[gmx-users] Vacuum Simulation of Alanine Dipeptide =>production run

[M. Emal Alekozai]

Hi,

to create some toy data I want to do a vacuum simulation of Alanine Dipeptide 
with Gromacs.
For the production run script I used the gmx-user mailing list thread [1a-d], 
the tutorial [2] and the corresponding sample script [3].

1a: http://www.gromacs.org/pipermail/gmx-users/2006-August/023245.html
1b: http://www.gromacs.org/pipermail/gmx-users/2006-August/023248.html
1c: http://www.gromacs.org/pipermail/gmx-users/2006-August/023250.html
1d: http://www.gromacs.org/pipermail/gmx-users/2006-August/023249.html
2: "Gromacs course in 2004 -> Gromacs exercises"
   
http://www.csc.fi/english/research/sciences/chemistry/courses/gmx2004/exercises/index_html
   https://extras.csc.fi/chem/courses/gmx2004/exercises/index.html
3: https://extras.csc.fi/chem/courses/gmx2004/exercises/exercise.tgz


I got three questions about my production run setup:

1. comm_mode
In [1c] David van der Spoel suggests to use "comm_mode=Angular" (... remove 
angular center of mass motion ...).
A few seconds later in [1d] Gerrit Gronhof suggests to use "comm_mode=linear"
(... In addition to Erik and my suggestions, you should also remove the 
overall rotation: comm_mode=linear. ...)
I'm know a little confused, I checked the Gromacs manual and it says if I use 
"comm_mode=Angular" the center of mass translation and rotation around the 
center of mass is removed.
Do I rally need to use  something like "comm_mode=Angular, linear" ???

2. comm_grps
If I use "comm_grps="  is the default value (all atoms of system) used?

3. I changed some settings in David van der Spoel's Vacuum production run 
script [3]. The modified script is attached. The main changes are:
;dt= 0.004 ; MEA
dt= 0.002 ; MEA
;epsilon-r= 1 ; MEA
epsilon-r= 80 ; MEA
Are they reasonable with the other options in the script (or do I have to 
adjust also other values)?

Thanks Emal

-- 
Pt! Schon das coole Video vom GMX MultiMessenger gesehen?
Der Eine für Alle: http://www.gmx.net/de/go/messenger03


prodVacuum.mdp
Description: Binary data
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Re: [gmx-users] Vacuum Simulation Alanine Dipeptide =>minimisation: ERROR "No default Ryckaert-Bell. types"

[M. Emal Alekozai]

Hi Chris,

> did you try searching the archives?
Yes I tried to search in archive for "No default Ryckaert-Bell. types", 
but I didn't find anything useful.
But I didn't had the idea to search for the string combination: 
"ACE+NAC+oplsaa" .


With the correction of topology file it worked.

Thanks for the links,
Emal

Chris Neale wrote:

 >What do I have to adjust to get rid of the error message?

did you try searching the archives?
http://www.gromacs.org/pipermail/gmx-users/2006-September/023875.html
http://www.gromacs.org/pipermail/gmx-users/2006-September/023872.html

Chris.


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[gmx-users] pull.pdo and AFM force

[xi zhao]

All users:
  I want to calculate the AFM force in afm pulling, is there a  script  to 
obtain forces from afm pulling! In fact, g_wham can not run, it is very 
depressed. Please help me!
  Thank you in advance! 




   
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[gmx-users] Help - No default Bond types dna

[Ragnarok sdf]

Hello. Ie been trying to run a DNA simulation with gromacs using amber99
force field. I've started with my DNA sequence complexed with the protein,
but then decided to separate them to know exactly what the problem was. Now
I am not even using the DNA sequence from my pdb file. I`ve used the NAB
server to create a DNA sequence which is exactly the same as the one I had.
I decided to do this in order to minimize the problems with the amber
forcefield. Well, that didn't work either.
I keep getting the "Error - No default Bond types.no default angle
typesetc "
On a previous email I asked the same question, and the answer was. Take a
look at the lines where the error appears. Just to be more specific on my
problem.ERROR 0 [file "1vkxdna_C.itp", line 71]:
  No default Bond types
ERROR 0 [file "1vkxdna_C.itp", line 196]:
  No default Angle types
Ok. I've taken the last advice and went ther to line 196. Except that on
line 196 there are 4 columns
"161819 1"  with values that I cannot spot the problem. I went
to the manual to see what each line means but came out without knowing
exactly what to do with them.
Another problem I've spotted is that the charge (no matter what i try)
always comes out as a non integral value. I've renamed all atoms exactly
like they should be...one by onereally...one by one.
I would like some advice on the problem if possible.

Ps: The amber Dickerson test works out just fine.
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[gmx-users] Vacuum Simulation Alanine Dipeptide =>minimisation: ERROR "No default Ryckaert-Bell. types"

[Chris Neale]

>What do I have to adjust to get rid of the error message?

did you try searching the archives?
http://www.gromacs.org/pipermail/gmx-users/2006-September/023875.html
http://www.gromacs.org/pipermail/gmx-users/2006-September/023872.html

Chris.

-- original message --

Hi,

to create some toy data I want to do a vacuum simulation of alanine dipeptide 
with Gromacs.
I used charmm ("generate" command) to build the structure of alanine dipeptide.
The structure in "charmm notation" is  "ACE-ALA-CT3" and in "gromacs notation" is 
"ACE-ALA-NAC" .
The charmm output is a pdb (in charmm dialect) of alanine dipeptide [see 1].
I looked up the notation in the corresponding OPLS-force field file 
"/usr/share/gromacs/top/ffoplsaa.rtp" and adjusted it in the pdb file [see 2].
To convert it to a gro file I used following command:

 $pdb2gmx -ter -f alanineDipeptide_gromacsOplsForceField.pdb -p 
alanineDipeptide_gromacsOplsForceField.top -o 
alanineDipeptide_gromacsOplsForceField.gro


I selected the "OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)" and 
as a "N-terminus" and a "C-terminus" I selected "None".

The output gro file is [3].

For the energy minimisation I use a sample vaccum script from David van der 
Spoel from:
 "Gromacs course in 2004 -> Gromacs exercises"
 https://extras.csc.fi/chem/courses/gmx2004/exercises/index.html
 https://extras.csc.fi/chem/courses/gmx2004/exercises/exercise.tgz


When I run the grompp command I get the error message "No default 
Ryckaert-Bell" (see [4] for full output):
 $grompp -v -zero -f energyMinimisation_steepSimple.mdp -c 
alanineDipeptide_gromacsOplsForceField.gro -p 
alanineDipeptide_gromacsOplsForceField.top -o 
alanineDipeptide_energyMinimisation.tpr


The corresponding topology file "alanineDipeptide_gromacsOplsForceField.top" is 
attached.

What do I have to adjust to get rid of the error message?


Thanks
Emal


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[gmx-users] g_rotacf

[rams rams]

Hi,

I want to clarify a few of the things about the usage of g_rotacf (for
rotational correlation function for molecules). In the manual it is given
like the following:

g_rotacf -P 1 -nparm 2 -fft -n index -o rotacf-x-P1 -fa expfit-x-P1
-beginfit 2.5 -endfit 20.0

I understood that -f, -s options are needed to be included in the above
list.

It is mentioned in the manual, that the above command will calculate the
rotational function using a first order Legendre polynomial of the angle of
a vector defined by the index file.
(as I understand, -P 1 option is taking care of this. If I want to use the
second order Legendre polynomials, -P 2 will do it for me I suppose)

The above command will also fit the calculated correlation function to a two
parameter exponential (-nparm 2 is taking care of this I suppose). Does it
mean that the calculated correlation function is expressed as a sum of three
exponential terms with two variables along two directions ? What is the fit
function by default is used here ? Is it exp(-l(l+1)Di) ?

There is also an option -fitfn in the list, what are these functions are
meant for ?

-fft option is for using FFT for the computation of the correlation function
if I am correct.

-fa option I dont have any idea about it.

Thanks and Regards in advance,

Ram.
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Re: [gmx-users] How to display simulation box in VMD?

[Nicolas Sapay]

You should have a look in the archives of the VMD mailing-list... Or 
check this page:

http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/pbcbox/

Nicolas

Suman Chakrabarty wrote:

How do I display the actual simulation box in VMD for a gromacs
configuration/trajectory? Is it possible? By default it shows only the axes.


Regards,
Suman Chakrabarty.

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[gmx-users] Re: The WARNING

[Vitaly Chaban]

>
> 1. If I have the correct information in my .top file and .gro file,
> I could successfully run "GROMPP" command without the warning.
>
> And, I could ignore the warning from the analysis tools.
> right?
>

If you have got .tpr submit it to the analysis tools.


