thes files ( .top, .gro, .ndx, .itp 
) with a starting structure (.pdb files)?


regards,
Jestin Mandumpal
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[gmx-users] stop mailing me

[Henry O Ify]

stop mailing me
Marius Retegan <[EMAIL PROTECTED]> wrote:  Hello
I would like to know what charges are in the ffopls.rtp in the case of HISA.
In the data below, on the 3rd column are the charges from Gromacs and
on the 4th column are the charges for the same residue from a personal
communication of opls parameters from prof. Jorgensen.

[ HISA ] ; HISD in OPLS terminology
[ atoms ]
N opls_238 -0.500 -0.5000
H opls_241 0.300 0.3000
CA opls_224B 0.140 0.1400
HA opls_140 0.060 0.0600
CB opls_505 -0.297 -0.0050
HB1 opls_140 0.060 0.0600
HB2 opls_140 0.060 0.0600
CG opls_508 -0.261 0.0150
ND1 opls_503 -0.291 -0.5700
HD1 opls_504 0.326 0.4200
CD2 opls_507 0.504 -0.0150
HD2 opls_146 0.183 0.1150
CE1 opls_506 0.182 0.2950
HE1 opls_146 0.098 0.1150
NE2 opls_511 -0.564 -0.4900
C opls_235 0.500 0.5000
O opls_236 -0.500 -0.5000

Thank you
Marius Retegan
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Re: [gmx-users] histidine charges in ffopls.rtp

[Ran Friedman]

Dear Marius,

Did you check the reference given for the FF? I assume the charges are
from there.

Ran.

Marius Retegan wrote:
> Hello
> I would like to know what charges are in the ffopls.rtp in the case of HISA.
> In the data below, on the 3rd column are the charges from Gromacs and
> on the 4th column are the charges for the same residue from a personal
> communication of opls parameters from prof. Jorgensen.
> 
> [ HISA ]   ; HISD in OPLS terminology
>  [ atoms ]
>  Nopls_238   -0.500-0.5000
>  Hopls_2410.300 0.3000
> CAopls_224B   0.140 0.1400
> HAopls_1400.060 0.0600
> CBopls_505   -0.297-0.0050
>HB1opls_1400.060 0.0600
>HB2opls_1400.060 0.0600
> CGopls_508   -0.261 0.0150
>ND1opls_503   -0.291-0.5700
>HD1opls_5040.326 0.4200
>CD2opls_5070.504-0.0150
>HD2opls_1460.183 0.1150
>CE1opls_5060.182 0.2950
>HE1opls_1460.098 0.1150
>NE2opls_511   -0.564-0.4900
>  Copls_2350.500 0.5000
>  Oopls_236   -0.500-0.5000
> 
> Thank you
> Marius Retegan
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-- 
--
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355593
Email: [EMAIL PROTECTED]
Skype: ran.friedman
--

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