[gmx-users] how to use the new potential

[Matthew Hoopes]

>He, Yang wrote:
>> Hi all users,
>> 
>> I am engaged in deal with the course grain model,in which the 
>> potential functions are not the same as in gromacs.Hence, If I want to 
>> use the new potentials , I guess I can change the source code or use 
>> the table. But I never have this experience about  that.Can anyone of 
>> you give me some suggestions or examples?
>
>Start with the manual. :-) Hopefully the version 4 manual will be out 
>soon, but even if not, the 3.3 manual will be fine for nonbonded 
>tabulated potentials.
>
>Mark

Here is an example:

#
# Tabulated WCA potentials, dr=0.002, rc=3.5, no coulomb
#
0.00e+00  0.00e+00  0.00e+00  0.00e+00
0.00e+00  0.00e+00  0.00e+00
2.00e-03  0.00e+00  0.00e+00  0.00e+00
0.00e+00  0.00e+00  0.00e+00
...
3.60e-02  0.00e+00  0.00e+00  0.00e+00
0.00e+00  0.00e+00  0.00e+00
3.80e-02  0.00e+00  0.00e+00  0.00e+00
0.00e+00  0.00e+00  0.00e+00
4.00e-02  0.00e+00  0.00e+00  0.00e+00
0.00e+00  2.3841857812e+17  7.1525573584e+19
4.20e-02  0.00e+00  0.00e+00  0.00e+00
0.00e+00  1.3276038530e+17  3.7931538762e+19
4.40e-02  0.00e+00  0.00e+00  0.00e+00
0.00e+00  7.5967506265e+16  2.0718410875e+19
4.60e-02  0.00e+00  0.00e+00  0.00e+00
0.00e+00  4.4562136749e+16  1.1624905294e+19
...
3.498000e+00  0.00e+00  0.00e+00  0.00e+00
0.00e+00  0.00e+00  0.00e+00
3.50e+00  0.00e+00  0.00e+00  0.00e+00
0.00e+00  0.00e+00  0.00e+00

Column 1) is r (distance between atoms) 6) h(r) the repulsive term of the
potential and 7) -h'(r) as defined in section 6.7.2

1) Just use your favorite script (I used octave) to generate the following
text file with printf statements or something similar.
2) If some of the early values are too large, it may cause an error so I
just zeroed them out.
3) The information you need is in a few places in the manual. The table
above is defined in section 6.7.2 on page 131 of the GROMACS 4.0 manual.
4) You will also want to read section 7.3.12 on page 148 about entries in
your parameter file (e.g. energy groups, table file naming conventions)
5) You will need an index file that has particle groups for your new
potentials. The group names in the index file are what you use for energy
groups.
6) Pay attention to which combination rules you use in the topology file
7) Note that in the LJC(12-6-1) table in the top directory of GROMACS, the
minimum of the LJ is -0.25 and not -1.0 so I guess there is a factor of
4*epsilon multiplied to the table values.

What I don't know, and perhaps someone else can answer this is what should
be done if you are unsure of how your potential is separated in to
attractive and repulsive terms (e.g. LJ with COS tail). First, it's
piecewise, and second the COS section is not the sum of two terms so how
should it be broken across g(r) and h(r) or is it always OK to use the g(r)
column for the whole potential?

Hope this helps.

-Matt

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[gmx-users] nematic phase disappears with reducing the time step

[Argyrios Karatrantos]

hi, 

i am doing simulations NVT simulations of rigid charged rods (with constrained 
bonds and stiff bending potential)in vacuum using PME for the electrostatics 
with a time step of 0.0015 ps (which i think is a pretty reasonable value for a 
corse grain model)
A nematic phase of the rods appears at specific concentration (i have checked 
the Total-energy, Pressure, Temperature of the system and it is seems the 
simulation is in equilibrium)

however when i do simulation of the same system with smaller time steps such as 
1.0 fs or 0.5 fs, the nematic phase disappears (there is only a small increase 
of the potential energy comparative to that of the nematic)

what is the reason that the time step can cause such an artifact phase?