-- 
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq., 4, Kharkiv 61077, Ukraine
email: [EMAIL PROTECTED]
skype: vvchaban
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[gmx-users] Vacuum Simulation Alanine Dipeptide =>minimisation: ERROR "No default Ryckaert-Bell. types"

[M. Emal Alekozai]

Hi,

to create some toy data I want to do a vacuum simulation of alanine dipeptide 
with Gromacs.
I used charmm ("generate" command) to build the structure of alanine dipeptide.
The structure in "charmm notation" is  "ACE-ALA-CT3" and in "gromacs notation" 
is "ACE-ALA-NAC" .
The charmm output is a pdb (in charmm dialect) of alanine dipeptide [see 1].
I looked up the notation in the corresponding OPLS-force field file 
"/usr/share/gromacs/top/ffoplsaa.rtp" and adjusted it in the pdb file [see 2].
To convert it to a gro file I used following command:

  $pdb2gmx -ter -f alanineDipeptide_gromacsOplsForceField.pdb -p 
alanineDipeptide_gromacsOplsForceField.top -o 
alanineDipeptide_gromacsOplsForceField.gro


I selected the "OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)" and 
as a "N-terminus" and a "C-terminus" I selected "None".
The output gro file is [3].

For the energy minimisation I use a sample vaccum script from David van der 
Spoel from:
  "Gromacs course in 2004 -> Gromacs exercises"
  https://extras.csc.fi/chem/courses/gmx2004/exercises/index.html
  https://extras.csc.fi/chem/courses/gmx2004/exercises/exercise.tgz


When I run the grompp command I get the error message "No default 
Ryckaert-Bell" (see [4] for full output):
  $grompp -v -zero -f energyMinimisation_steepSimple.mdp -c 
alanineDipeptide_gromacsOplsForceField.gro -p 
alanineDipeptide_gromacsOplsForceField.top -o 
alanineDipeptide_energyMinimisation.tpr


The corresponding topology file "alanineDipeptide_gromacsOplsForceField.top" is 
attached.

What do I have to adjust to get rid of the error message?


Thanks
Emal


=1. PDB IN CHARMM DIALECT
REMARK  COORDINATES FOR FRAGMENT/ PEPTIDE WITH TERMINI  
  
REMARK   DATE: 8/20/ 8  1: 4: 7  CREATED BY USER: emal  
  
ATOM  1  CAY ALA 1 -10.138  -4.600   4.190  1.00  0.00  ALAD
ATOM  2  HY1 ALA 1 -11.149  -4.333   3.817  1.00  0.00  ALAD
ATOM  3  HY2 ALA 1  -9.523  -4.958   3.336  1.00  0.00  ALAD
ATOM  4  HY3 ALA 1  -9.654  -3.701   4.627  1.00  0.00  ALAD
ATOM  5  CY  ALA 1 -10.229  -5.671   5.206  1.00  0.00  ALAD
ATOM  6  OY  ALA 1  -9.447  -6.612   5.208  1.00  0.00  ALAD
ATOM  7  N   ALA 1 -11.211  -5.565   6.107  1.00  0.00  ALAD
ATOM  8  HN  ALA 1 -11.843  -4.801   6.075  1.00  0.00  ALAD
ATOM  9  CA  ALA 1 -11.421  -6.529   7.170  1.00  0.00  ALAD
ATOM 10  HA  ALA 1 -10.458  -6.861   7.536  1.00  0.00  ALAD
ATOM 11  CB  ALA 1 -12.168  -5.848   8.335  1.00  0.00  ALAD
ATOM 12  HB1 ALA 1 -12.307  -6.558   9.179  1.00  0.00  ALAD
ATOM 13  HB2 ALA 1 -13.171  -5.499   8.007  1.00  0.00  ALAD
ATOM 14  HB3 ALA 1 -11.590  -4.974   8.702  1.00  0.00  ALAD
ATOM 15  C   ALA 1 -12.172  -7.778   6.699  1.00  0.00  ALAD
ATOM 16  O   ALA 1 -13.319  -8.018   7.067  1.00  0.00  ALAD
ATOM 17  NT  ALA 1 -11.511  -8.601   5.861  1.00  0.00  ALAD
ATOM 18  HNT ALA 1 -10.598  -8.316   5.559  1.00  0.00  ALAD
ATOM 19  CAT ALA 1 -12.058  -9.831   5.329  1.00  0.00  ALAD
ATOM 20  HT1 ALA 1 -13.146  -9.935   5.547  1.00  0.00  ALAD
ATOM 21  HT2 ALA 1 -11.927  -9.864   4.225  1.00  0.00  ALAD
ATOM 22  HT3 ALA 1 -11.534 -10.708   5.770  1.00  0.00  ALAD
TER  23  ALA 1 
END


=2. PDB IN GROMACS DIALECT
REMARK  COORDINATES FOR FRAGMENT/ PEPTIDE WITH TERMINI  
  
REMARK   DATE: 8/20/ 8  1: 4: 7  CREATED BY USER: emal  
  
ATOM  1  CH3 ACE 1 -10.138  -4.600   4.190  1.00  0.00
ATOM  2 HH31 ACE 1 -11.149  -4.333   3.817  1.00  0.00
ATOM  3 HH32 ACE 1  -9.523  -4.958   3.336  1.00  0.00
ATOM  4 HH33 ACE 1  -9.654  -3.701   4.627  1.00  0.00
ATOM  5  C   ACE 1 -10.229  -5.671   5.206  1.00  0.00
ATOM  6  O   ACE 1  -9.447  -6.612   5.208  1.00  0.00
ATOM  7  N   ALA 2 -11.211  -5.565   6.107  1.00  0.00
ATOM  8  H   ALA 2 -11.843  -4.801   6.075  1.00  0.00
ATOM  9  CA  ALA 2 -11.421  -6.529   7.170  1.00  0.00
ATOM 10  HA  ALA 2 -10.458  -6.861   7.536  1.00  0.00
ATOM 11  CB  ALA 2 -12.168  -5.848   8.335  1.00  0.00
ATOM 12  HB1 ALA 2 -12.307  -6.558   9.179  1.00  0.00
ATOM 13  HB2 ALA 2 -13.171  -5.499   8.007  1.00  0.00
ATOM 14  HB3 ALA 2 -11.590  -4.974   8.702  1.00  0.00
ATOM 15  C   ALA 2 -12.172  -7.778   6.699  1.00  0.00
ATOM 16  O   ALA 2 -13.319  -8.018   7.067  1.00  0.00
ATOM 17  N   NAC 3 -11.511  -8.601   5.861  1.00  0.00
ATOM 18  H   NAC 3 -10.598  -8.316   5.559  1.00  0.00
ATOM 19  CH3 NAC 3 

[gmx-users] How to display simulation box in VMD?

[Suman Chakrabarty]

How do I display the actual simulation box in VMD for a gromacs
configuration/trajectory? Is it possible? By default it shows only the axes.


Regards,
Suman Chakrabarty.

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Re: [gmx-users] rb1 test failed after recompiling gromacs 3.3.2

[Nicolas Sapay]

Justin A. Lemkul wrote:



Nicolas Sapay wrote:

Nicolas Sapay wrote:

Hello,

I've run the gmxtest on Gromacs-3.3.2. One simple test failed:

   Testing rb1 . . . *** glibc detected *** realloc(): invalid next
   size: 0x082c0180 ***
   sh: line 1: 27398 Aborted mdrun >mdrun.out 2>&1
   FAILED. Check files in rb1

I have more closely looked the compilation logs and the files used 
for the test. There is nothing particular to say about the 
compilation (no error, no warning). note that I'm using glibc 2.3.4 
compiled on a Linux 2.4.20 system. The error seems to be due to the 
-DMOL1 define in grompp.mdp of the rb1 test. When I replace it by 
-DBONDS (as in the rb125 test), the test is successful. What the 
-DMOL1 statement means? I though you can only use -DFLEXIBLE or 
-DPOSRES as defines in a mdp file. I had a look in the 3.3.2 manual, 
but found nothing about it.




Anything can be defined in the topology.  Look for the #ifdef 
statements in topol.top.  I checked the test suite (for mine it's 
3.3.3), and found several instances where there is a -DMOL1 flag, but 
no corresponding definition in the topology:


angles1
dih1
rb1

In other tests, where it is defined, it appears to mean that the 
system should contain one molecule of interest.  No idea why it's 
missing from these others, and why it doesn't seem to cause problems, 
at least in angles1 and dih1.


-Justin

Thanks for the answer. I can indeed use ANGLES an BONDS (defined in 
topol.top) in place of MOL1, but not RYCKAERT alone... Anyway, if the 
rb125 test is passed, I guess my compilation is safe enough, even for 
the R-B potential.


Nicolas


And two complex tests failed as well:

   Testing acetonitrilRF . . . FAILED. Check files in acetonitrilRF
   Testing dec+water . . . FAILED. Check files in dec+water


In the case of the rb1 test, I checked all the .out .log files but 
found anything wrong. For acetonitrilRF, I obtain this:


   ---
   Program mdrun, VERSION 3.3.2
   Source code file: network.c, line: 437

   Routine should not have been called:
   gmx_sumi
   --


According to the mailing list, there is something to fix in 
src/mdlib/rf_util.c. For dec+water, I've got the same error than on 
the wiki, so nothing to worry about apparently.Following the advices 
found on the wiki or the mailing list, I have re-compiled FFTW and 
Gromacs (with fixed rf_util.c) from the sources. For FFTW, I've used 
the following command:


   ./configure --prefix /usr/export/fftw-3.1.2/ --enable-float
   --enable-threads CC=/usr/bin/gcc


And for Gromacs:

   ./configure --prefix /usr/export/gromacs-3.3.2 --without-x
   CC=/usr/bin/gcc CPPFLAGS=-I/usr/export/fftw-3.1.2/include/
   LDFLAGS=-L/usr/export/fftw-3.1.2/lib/


I have rerun the test but I still obtain the same error with the rb1 
test (and the dec+water test). Can someone explain to me what the it 
means exactly and how to fix it? (I guess it's related to the 
Ryckaert-Bellemans potential?).


   Thanks,
   Nicolas


ps: I'm using RHE 4.7 and gcc 3.4.6

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[gmx-users] Re: The WARNING

[Tsjerk Wassenaar]

Lin,

A .gro file does not have information regarding masses. Therefore, any
operation involving masses (mass-weighted fitting) will not be
performed optimally.

Cheers,

Tsjerk

On Thu, Aug 21, 2008 at 9:19 PM, Chih-Ying Lin <[EMAIL PROTECTED]> wrote:
> Hi
> As you described...
> This is not a grompp warning, but a warning from one of the analysis
> tools. grompp will never take masses 'out of the blue', but will
> always use the force field description (atom type definitions) or the
> mass specified in the .top/.itp file. It will bail out if no mass is
> properly defined for a specified atom. As David pointed out, these
> tools would benefit from reading in a .tpr (run input) file, not a
> .top file.
>
>
> 1. If I have the correct information in my .top file and .gro file,
> I could successfully run "GROMPP" command without the warning.
>
> And, I could ignore the warning from the analysis tools.
> right?
>
>
>
> 2. you described " these tools would benefit from reading in a .tpr
> (run input) file, not a .top file.. "
> how about the .gro file? I see nothing wrong with my .gro file.
>
>
> Thank you
> Lin
>



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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[gmx-users] The WARNING

[Chih-Ying Lin]

Hi
As you described...
This is not a grompp warning, but a warning from one of the analysis
tools. grompp will never take masses 'out of the blue', but will
always use the force field description (atom type definitions) or the
mass specified in the .top/.itp file. It will bail out if no mass is
properly defined for a specified atom. As David pointed out, these
tools would benefit from reading in a .tpr (run input) file, not a
.top file.


1. If I have the correct information in my .top file and .gro file,
I could successfully run "GROMPP" command without the warning.

And, I could ignore the warning from the analysis tools.
right?



2. you described " these tools would benefit from reading in a .tpr
(run input) file, not a .top file.. "
how about the .gro file? I see nothing wrong with my .gro file.


Thank you
Lin
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Re: [gmx-users] rb1 test failed after recompiling gromacs 3.3.2

[Justin A. Lemkul]

Nicolas Sapay wrote:

Nicolas Sapay wrote:

Hello,

I've run the gmxtest on Gromacs-3.3.2. One simple test failed:

   Testing rb1 . . . *** glibc detected *** realloc(): invalid next
   size: 0x082c0180 ***
   sh: line 1: 27398 Aborted mdrun >mdrun.out 2>&1
   FAILED. Check files in rb1

I have more closely looked the compilation logs and the files used for 
the test. There is nothing particular to say about the compilation (no 
error, no warning). note that I'm using glibc 2.3.4 compiled on a Linux 
2.4.20 system. The error seems to be due to the -DMOL1 define in 
grompp.mdp of the rb1 test. When I replace it by -DBONDS (as in the 
rb125 test), the test is successful. What the -DMOL1 statement means? I 
though you can only use -DFLEXIBLE or -DPOSRES as defines in a mdp file. 
I had a look in the 3.3.2 manual, but found nothing about it.




Anything can be defined in the topology.  Look for the #ifdef statements in 
topol.top.  I checked the test suite (for mine it's 3.3.3), and found several 
instances where there is a -DMOL1 flag, but no corresponding definition in the 
topology:


angles1
dih1
rb1

In other tests, where it is defined, it appears to mean that the system should 
contain one molecule of interest.  No idea why it's missing from these others, 
and why it doesn't seem to cause problems, at least in angles1 and dih1.


-Justin



And two complex tests failed as well:

   Testing acetonitrilRF . . . FAILED. Check files in acetonitrilRF
   Testing dec+water . . . FAILED. Check files in dec+water


In the case of the rb1 test, I checked all the .out .log files but 
found anything wrong. For acetonitrilRF, I obtain this:


   ---
   Program mdrun, VERSION 3.3.2
   Source code file: network.c, line: 437

   Routine should not have been called:
   gmx_sumi
   --


According to the mailing list, there is something to fix in 
src/mdlib/rf_util.c. For dec+water, I've got the same error than on 
the wiki, so nothing to worry about apparently.Following the advices 
found on the wiki or the mailing list, I have re-compiled FFTW and 
Gromacs (with fixed rf_util.c) from the sources. For FFTW, I've used 
the following command:


   ./configure --prefix /usr/export/fftw-3.1.2/ --enable-float
   --enable-threads CC=/usr/bin/gcc


And for Gromacs:

   ./configure --prefix /usr/export/gromacs-3.3.2 --without-x
   CC=/usr/bin/gcc CPPFLAGS=-I/usr/export/fftw-3.1.2/include/
   LDFLAGS=-L/usr/export/fftw-3.1.2/lib/


I have rerun the test but I still obtain the same error with the rb1 
test (and the dec+water test). Can someone explain to me what the it 
means exactly and how to fix it? (I guess it's related to the 
Ryckaert-Bellemans potential?).


   Thanks,
   Nicolas


ps: I'm using RHE 4.7 and gcc 3.4.6

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--


Justin A. Lemkul
Graduate Research Assistant
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] rb1 test failed after recompiling gromacs 3.3.2

[Nicolas Sapay]

Nicolas Sapay wrote:

Hello,

I've run the gmxtest on Gromacs-3.3.2. One simple test failed:

   Testing rb1 . . . *** glibc detected *** realloc(): invalid next
   size: 0x082c0180 ***
   sh: line 1: 27398 Aborted mdrun >mdrun.out 2>&1
   FAILED. Check files in rb1

I have more closely looked the compilation logs and the files used for 
the test. There is nothing particular to say about the compilation (no 
error, no warning). note that I'm using glibc 2.3.4 compiled on a Linux 
2.4.20 system. The error seems to be due to the -DMOL1 define in 
grompp.mdp of the rb1 test. When I replace it by -DBONDS (as in the 
rb125 test), the test is successful. What the -DMOL1 statement means? I 
though you can only use -DFLEXIBLE or -DPOSRES as defines in a mdp file. 
I had a look in the 3.3.2 manual, but found nothing about it.




And two complex tests failed as well:

   Testing acetonitrilRF . . . FAILED. Check files in acetonitrilRF
   Testing dec+water . . . FAILED. Check files in dec+water


In the case of the rb1 test, I checked all the .out .log files but 
found anything wrong. For acetonitrilRF, I obtain this:


   ---
   Program mdrun, VERSION 3.3.2
   Source code file: network.c, line: 437

   Routine should not have been called:
   gmx_sumi
   --


According to the mailing list, there is something to fix in 
src/mdlib/rf_util.c. For dec+water, I've got the same error than on 
the wiki, so nothing to worry about apparently.Following the advices 
found on the wiki or the mailing list, I have re-compiled FFTW and 
Gromacs (with fixed rf_util.c) from the sources. For FFTW, I've used 
the following command:


   ./configure --prefix /usr/export/fftw-3.1.2/ --enable-float
   --enable-threads CC=/usr/bin/gcc


And for Gromacs:

   ./configure --prefix /usr/export/gromacs-3.3.2 --without-x
   CC=/usr/bin/gcc CPPFLAGS=-I/usr/export/fftw-3.1.2/include/
   LDFLAGS=-L/usr/export/fftw-3.1.2/lib/


I have rerun the test but I still obtain the same error with the rb1 
test (and the dec+water test). Can someone explain to me what the it 
means exactly and how to fix it? (I guess it's related to the 
Ryckaert-Bellemans potential?).