  
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[gmx-users] Smallest allowed cell size

[Matthew Hoopes]

Hi,

I received the following error

---
Program mdrun, VERSION 4.0
Source code file: domdec.c, line: 2933

Fatal error:
Step 10: The X-size (-32.295326) times the triclinic skew factor (1.00)
is smaller than the smallest allowed cell size (1.20) for domain
decomposition grid cell 0 0 0
---

under the following conditions

GROMACS 4.0 installed on a Cray XT4 at nics.utk.edu

#PBS -l walltime=12:00:00,size=16
aprun -n 16 mdrun -maxh 29.5

The system has 84272 atoms in a box that is approx. 10x10x10. It works with
8 processors but I would think that this is fine divided up between 16
processors.

Any suggestions for understanding this error message would be appreciated.

Thanks,
Matt

-
Matthew Hoopes
Biophysics Graduate Group
University of California, Davis

[EMAIL PROTECTED]
530-752-6452
- 


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Re: [gmx-users] g_rotacf

[Daniel K]

How should I change it so it calculates the 40 ps?

On Wed, Oct 22, 2008 at 6:34 PM, Xavier Periole <[EMAIL PROTECTED]> wrote:

> On Wed, 22 Oct 2008 17:38:58 -0400
>  "Daniel K" <[EMAIL PROTECTED]> wrote:
>
>> I have been trying to use g_rotacf with a simulation run for 40 ps (2)
>> with steps of 2fs and the frames where extracted every 50 fs (25 frames).
>> The trajectory file is correct because it has 801 frames. When I calculate
>> the g_rotacf I only get 20 ps and the time step is 50 fs. Does any body no
>> why?
>>
> What is wrong with this? By default g_rotacf plots only half of the time
> correlation function ...
> I do not know what you looking at but 40 ps is pretty short simulation.
>
>
>> This is the header and end of the file that I get
>> # This file was created Mon Oct 20 11:38:06 2008
>> # by the following command:
>> # g_rotacf -P 2 -f md_noT.trr -s md_noT.tpr -n NC.ndx -o md_noT_ACF.xvg -d
>> #
>> # g_rotacf is part of G R O M A C S:
>> #
>> # Glycine aRginine prOline Methionine Alanine Cystine Serine
>> #
>> @title "Rotational Correlation Function"
>> @xaxis  label "Time (ps)"
>> @yaxis  label "C(t)"
>> @TYPE xy
>>0.000 1.0
>>0.050 0.95376
>>0.100 0.90907
>>  
>>   19.800-0.22896
>>   19.850-0.22921
>>   19.900-0.23028
>>   19.950-0.23078
>>   20.000-0.23111
>> &
>>
>
> -
> XAvier Periole - PhD
>
> - Molecular Dynamics Group -
> NMR and Computation
> University of Groningen
> The Netherlands
> -
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[gmx-users] m) Re: modify bondfree.c and recompile

[Jian Zou]

Hi Berk and Mark,

Thank you all for the suggestions. I will follow the safe way (make
under src or top-level dir).

> Date: Thu, 23 Oct 2008 02:29:14 +1100
> From: Mark Abraham <[EMAIL PROTECTED]>
> Subject: Re: [gmx-users] Re: modify bondfree.c and recompile
> To: Discussion list for GROMACS users 
> Message-ID: <[EMAIL PROTECTED]>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> Jian Zou wrote:
>> Hi Mark, David and Bess,
>>
>> Thank you all for the suggestions.
>>
>>
>> I know the dependency has to be somewhere in the Makefiles or the
>> files they include but I cannot find it. What I am doing is simply
>> "make" under top-level source directory followed by make install. In
>> this case, the content of all the files (except the RC files) under
>> bin and lib will be rebuild and differ from the previous build, even
>> from the same source.
>
> Great. So what's the problem?

I assume Gromacs put time stamp in the content of library and binary.
If this is true, it is difficult to identify whether the difference
comes from the change in the source or only from the time stamp.