   Thanks,
   Nicolas


ps: I'm using RHE 4.7 and gcc 3.4.6

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begin:vcard
fn:Nicolas SAPAY
n:SAPAY;Nicolas
org:University of Calgary;Biological Sciences
adr:;;2500 University drive NW;Calgary;AB;T2N 1N4;Canada
email;internet:[EMAIL PROTECTED]
title:PhD
tel;work:(403) 220-6869
tel;fax:(403) 289-9311
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[gmx-users] Re: Salt molecule - ion bond

[Vitaly Chaban]

> The salt R-N(CH3)3-Br.
> And, any differences for assigning the Van-der waal and LJ parameters
> between salt and organic molecules?

no difference.
-
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq., 4, Kharkiv 61077, Ukraine
email: [EMAIL PROTECTED]
skype: vvchaban
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Re: [gmx-users] Salt molecule - ion bond

[Justin A. Lemkul]

Chih-Ying Lin wrote:

Hi
The salt R-N(CH3)3-Br.

Could anyone tell me how to assign the force field parameter for the
salt molecule ; especially for the ion bond/ ion angle/



There will be no such thing, unless the force field has already assigned it. 
But since a covalent bond is probably unlikely to exist within such a compound 
(at least, in aqueous solution, for which most force fields are derived), you 
will likely not find a force constant (at the very least) for such a species.



Does there exist "dihedral angle " between the ion Br and R ?
And, any differences for assigning the Van-der waal and LJ parameters
between salt and organic molecules?


If there's no bond, there's no dihedral either.  Again, I'm assuming aqueous 
solution.


L-J parameters are defined by the force field.  Investigate such issues in the 
the primary reference for the force field you want to use, and look in the 
*nb.itp for that force field, as well.


-Justin



Thanks
Lin
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--


Justin A. Lemkul
Graduate Research Assistant
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] tfe and gromos9653a

[Justin A. Lemkul]

shahrbanoo karbalaee wrote:

Dear justin
I guess I did right.I add in my topoly file tfe   in part of dehedrals
" gd_24".(from your edit  in  dmso topolgy  last another mail)and I
could minimize. what do you think this adding ?.any way thank you for
every thing.now about my peptide I have this error .(in c terminal
peptide   is amidated) and in this force field ffG53a5,I tried to edit
this error (refine pdb file and ...). but  didnot.(the 14 residue is
phe)


I don't know, does gd_24 correspond to the missing dihedral involving your 
atoms?


C-terminus: None
Now there are 14 residues with 138 atoms
Making bonds...
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Number of bonds was 142, now 139
Generating angles, dihedrals and pairs...
Before cleaning: 210 pairs

---
Program pdb2gmx, VERSION 3.3.2
Source code file: pgutil.c, line: 87

Fatal error:
Atom H not found in residue 14 while adding improper

---



Without seeing your command line, I have absolutely no idea what you've done. 
Please, take my advice (that I've given about ten times) - post command lines if 
you post errors.  You probably didn't specify -ignh, but that's just a guess 
because I can't get into your head!


-Justin

--


Justin A. Lemkul
Graduate Research Assistant
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] regarding 2002 post showing protein unfolding with long timesteps

[David van der Spoel]

[EMAIL PROTECTED] wrote:

David van der Spoel, can you please comment on this post of your from 2002:

"long timesteps combined with dummies give me unfolding proteins while 
without

dummies and 2 fs the systems are stable. These are long-time effects (i.e.
after a couple of ns things start to happen). I have to do more test
before I can conclude anything."

reference: http://www.gromacs.org/pipermail/gmx-users/2002-July/002171.html

I searched your name with the work timestep and looked through the ~200 
titles of posts, but couldn't find anything.


I am currently considering a 5fs timestep and, even though it is nicely 
described in the gromacs 4 paper, I wanted to ensure that whatever 
problem you might have been experiencing is now solved. Alternatively, 
if it was a particular type of system that appears to be refractory to 
the 5fs timestep options (properly instituted with dummies, etc) then 
that information would also be valuable to me.


My usage will be for free energy calculations of a protein in a lipid 
bilayer so obtaining information on the dynamic processes is not 
important to me here.


Thanks,
Chris.


I don't recall this to be honest, but obviously there are a lot of 
factors playing in. The most important one is the force field of course, 
but also the treatment of cutoffs. Many problems of instabilities go 
away when one uses PME instead of cutoffs. I think that many people use 
at least 4 fs time steps routinely, and the integration algorithm is 
fine with that. If you want to know more than you should probably test 
it explicitly.




--
David van der Spoel, Ph.D., Professor of Biology
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] cgnr

[LuLanyuan]

Hi Lin,
Please read the manual. By checking the "Index" section you'll find charge 
group.
For example, there is a paragraph in page 20.
Lanyuan Lu


> Date: Thu, 21 Aug 2008 09:52:35 -0700
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: [gmx-users] cgnr
> 
> Hi
> As Justin described,
> cgnr = charge group number
> 
> could anyone explain more about this ?
> and, how to determin cgnr?
> 
> Thanks
> Lin
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[gmx-users] Salt molecule - ion bond

[Chih-Ying Lin]

Hi
The salt R-N(CH3)3-Br.

Could anyone tell me how to assign the force field parameter for the
salt molecule ; especially for the ion bond/ ion angle/

Does there exist "dihedral angle " between the ion Br and R ?
And, any differences for assigning the Van-der waal and LJ parameters
between salt and organic molecules?

Thanks
Lin
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[gmx-users] cgnr

[Chih-Ying Lin]

Hi
As Justin described,
cgnr = charge group number

could anyone explain more about this ?
and, how to determin cgnr?

Thanks
Lin
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[gmx-users] tfe and gromos9653a

[shahrbanoo karbalaee]

Dear justin
I guess I did right.I add in my topoly file tfe   in part of dehedrals
" gd_24".(from your edit  in  dmso topolgy  last another mail)and I
could minimize. what do you think this adding ?.any way thank you for
every thing.now about my peptide I have this error .(in c terminal
peptide   is amidated) and in this force field ffG53a5,I tried to edit
this error (refine pdb file and ...). but  didnot.(the 14 residue is
phe)
C-terminus: None
Now there are 14 residues with 138 atoms
Making bonds...
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Number of bonds was 142, now 139
Generating angles, dihedrals and pairs...
Before cleaning: 210 pairs

---
Program pdb2gmx, VERSION 3.3.2
Source code file: pgutil.c, line: 87

Fatal error:
Atom H not found in residue 14 while adding improper

---

-- 
sh-karbalaee
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[gmx-users] Re: Using Morse potentials with ENCAD force field

[Vitaly Chaban]

It seems because your box should be a bit longer to succeed. Try to
enlarge the side (13.2 nm) length.


2008/8/21 Andy Shelley <[EMAIL PROTECTED]>:
> No problem the term flattens is porbably not the best technical
> description.  A better one would be the cnt collapses.
>
> Andy
>
> On Thu, Aug 21, 2008 at 8:34 AM, Vitaly Chaban <[EMAIL PROTECTED]>
> wrote:
>>
>> >
>> > Actually I think I am using the gromos force field. I have been using
>> > Christopher Stiles page as a guide to get started with using CNT
>> > http://cs86.com/CNSE/SWNT.htm. I realize now that all the modifications
>> > were
>> > made to ffgmx files.  So I believe I am using the gromos forcefield. Is
>> > the
>> > forcefield used defined by the parameters? I have added nonbonded
>> > parameters
>> > to ffgmxnb.itp as the following:
>> > [ nonboned_params ]
>> >   ON1 0.00691.4016E-05
>> >OO1 0.00619.9676E-06
>> >NN1 0.00761.8778E-05
>> >CO1 0.00304.7908E-06
>> >CN1 0.00336.5271E-06
>> >
>> > and the same for pairtypes
>> >  [ pairtypes ]
>> >CN1  0.0033   6.5271E-06
>> >CO1  0.0030   4.7908E-06
>> >NN1  0.0076   1.8778E-05
>> >OO1  0.0061   9.9676E-06
>> >ON1  0.0069   1.4016E-05
>> >
>> > I have put just 200 nitrogen molecules in a 24.7nm x 24.7nm x 12.3nm box
>> > with a 10,10 cnt length 12.3nm.  The nitrogen molecules appear to not
>> > even
>> > interact with the cnt but it still flattens.  Any ideas?
>> >
>>
>> Andy,
>>
>> Hi. Sorry for my English, what do you mean saying "cnt flattens"?
>>
>> Again, is everything right with your box side length. I mean if the
>> cnt fits in the box (the rim atoms)?
>>
>>
>> --
>> Vitaly V. Chaban
>> School of Chemistry
>> National University of Kharkiv
>> Svoboda sq., 4, Kharkiv 61077, Ukraine
>> email: [EMAIL PROTECTED]
>> skype: vvchaban
>
>



-- 
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq., 4, Kharkiv 61077, Ukraine
email: [EMAIL PROTECTED]
skype: vvchaban
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[gmx-users] regarding 2002 post showing protein unfolding with long timesteps

[chris . neale]

David van der Spoel, can you please comment on this post of your from 2002:

"long timesteps combined with dummies give me unfolding proteins while without
dummies and 2 fs the systems are stable. These are long-time effects (i.e.
after a couple of ns things start to happen). I have to do more test
before I can conclude anything."

reference: http://www.gromacs.org/pipermail/gmx-users/2002-July/002171.html

I searched your name with the work timestep and looked through the  
~200 titles of posts, but couldn't find anything.