Regards,

Jian
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Re: [gmx-users] g_rotacf

[Xavier Periole]

On Wed, 22 Oct 2008 17:38:58 -0400
 "Daniel K" <[EMAIL PROTECTED]> wrote:

I have been trying to use g_rotacf with a simulation run for 40 ps (2)
with steps of 2fs and the frames where extracted every 50 fs (25 frames).
The trajectory file is correct because it has 801 frames. When I calculate
the g_rotacf I only get 20 ps and the time step is 50 fs. Does any body no
why?

What is wrong with this? By default g_rotacf plots only half of the time
correlation function ...
I do not know what you looking at but 40 ps is pretty short simulation.
 

This is the header and end of the file that I get
# This file was created Mon Oct 20 11:38:06 2008
# by the following command:
# g_rotacf -P 2 -f md_noT.trr -s md_noT.tpr -n NC.ndx -o md_noT_ACF.xvg -d
#
# g_rotacf is part of G R O M A C S:
#
# Glycine aRginine prOline Methionine Alanine Cystine Serine
#
@title "Rotational Correlation Function"
@xaxis  label "Time (ps)"
@yaxis  label "C(t)"
@TYPE xy
0.000 1.0
0.050 0.95376
0.100 0.90907
 
   19.800-0.22896
   19.850-0.22921
   19.900-0.23028
   19.950-0.23078
   20.000-0.23111
&


-
XAvier Periole - PhD

- Molecular Dynamics Group -
NMR and Computation
University of Groningen
The Netherlands
-
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[gmx-users] g_rotacf

[Daniel K]

I have been trying to use g_rotacf with a simulation run for 40 ps (2)
with steps of 2fs and the frames where extracted every 50 fs (25 frames).
The trajectory file is correct because it has 801 frames. When I calculate
the g_rotacf I only get 20 ps and the time step is 50 fs. Does any body no
why?
This is the header and end of the file that I get
# This file was created Mon Oct 20 11:38:06 2008
# by the following command:
# g_rotacf -P 2 -f md_noT.trr -s md_noT.tpr -n NC.ndx -o md_noT_ACF.xvg -d
#
# g_rotacf is part of G R O M A C S:
#
# Glycine aRginine prOline Methionine Alanine Cystine Serine
#
@title "Rotational Correlation Function"
@xaxis  label "Time (ps)"
@yaxis  label "C(t)"
@TYPE xy
 0.000 1.0
 0.050 0.95376
 0.100 0.90907
  
19.800-0.22896
19.850-0.22921
19.900-0.23028
19.950-0.23078
20.000-0.23111
&
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Re: [gmx-users] How to make a pdb file for methane pair?

[xianghong qi]

Hi, Justin:
I put a residue name ( ALA) there, but pdb2gmx told me that there is a fatal
error:

Atom H4 in residue ALA 1 not found in rtp entry with 6 atoms
 while sorting atoms. Maybe different protonation state.
 Remove this hydrogen or choose a different protonation state.
 Option -ignh will ignore all hydrogens in the input.
If I creat one ( CH4), it said that :
Residue 'CH4' not found in residue topology database.

my pdb file for methane pair is ( I created from MOE), original residue name
is *, now I change to CH4:
REMARK  99 MOE v2007.09 (Chemical Computing Group Inc)  Mon Oct 20 12:31:39
2008
HETATM1  C   CH4 1  -0.415  -0.007   0.005  0.00  0.00
C
HETATM2  H2  CH4 1  -0.778   0.720   0.731  0.00  0.00
H
HETATM3  H3  CH4 1  -0.778  -0.999   0.271  0.00  0.00
H
HETATM4  H4  CH4 1  -0.778   0.259  -0.988  0.00  0.00
H
HETATM5  H1  CH4 1   0.675  -0.007   0.005  0.00  0.00
H
HETATM6  C   CH4 2   9.588  -0.007   0.005  0.00  0.00
C
HETATM7  H1  CH4 2  10.678  -0.007   0.005  0.00  0.00
H
HETATM8  H2  CH4 2   9.225   0.720   0.731  0.00  0.00
H
HETATM9  H3  CH4 2   9.225  -0.999   0.271  0.00  0.00
H
HETATM   10  H4  CH4 2   9.225   0.259  -0.988  0.00  0.00
H
CONECT12345
CONECT6789   10
END