I am currently considering a 5fs timestep and, even though it is  
nicely described in the gromacs 4 paper, I wanted to ensure that  
whatever problem you might have been experiencing is now solved.  
Alternatively, if it was a particular type of system that appears to  
be refractory to the 5fs timestep options (properly instituted with  
dummies, etc) then that information would also be valuable to me.


My usage will be for free energy calculations of a protein in a lipid  
bilayer so obtaining information on the dynamic processes is not  
important to me here.


Thanks,
Chris.

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Re: [gmx-users] simulations backward in time

[Jussi Lehtola]

On Thu, 2008-08-21 at 10:32 -0400, Sumanth Jamadagni wrote:
> Using a negative 'dt' in the mdp file does not not seem to cause any
> simulation problems (tested on a waterbox- doesn't crash). I am not sure
> if the system is evolving backwards in time though. I am not sure how to
> check that.  

So is the purpose of this to run an NVE simulation? Since if you have
any thermostats enabled the sign of the time step doesn't matter since
the simulation is "screwed up" anyhow..

Also when using thermostats inverting the sign of the time step may
cause wrong behaviour since then the difference to the desired value may
increase if the time step is assumed positive in the algorithm.

Physically, inverting the initial velocity corresponds to inverting the
direction of time. Of course you will not get back the same
configurations as before due to rounding errors and a chaotic system.
-- 
--
Jussi Lehtola, FM, Tohtorikoulutettava
Fysiikan laitos, Helsingin Yliopisto
[EMAIL PROTECTED], p. 191 50673
--
Mr. Jussi Lehtola, M. Sc., Doctoral Student
Department of Physics, University of Helsinki, Finland
[EMAIL PROTECTED]
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Re: [gmx-users] Visualizing gromacs result

[Jochen Hub]

vivek sharma wrote:

Hi,
Can anybody tell which visualization tool is better out of 
vmd/pymol/gopenmol to visualize gromacs result.?

- watch long trajectories: VMD (reads xtc)
- fancy pictures and short movies: pymol (does not read xtc)
gopenmol: I don't know.

cheers, jochen




Thanks in advance,
Vivek


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--

Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312
 


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[gmx-users] [Fwd: WARNING: Found more than 12 triclinic correction vectors, ignoring some.]

[Justin A. Lemkul]

Hi all,

I tried to send this to the gmx-developers list several hours ago, but it never 
showed up, so I'll try here.  There also appears to be problems with the Admin 
pages for the mailing lists (I went to check and make sure my subscription to 
that list was active).


I am simulating a simple protein/ligand in water using an octahedral box.  For
visualization purposes, I am rendering the box in its true octahedral shape
using the following command:

trjconv -s md.tpr -f 20ns.xtc -o compact.xtc -ur compact -pbc mol

When I do this, I receive a series of warnings like the following:

WARNING: Found more than 12 triclinic correction vectors, ignoring some.
  There is probably something wrong with your box.
 Box (3x3):
Box[0]={ 6.87729e+00,  0.0e+00,  0.0e+00}
Box[1]={ 3.23209e+00,  6.46199e+00,  0.0e+00}
Box[2]={-2.97018e-01,  1.10216e-03,  5.59953e+00}

I saw a previous discussion across the list here:

http://www.gromacs.org/pipermail/gmx-developers/2006-November/001953.html

The result was a request for a bugzilla and a potential fix.  I am using GMX
3.3.3, and the warnings only seem to come up when I use -pbc mol.  Other PBC
corrections (like nojump) don't seem to result in these warnings.

When I visualize the trajectory, the box seems to smoothly morph between an
octahedron and a rectangular shape.  I don't know if that's relevant or just a
consequence of visualization.

Any ideas as to what's going on?  Is there a problem with this type of 
manipulation?

Thanks in advance for any comments.

-Justin

--


Justin A. Lemkul
Graduate Research Assistant
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] New Gromacs-CPMD QMMM webpage

[Pradip Biswas]

Hi Vidhya,

You can also find the qmmm_examples in your downloaded gromacs source code:
gmx-3.3.1_qmmm-1.3.2.

location:
gmx-3.3.1_qmmm-1.3.2/share/qmmm_examples

You will find the templates of  'CPMD_inp.tmpl'  and 'runcpmd' there in the
examples. However, all the runcpmd templates seem to be for parallel run. If
you use a serial version for CPMD, just use the following line in your
runcpmd (instead all those lamboot, lamclean, mpirun)

 (path to cpmd executable)/cpmd.x CPMD_inp.run

or simply

 cpmd.x CPMD_inp.run

if cpmd.x is globally accessible.

pb.

On Wed, Aug 20, 2008 at 6:55 AM, vidhya sankar <[EMAIL PROTECTED]>wrote:

>
> dear sir,
> i am vidhya sankar speaking . i am not able to down load QM/MM
> exampiles files since it take much time and huge memory (156Mb) often net is
> disconnected
> could you please send some example input files of CPMD part  mainly 
> 'CPMD_inp.tmpl'
> 'runcpmd' ?
> please i am expecting your reply soon
>
>
>
>
>
> --- On *Fri, 15/8/08, Pradip Biswas <[EMAIL PROTECTED]>* wrote:
>
> From: Pradip Biswas <[EMAIL PROTECTED]>
> Subject: [gmx-users] New Gromacs-CPMD QMMM webpage
> To: gmx-users@gromacs.org
> Date: Friday, 15 August, 2008, 4:41 AM
>
>
>  Dear Users,
> The modified Gromacs code for Gromacs-CPMD QMMM is now available at:
>
> http://www.tougaloo.edu/research/qmmm/
>
> Please note that we fixed a bug related to MM layering in the version
> gmx-3.3.1_qmmm-1.3.1 and uploaded a new version, gmx-3.3.1_qmmm-1.3.2. If
> you are using version 1.3.1, you should upgrade to v-1.3.2 or contact us (
> [EMAIL PROTECTED]) to fix the typos in v-1.3.1.
>
> The site http://comppsi.csuohio.edu/groups/qmmm.html is offline because of
> lab renovation and will not be maintained hereafter. The Gromacs-CPMD page
> will henceforth be continued in the above mentioned site.
>
> Cheers,
> Pradip K Biswas.
>
>
> ___
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[gmx-users] simulations backward in time

[Sumanth Jamadagni]

Using a negative 'dt' in the mdp file does not not seem to cause any
simulation problems (tested on a waterbox- doesn't crash). I am not sure
if the system is evolving backwards in time though. I am not sure how to
check that.  

But I think, all I require is that the equations of motion be integrated
backwards. The ensemble of trajectories which will end up in one  state A 
(an attractor) when integrated backwards and in state B (another
attractor) when integrated forwards will be the ensemble I need for
transition path sampling. 

Sumanth N Jamadagni
Graduate Student 
Isermann Dept of Chemical and Biological Engg
Rensselaer Polytechnic Institute

[EMAIL PROTECTED]
(Cell)518-598-2786


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Re: [gmx-users] Re: Simulations backward in time

[Vitaly Chaban]

Yes. Namely at the very step the velocities should be inverted to
invert a time flow.

My remark was addressed namely to the word "initial".


2008/8/21 Berk Hess <[EMAIL PROTECTED]>:
> Surely inverting the velocities changes the direction of the system
> evolution.
> The state of the system is given by x and v. The evolution is determined
> by the state and the potential. The only time direction information is in
> the sign of v.
> Note that due to numerical issues you will never get back the inverse of
> an original trajectory when inverting the velocities.
>
> Berk
>
>
> 
>> Date: Thu, 21 Aug 2008 16:53:07 +0300
>> From: [EMAIL PROTECTED]
>> To: [EMAIL PROTECTED]; gmx-users@gromacs.org
>> Subject: Re: [gmx-users] Re: Simulations backward in time
>> CC:
>>
>> In conf.gro? It will change only the first steps but will not change
>> the direction of the system evolution.
>>
>> As I understand, the topicstarter wanted to perform the simulation
>> "backwards"...
>>
>> Vitaly
>>
>> 2008/8/21 Jochen Hub <[EMAIL PROTECTED]>:
>> > Vitaly Chaban wrote:
>> >>>
>> >>> I wanted to perform some simulations backward and forward in time (for
>> >>> transition path sampling ). If I specify a negative value for 'dt' in
>> >>> the
>> >>> mdp file, would that work for backward integration of the equations of
>> >>> motion ?
>> >>>
>> >
>> > You could also invert the initial velocities. Shouldn't that be the same
>> > as
>> > using a negative dt ?
>> >
>> > jochen
>> >
>> > --
>> > 
>> > Dr. Jochen Hub
>> > Max Planck Institute for Biophysical Chemistry
>> > Computational biomolecular dynamics group
>> > Am Fassberg 11
>> > D-37077 Goettingen, Germany
>> > Email: jhub[at]gwdg.de
>> > Tel.: +49 (0)551 201-2312
>> > 
>> >
>>
>>
>>
>> --
>> Vitaly V. Chaban
>> School of Chemistry
>> National University of Kharkiv
>> Svoboda sq., 4, Kharkiv 61077, Ukraine
>> email: [EMAIL PROTECTED]
>> skype: vvchaban
>> ___
>> gmx-users mailing list gmx-users@gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
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>
> 
> Express yourself instantly with MSN Messenger! MSN Messenger



-- 
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq., 4, Kharkiv 61077, Ukraine
email: [EMAIL PROTECTED]
skype: vvchaban
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FW: [gmx-users] Re: Simulations backward in time

[Berk Hess]

From: [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
Subject: RE: [gmx-users] Re: Simulations backward in time
Date: Thu, 21 Aug 2008 16:11:56 +0200







Surely inverting the velocities changes the direction of the system evolution.
The state of the system is given by x and v. The evolution is determined
by the state and the potential. The only time direction information is in the 
sign of v.
Note that due to numerical issues you will never get back the inverse of
an original trajectory when inverting the velocities.