What kind of residue name I should put there?  thanks lot.
-Xianghong Qi


On Wed, Oct 22, 2008 at 9:56 AM, xianghong qi <[EMAIL PROTECTED]>wrote:

> Thanks so much , Justin. I will try.
> -Xianghong Qi
>
>
> On Wed, Oct 22, 2008 at 7:41 AM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:
>
>>
>>
>> xianghong qi wrote:
>>
>>> Thanks, so how to edit  a residue name ? I am confused.  sorry about such
>>> simple question.
>>>
>>
>> Use a text editor.  Be sure to keep the formatting right when doing so:
>>
>> http://www.wwpdb.org/documentation/format32/sect9.html
>>
>> -Justin
>>
>>  -Xianghong Qi
>>>
>>> On Tue, Oct 21, 2008 at 9:01 PM, Mark Abraham <[EMAIL PROTECTED]>> [EMAIL PROTECTED]>> wrote:
>>>
>>>xianghong qi wrote:
>>>
>>>Hello, everyone,
>>>I want to create a pdb file for methane pair . I can make
>>>methane pair from MOE and then save to pdb file format without
>>>any residue name there.
>>>The question is that I can't convert pdb file to .gro file from
>>>gromacs without residue name.  Anyone has any idea about this
>>>question. I appreciate
>>>your help.
>>>
>>>
>>>You don't need a .gro file for itself.. see
>>>
>>> http://wiki.gromacs.org/index.php/Coordinate_File#On_the_need_for_a_.gro_file
>>>
>>>You'll need a residue name to get a topology defined, so edit one in.
>>>
>>>Mark
>>>___
>>>gmx-users mailing listgmx-users@gromacs.org
>>>
>>>http://www.gromacs.org/mailman/listinfo/gmx-users
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>>>posting!
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>>>interface or send it to [EMAIL PROTECTED]
>>>.
>>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>>>
>>>
>>>
>>> --
>>> Some people make the world more special just by being in it.
>>>
>>>
>>> 
>>>
>>> ___
>>> gmx-users mailing listgmx-users@gromacs.org
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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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>>
>
>
>
> --
> Some people make the world more special just by being in it.
>



-- 
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[gmx-users] Setting constant velocity

[Andy Shelley]

Is there a way to set a constant velocity to simulate fluid flow? I know I
can apply a force to increase velocity, but can I keep the velocity constant
after that?

Thanks,
Andy
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Re: [gmx-users] spliting clusters.pdb

[Jochen Hub]

Abu Naser wrote:
> Hi All,
>  
> I have been wondering whether there is any tools for spliting clusters.pdb 
> file into individual snapshots.

If there is a TER between the structures, the shell command csplit may
be useful for you.

Jochen


>  
> With regards,
>  
> Abu
> 
> 
> 
> 
> 
> 
>  
> _
> Win an Xbox 360 or £200 Top Shop Vouchers 
> http://clk.atdmt.com/GBL/go/115454062/direct/01/
> 
> 
> 
> 
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-- 

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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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Re: [gmx-users] How to make a pdb file for methane pair?

[Justin A. Lemkul]

xianghong qi wrote:

Hi, Justin:
I put a residue name ( ALA) there, but pdb2gmx told me that there is a 
fatal error:


Atom H4 in residue ALA 1 not found in rtp entry with 6 atoms
 while sorting atoms. Maybe different protonation state.
 Remove this hydrogen or choose a different protonation state.
 Option -ignh will ignore all hydrogens in the input.


Right, if it's not alanine, then that won't work.


If I creat one ( CH4), it said that :
Residue 'CH4' not found in residue topology database.



Pretty common error; see here:

http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database

If the residue/molecule name is not already parameterized and entered into the 
.rtp file, you'll have to come up with the topology yourself.  For methane, this 
should be quite easy to do by hand.