Berk


> Date: Thu, 21 Aug 2008 16:53:07 +0300
> From: [EMAIL PROTECTED]
> To: [EMAIL PROTECTED]; gmx-users@gromacs.org
> Subject: Re: [gmx-users] Re: Simulations backward in time
> CC: 
> 
> In conf.gro? It will change only the first steps but will not change
> the direction of the system evolution.
> 
> As I understand, the topicstarter wanted to perform the simulation
> "backwards"...
> 
> Vitaly
> 
> 2008/8/21 Jochen Hub <[EMAIL PROTECTED]>:
> > Vitaly Chaban wrote:
> >>>
> >>>  I wanted to perform some simulations backward and forward in time (for
> >>> transition path sampling ). If I specify a negative value for 'dt' in the
> >>> mdp file, would that work for backward integration of the equations of
> >>> motion ?
> >>>
> >
> > You could also invert the initial velocities. Shouldn't that be the same as
> > using a negative dt ?
> >
> > jochen
> >
> > --
> > 
> > Dr. Jochen Hub
> > Max Planck Institute for Biophysical Chemistry
> > Computational biomolecular dynamics group
> > Am Fassberg 11
> > D-37077 Goettingen, Germany
> > Email: jhub[at]gwdg.de
> > Tel.: +49 (0)551 201-2312
> > 
> >
> 
> 
> 
> -- 
> Vitaly V. Chaban
> School of Chemistry
> National University of Kharkiv
> Svoboda sq., 4, Kharkiv 61077, Ukraine
> email: [EMAIL PROTECTED]
> skype: vvchaban
> ___
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[gmx-users] Re: Simulations backward in time

[Vitaly Chaban]

>
>
> Vitaly Chaban wrote:
>>>  I wanted to perform some simulations backward and forward in time (for
>>> transition path sampling ). If I specify a negative value for 'dt' in the
>>> mdp file, would that work for backward integration of the equations of
>>> motion ?
>>
>> Time does not run back. :) It's a bad idea.
>>
> I think it will work, but I'm not sure whether this is the best solution
> to the problem of transition path sampling.

No doubt, the integration itself will work. But will all the attendant
algorithms work correctly while the system moves from more favourable
state to less favourable ones?


Just for interest, I started such run (dt = -0.001) for liquid
acetonitrile box and after a few picoseconds obtained a series of pdb
files and a complete crash.

About transition path sampling... I don't know. :)


-- 
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq., 4, Kharkiv 61077, Ukraine
email: [EMAIL PROTECTED]
skype: vvchaban
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[gmx-users] Re: gmx-users Digest, Vol 52, Issue 89

[Vitaly Chaban]

> Hi,
> Can anybody tell which visualization tool is better out of
> vmd/pymol/gopenmol to visualize gromacs result.?
>
> Thanks in advance,
> Vivek

I am a fan of VMD. But for quick looking at the trajectory ngmx is a
bit more convenient.


-- 
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq., 4, Kharkiv 61077, Ukraine
email: [EMAIL PROTECTED]
skype: vvchaban
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Re: [gmx-users] Re: Simulations backward in time

[Vitaly Chaban]

In conf.gro? It will change only the first steps but will not change
the direction of the system evolution.

As I understand, the topicstarter wanted to perform the simulation
"backwards"...

Vitaly

2008/8/21 Jochen Hub <[EMAIL PROTECTED]>:
> Vitaly Chaban wrote:
>>>
>>>  I wanted to perform some simulations backward and forward in time (for
>>> transition path sampling ). If I specify a negative value for 'dt' in the
>>> mdp file, would that work for backward integration of the equations of
>>> motion ?
>>>
>
> You could also invert the initial velocities. Shouldn't that be the same as
> using a negative dt ?
>
> jochen
>
> --
> 
> Dr. Jochen Hub
> Max Planck Institute for Biophysical Chemistry
> Computational biomolecular dynamics group
> Am Fassberg 11
> D-37077 Goettingen, Germany
> Email: jhub[at]gwdg.de
> Tel.: +49 (0)551 201-2312
> 
>



-- 
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq., 4, Kharkiv 61077, Ukraine
email: [EMAIL PROTECTED]
skype: vvchaban
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Re: [gmx-users] HELP::Running Gromacs in parellel

[Justin A. Lemkul]

vivek sharma wrote:

Hi There,

I am running gromacs on parellel system using the submit command. 
Commands are running fine, but the .trr file I got is not matching with 
the trr file I got while running command in serial.


Based on what analysis?  Have you done gmxcheck -f1 -f2 on these .trr files?

Also, I am getting a number of log files(equal to number of nodes I am 
choosing).
How should I analyze them or check whether results with parellel run are 
consistent with the serial run, to validate my procedure.


The md0.log contains the most detailed information.  Have a look at the contents 
with a text editor.


-Justin



Anybody having experience in related topic, please suggest me the proper 
way of sorting it out. I am using submit command for submitting my job 
in parellel run.




With Thanks,
Vivek




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--


Justin A. Lemkul
Graduate Research Assistant
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] Visualizing gromacs result

[vivek sharma]

Hi,
Can anybody tell which visualization tool is better out of
vmd/pymol/gopenmol to visualize gromacs result.?

Thanks in advance,
Vivek
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Re: [gmx-users] Re: Simulations backward in time

[Jochen Hub]

Vitaly Chaban wrote:

 I wanted to perform some simulations backward and forward in time (for
transition path sampling ). If I specify a negative value for 'dt' in the
mdp file, would that work for backward integration of the equations of
motion ?



You could also invert the initial velocities. Shouldn't that be the same 
as using a negative dt ?


jochen

--

Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312
 


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[gmx-users] Re: New Gromacs-CPMD QMMM webpage

[Vitaly Chaban]

>> Â
>> dear sir,
>> Â Â Â Â Â Â Â Â Â Â Â  i am vidhya sankar speaking . i am not able to down 
>> load QM/MM exampiles files since it take much time and huge memory (156Mb) 
>> often net is disconnected
>> could you please send some example input files of CPMD part  mainly 
>> 'CPMD_inp.tmpl'Â  'runcpmd'Â ?
>> please i am expecting your reply soonÂ


Sent personally.


>
> --
> Vitaly V. Chaban
> School of Chemistry
> National University of Kharkiv
> Svoboda sq., 4, Kharkiv 61077, Ukraine
> email: [EMAIL PROTECTED]
> skype: vvchaban
>



-- 
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq., 4, Kharkiv 61077, Ukraine
email: [EMAIL PROTECTED]
skype: vvchaban
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[gmx-users] Re: Using Morse potentials with ENCAD force field

[Vitaly Chaban]

>
> Actually I think I am using the gromos force field. I have been using
> Christopher Stiles page as a guide to get started with using CNT
> http://cs86.com/CNSE/SWNT.htm. I realize now that all the modifications were
> made to ffgmx files.  So I believe I am using the gromos forcefield. Is the
> forcefield used defined by the parameters? I have added nonbonded parameters
> to ffgmxnb.itp as the following:
> [ nonboned_params ]
>   ON1 0.00691.4016E-05
>OO1 0.00619.9676E-06
>NN1 0.00761.8778E-05
>CO1 0.00304.7908E-06
>CN1 0.00336.5271E-06
>
> and the same for pairtypes
>  [ pairtypes ]
>CN1  0.0033   6.5271E-06
>CO1  0.0030   4.7908E-06
>NN1  0.0076   1.8778E-05
>OO1  0.0061   9.9676E-06
>ON1  0.0069   1.4016E-05
>
> I have put just 200 nitrogen molecules in a 24.7nm x 24.7nm x 12.3nm box
> with a 10,10 cnt length 12.3nm.  The nitrogen molecules appear to not even
> interact with the cnt but it still flattens.  Any ideas?
>

Andy,

Hi. Sorry for my English, what do you mean saying "cnt flattens"?

Again, is everything right with your box side length. I mean if the
cnt fits in the box (the rim atoms)?


-- 
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq., 4, Kharkiv 61077, Ukraine
email: [EMAIL PROTECTED]
skype: vvchaban
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[gmx-users] HELP::Running Gromacs in parellel

[vivek sharma]

Hi There,

I am running gromacs on parellel system using the submit command. Commands
are running fine, but the .trr file I got is not matching with the trr file
I got while running command in serial.
Also, I am getting a number of log files(equal to number of nodes I am
choosing).
How should I analyze them or check whether results with parellel run are
consistent with the serial run, to validate my procedure.

Anybody having experience in related topic, please suggest me the proper way
of sorting it out. I am using submit command for submitting my job in
parellel run.



With Thanks,
Vivek
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[gmx-users] simulation problems

[baloilgiullare]

Hello gmx users

I am simulating a system composed of of an organic molecule
(a 10 -CH=CH- thread with polyciclyc ends) in CH3CN. The system is made
up of 6000 atoms in a cubic box. I am using the gromos the 96 force field.
The solute molecule is elongated like : A-B where A and B are 
the ends

but (via h-bond) can fold like:
--A-B--
| |
---
(sorry for poor ASCII art but I hope it helps).
Since I want to study
the kinetics of this process I have performed several simulations of the
system starting from different staring conditions. The problem I have
is that some of simulations (4 out of 15) crash due to problems with
lincs. The strange thing is that this happens after the simulation has
go on for quite a long time (never less than 5 ns) so I do not think
that it is related to the equilibration at the start of the simulation.
The initial lincs warning always concerns different bonds and the
energies some 1 ps intervals before the crash seem not to show
"patological" behavior.
I would discard machine and/or compiler problems too, since i have used
two different gromacs versions (3.3.2 and 3.3.3) and both gave the same
problem. Both versions were tested with the gmxtest suite using
gcc-3.4.6. The simulations were run of 1 to 4 cpus on a single AMD
Opteron node.

Here is my mdp file:

cpp  = /lib/cpp
include  =
define   =

integrator   = md
tinit= .0
dt   = 0.002
nsteps   = 10
nstcomm  = 1
comm-grps= System
comm_mode= Linear

emtol= 100
emstep   = 0.01
niter= 0
nstcgsteep   = 1000

nstxout  = 2500
nstvout  = 2500
nstfout  = 0
nstlog   = 2500
nstenergy= 250
nstxtcout= 250
xtc_precision= 1000
xtc_grps = System
; Selection of energy groups =
energygrps   = System

nstlist  = 5
ns_type  = grid
pbc  = xyz
rlist= 1.1
domain-decomposition = no

coulombtype  = PME
rcoulomb_switch  = 0
rcoulomb = 1.00
epsilon_r= 1
vdw_type = Cut-off
rvdw_switch  = 0
rvdw = 1.00
DispCorr = no
fourierspacing   = 0.12
fourier_nx   =
fourier_ny   =
fourier_nz   =
pme_order= 4
ewald_rtol   = 1e-05
epsilon_surface  = 0
optimize_fft = no

tcoupl   = Berendsen
tc-grps  = System
tau_t= 0.1
ref_t= 300.
Pcoupl   = No
Pcoupltype   = Isotropic
tau_p= 5.0
compressibility  = 11.2e-5
ref_p= 1.0


annealing= no
annealing_npoints=
annealing_time   =
annealing_temp   =

gen_vel  = no
gen_temp = 300
gen_seed = 135907

constraints  = all-bonds

constraint-algorithm = Lincs
unconstrained-start  = yes
Shake-SOR= no
shake-tol= 0.0001
lincs_order  = 4
lincs-iter   = 1
lincs_warnangle  = 30
morse= no

Any ideas? Should I keep separated thermostats for solute and solvent?
Even increasing lincs-order to 2 did not help.

Greetings,
giordano



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Re: [gmx-users] tfe

[Justin A. Lemkul]

shahrbanoo karbalaee wrote:

Dear justin
 for have  tfe30% after I got tfedrg.top with pdb2gmx and force field
gromos965a.
I do t this command :
editconf -f tfedrg.gro -bt dodecahedron -d 0.71 -o box.gro
genbox -cp box.gro -cs spc216.gro  ci tfedrg.gro - nmol 40  -p
topol.top -o solvated.gro
 I did that command with spc.gro(I rename spc216 to spc.gro) so.


I don't understand what you mean.  You show the use of spc216.gro...


I got this  error:creating statusfile for 1 node...
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 165 of the 1596 non-bonded parameter combinations
ERROR 0 [file "topol.top", line 57]:
  No default Proper Dih. types


grompp is telling you where the error is.  What is on line 57?  What atoms are 
involved?  Are these parameters in the *bon.itp file for your force field?



Excluding 1 bonded neighbours for TFE 18


I thought you tryed to insert 40 of these...you might want to check what went 
wrong.


Excluding 2 bonded neighbours for SOL 5777
processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
#   G96BONDS:   108
#  G96ANGLES:   144
#  PDIHS:   36
#   LJ14:   72
# SETTLE:   5777

---
Program grompp, VERSION 3.3.2
Source code file: grompp.c, line: 1182

Fatal error:
There was 1 error in input file(s)

---

the top file is attached.
another question  please: if i use opls doI must have rtp file.  and
add tfe. information  to this file?


This is not specific to OPLS.  If you want to use pdb2gmx to create your 
topology (under any force field), then yes, you need an .rtp file.  Otherwise, 
you make the topology by hand.


-Justin


thank u for suggestion and help





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--


Justin A. Lemkul
Graduate Research Assistant
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] tfe

[shahrbanoo karbalaee]

Dear justin
 for have  tfe30% after I got tfedrg.top with pdb2gmx and force field
gromos965a.
I do t this command :
editconf -f tfedrg.gro -bt dodecahedron -d 0.71 -o box.gro
genbox -cp box.gro -cs spc216.gro  ci tfedrg.gro - nmol 40  -p
topol.top -o solvated.gro
 I did that command with spc.gro(I rename spc216 to spc.gro) so.
I got this  error:creating statusfile for 1 node...
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 165 of the 1596 non-bonded parameter combinations
ERROR 0 [file "topol.top", line 57]:
  No default Proper Dih. types
Excluding 1 bonded neighbours for TFE 18
Excluding 2 bonded neighbours for SOL 5777
processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
#   G96BONDS:   108
#  G96ANGLES:   144
#  PDIHS:   36
#   LJ14:   72
# SETTLE:   5777

---
Program grompp, VERSION 3.3.2
Source code file: grompp.c, line: 1182

Fatal error:
There was 1 error in input file(s)

---

the top file is attached.
another question  please: if i use opls doI must have rtp file.  and
add tfe. information  to this file?
thank u for suggestion and help

-- 


best
-- 
sh-karbalaee


topol.top
Description: Binary data
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Re: [gmx-users] Re: Simulations backward in time

[David van der Spoel]

Vitaly Chaban wrote:

 I wanted to perform some simulations backward and forward in time (for
transition path sampling ). If I specify a negative value for 'dt' in the
mdp file, would that work for backward integration of the equations of
motion ?


Time does not run back. :) It's a bad idea.

I think it will work, but I'm not sure whether this is the best solution 
to the problem of transition path sampling.


--
David van der Spoel, Ph.D., Professor of Biology
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: Simulations backward in time

[Vitaly Chaban]

>  I wanted to perform some simulations backward and forward in time (for
> transition path sampling ). If I specify a negative value for 'dt' in the
> mdp file, would that work for backward integration of the equations of
> motion ?

Time does not run back. :) It's a bad idea.

-- 
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq., 4, Kharkiv 61077, Ukraine
email: [EMAIL PROTECTED]
skype: vvchaban
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Re: [gmx-users] Re: The WARNING

[Vitaly Chaban]

Tsjerk, probably you are right about grompp. I thought the user had
received this warning when preparing a system. Like genbox and so
on... So, I mean maybe he had not .tpr at that moment...

Vitaly

2008/8/21 Tsjerk Wassenaar <[EMAIL PROTECTED]>:
> Vitaly,
>
> This is not a grompp warning, but a warning from one of the analysis
> tools. grompp will never take masses 'out of the blue', but will
> always use the force field description (atom type definitions) or the
> mass specified in the .top/.itp file. It will bail out if no mass is
> properly defined for a specified atom. As David pointed out, these
> tools would benefit from reading in a .tpr (run input) file, not a
> .top file.
>
> Tsjerk
>
> On Thu, Aug 21, 2008 at 10:12 AM, Vitaly Chaban
> <[EMAIL PROTECTED]> wrote:
>>> WARNING: masses will be determined based on residue and atom names,
>>> this can deviate from the real mass of the atom type
>>>
>>> Is this warning serious?
>>> Could any one tell me how to fix the warning?
>>> I see nothing wrong with my .top and my .gro file.
>>>
>>
>> You should have right masses in your .top file - it's serious for
>> adequate simulation.
>>
>> If you get this warning NOT WITH GROMPP but while constructing  a
>> system it's not critical. Provide a valid .top file for the utility
>> generating the warning.
>>
>>
>> --
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Re: [gmx-users] Re: The WARNING

[Tsjerk Wassenaar]

Vitaly,

This is not a grompp warning, but a warning from one of the analysis
tools. grompp will never take masses 'out of the blue', but will
always use the force field description (atom type definitions) or the
mass specified in the .top/.itp file. It will bail out if no mass is
properly defined for a specified atom. As David pointed out, these
tools would benefit from reading in a .tpr (run input) file, not a
.top file.

Tsjerk

On Thu, Aug 21, 2008 at 10:12 AM, Vitaly Chaban
<[EMAIL PROTECTED]> wrote:
>> WARNING: masses will be determined based on residue and atom names,
>> this can deviate from the real mass of the atom type
>>
>> Is this warning serious?
>> Could any one tell me how to fix the warning?
>> I see nothing wrong with my .top and my .gro file.
>>
>
> You should have right masses in your .top file - it's serious for
> adequate simulation.
>
> If you get this warning NOT WITH GROMPP but while constructing  a
> system it's not critical. Provide a valid .top file for the utility
> generating the warning.
>
>
> --
> Vitaly V. Chaban
> School of Chemistry
> National University of Kharkiv
> Svoboda sq., 4, Kharkiv 61077, Ukraine
> email: [EMAIL PROTECTED]
> skype: vvchaban
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>



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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Re: [gmx-users] pdb file ???

[Tsjerk Wassenaar]

Hi Lin,

If you include bromide, you won't have excess charge... So, no need
for adding more counterions.

Cheers,

Tsjerk

On Thu, Aug 21, 2008 at 8:20 AM, Chih-Ying Lin <[EMAIL PROTECTED]> wrote:
> Hi
> It is the water-molecule system.
> For a molecule, like  R-N(CH3)3-Br,  I could make a pdb file  either
> include Br ion or exclude Br ion.
>
> If I exclude Br ion, I have to make Br ion as the counter ion for my system.
> If I include Br ion, I do NOT have to make Br ion as the counter ion
> since it will automatically become the counter ion.
> Am I right?
>
>
> Thank you
> Lin
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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[gmx-users] Re: tfe.itp

[Vitaly Chaban]

> after edit tfe.itp , I did the command grompp  and I got  this error :
> error  input solvated.gro. Do  I   have to make spc.gro  with tis
> forcefield(gromos965a)?
>

No solvated.gro? Access rights? dos format?


-- 
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq., 4, Kharkiv 61077, Ukraine
email: [EMAIL PROTECTED]
skype: vvchaban
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[gmx-users] RE: [ atomtypes ] are not case sensitive?

[Alan]

Well, I didn't developed Amber FF neither GAFF and although only Amber FF is
ported to GMX, one of the greatest appealing of Amber is its antechamber and
GAFF for generating topology for non usual compounds.

Looking at the way GAFF was developed (remember G is for generalised) is
seemed a natural step to me to use the same name for atom types but using a
different cases.

So have said that, I did a look at my converted topology file by
amb2gmx/acpypi and found that, although for vdw parameters they seem the
same, this doesn't hold for bonds for example. I have this in my GMX top
file:

[ bonds ]
...
96 97   11.0800e-013.0711e+05 ;CZ2 - HZ2 (AT CA - HA)
Protein
...
3154   3194   11.0870e-012.8811e+05 ;C76 - H76 (AT ca - ha)
Ligand

Anyway, after all this discussion, I realized (correct if I am wrong please)
that as long as the vdw parameters are the same, anything else is NOT
affected because even for the example of bonds above atom types change
nothing since parameters are explicit.

Then, I decided to compare gaff.dat and parm99.dat (topology parameters
files for Amber package) for vdw. I did found 2 atom types with same name
(diff case though) and diff parameters:

parm99.dat
   HP  1.1000  0.0157 Veenstra et al JCC,8,(1992),963
   Na  1.8680  0.00277Na+ Aqvist JPC 1990,94,8021.
(adapted)

gaff.dat
   hp  0.6000  0.0157 same to hs (be careful !)
   na  1.8240  0.1700 OPLS

Observe by the comments (4th column) that although they have the same name
(but diff by case) they are completely unrelated, hence the diff values for
r0 and epsilon.

So, in the end, at least for example gaff.dat x parm99.dat (note that Amber
has several others parm*.dat and glycam*.dat), I do have a conflicting case
issue that would affect my topology in GMX format if using amb2gmx/acpypi
tool for conversion.

Pondering a bit more, I came to the conclusion that at least for acpypi
(which I am developing), I can make it aware of this conflicting atom type
naming issue and rename it when converting from Amber to GMX.

About changing something in GMX? Frankly I don't know, but I hope that this
thread can be of some use for someone else who stumbles in this problem.

Cheers and many thanks for attention dear Berk.

Alan


From: Berk Hess <[EMAIL PROTECTED]>
> Subject: RE: [gmx-users] RE: [ atomtypes ] are not case sensitive?
> Hi,
>
> I don't know if any thinking went into the (non) case specifity of atom
> types.
> Nearly all string comparisons in Gromacs are not case specific.
> For things like atom names this makes sense.
>
> We could change the atom type comparisons to case specific.
> I think that all force field files supplied with Gromacs have consistent
> cases.
> But some users might have made force fields where this would cause
> problems.
>
> I think it is bad practice to distinguish atom types just by case,
> this makes things quite error prone.
> But allowing this probably does not mean that many people would do this.
>
> Another option would be to add an option to grompp.
>
> Berk.
>
>
> Date: Tue, 19 Aug 2008 12:03:57 +0100
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: [gmx-users] RE: [ atomtypes ] are not case sensitive?
>
> Dear Berk,
> Thanks for your attention.
> I don't know how familiar are you to amb2gmx and ffamber port to GMX. I am
> just learning since I am trying to test an application that is related to
> amb2gmx and ffamber (acpypi).
>
> So, for Amber MD (MD to contrast with FF), Generalised Amber Force Field
> (GAFF) uses all the atom types (AT) usually defined for Amber FF and several
> more AT but in lower case. I cannot assure 100% but I believe that for all
> common AT (being upper or lower), they share the same parameters including
> when found in bonds, angles etc. parameters.
>
> If so, then, it's not a problem if GMX is not sensitive about AT lower or
> upper case, because in the end they are the same. But, as I said before, I
> am not 100% sure about it. However, for Amber MD, case matters!
>
> Anyway, I am just worried about integrating Amber FF in GMX. If using
> ffamber port this problem doesn't appear because for Amber FF (ffamber*.itp
> files in GMX/top folder), AT are defined as, e.g., 'amber99_27', and so if I
> add a ligand.itp build with help of antechamber with GAFF to my system, the
> AT types will never conflict with ffamber*.itp.
>
> So, to summarise, I am really concerned that GMX is not case sensitive in
> the matter of AT. Is there any special reason for doing so?
>
> From: Berk Hess <[EMAIL PROTECTED]>
> In this case at least the non-bonded parameters seem to be the identical.
>
> Are there some different parameters for atom types which only differ in
> case?
>
>
> Hence, I don't have a clear example to answer your question, but I am
> investigating.  Cheers,Alan
>
> That is bad practice IMHO.
>
> But if so, we should consider changing this or adding an opti

[gmx-users] Re: The WARNING

[Vitaly Chaban]

> WARNING: masses will be determined based on residue and atom names,
> this can deviate from the real mass of the atom type
>
> Is this warning serious?
> Could any one tell me how to fix the warning?
> I see nothing wrong with my .top and my .gro file.
>

You should have right masses in your .top file - it's serious for
adequate simulation.

If you get this warning NOT WITH GROMPP but while constructing  a
system it's not critical. Provide a valid .top file for the utility
generating the warning.


-- 
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq., 4, Kharkiv 61077, Ukraine
email: [EMAIL PROTECTED]
skype: vvchaban
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[gmx-users] call for help

[曹臻]

Hello, everyone,

I meet a problem when I perform the gromacs. 
I fixed two C60 molecule at a certain distance(2.02 nm) by SHAKE algorithm. The
atoms have no charge on them. So the interaction between the molecules should be
the van der Waals interactions. I set the van der Waals cut off to be 1.2nm. The
intramolecular interaction was set to be zero. The intermolecular distance 
should
be further than 1.2nm. The length of the pbc box was 4.7nm. I run pullcode 
within
NVE ensemble. The ensemble average of force between the two C60 molecules should
be zero.  However, it is not. What mistake did I commit?

Thank you in advance.

Cao, Zhen


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