-Justin

my pdb file for methane pair is ( I created from MOE), original residue 
name is *, now I change to CH4:
REMARK  99 MOE v2007.09 (Chemical Computing Group Inc)  Mon Oct 20 
12:31:39 2008
HETATM1  C   CH4 1  -0.415  -0.007   0.005  0.00  
0.00   C
HETATM2  H2  CH4 1  -0.778   0.720   0.731  0.00  
0.00   H
HETATM3  H3  CH4 1  -0.778  -0.999   0.271  0.00  
0.00   H
HETATM4  H4  CH4 1  -0.778   0.259  -0.988  0.00  
0.00   H
HETATM5  H1  CH4 1   0.675  -0.007   0.005  0.00  
0.00   H
HETATM6  C   CH4 2   9.588  -0.007   0.005  0.00  
0.00   C
HETATM7  H1  CH4 2  10.678  -0.007   0.005  0.00  
0.00   H
HETATM8  H2  CH4 2   9.225   0.720   0.731  0.00  
0.00   H
HETATM9  H3  CH4 2   9.225  -0.999   0.271  0.00  
0.00   H
HETATM   10  H4  CH4 2   9.225   0.259  -0.988  0.00  
0.00   H

CONECT12345
CONECT6789   10
END

What kind of residue name I should put there?  thanks lot. 
-Xianghong Qi



On Wed, Oct 22, 2008 at 9:56 AM, xianghong qi <[EMAIL PROTECTED] 
> wrote:


Thanks so much , Justin. I will try. 
-Xianghong Qi



On Wed, Oct 22, 2008 at 7:41 AM, Justin A. Lemkul <[EMAIL PROTECTED]
> wrote:



xianghong qi wrote:

Thanks, so how to edit  a residue name ? I am confused.
 sorry about such simple question.


Use a text editor.  Be sure to keep the formatting right when
doing so:

http://www.wwpdb.org/documentation/format32/sect9.html

-Justin

-Xianghong Qi


On Tue, Oct 21, 2008 at 9:01 PM, Mark Abraham
<[EMAIL PROTECTED] 
>> wrote:

   xianghong qi wrote:

   Hello, everyone,
   I want to create a pdb file for methane pair . I can make
   methane pair from MOE and then save to pdb file
format without
   any residue name there.
   The question is that I can't convert pdb file to .gro
file from
   gromacs without residue name.  Anyone has any idea
about this
   question. I appreciate
   your help.


   You don't need a .gro file for itself.. see
 
 http://wiki.gromacs.org/index.php/Coordinate_File#On_the_need_for_a_.gro_file


   You'll need a residue name to get a topology defined, so
edit one in.

   Mark
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Re: [gmx-users] how to use the new potential

[Mark Abraham]

He, Yang wrote:

Hi all users,

I am engaged in deal with the course grain model,in which the potential 
functions are not the same as in gromacs.Hence, If I want to use the new 
potentials , I guess I can change the source code or use the table. But I never 
have this experience about  that.Can anyone of you give me some suggestions or 
examples?


Start with the manual. :-) Hopefully the version 4 manual will be out 
soon, but even if not, the 3.3 manual will be fine for nonbonded 
tabulated potentials.


Mark
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Re: [gmx-users] Re: modify bondfree.c and recompile

[Mark Abraham]

Jian Zou wrote:

Hi Mark, David and Bess,

Thank you all for the suggestions.


I know the dependency has to be somewhere in the Makefiles or the
files they include but I cannot find it. What I am doing is simply
"make" under top-level source directory followed by make install. In
this case, the content of all the files (except the RC files) under
bin and lib will be rebuild and differ from the previous build, even
from the same source.


Great. So what's the problem?


Berk told me to do "make" in src/gmxlib. I checked the top-level
Makefile and the the rules for "make mdrun" is "make" under
src/gmxlib, src/mdlib and src/kernel, so it seems for my case "make
mdrun" then "make install-mdrun" should be enough to update the
binary, but how about the library?


The libraries needed for building static executables (or running if you 
enabled shared libraries) are all built in the usual make manner in 
response to a top-level "make". You could have verified this by looking 
at the timestamps.


Mark
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Re: [gmx-users] monomer's conectivity

[Mark Abraham]

Andrea Muntean wrote:
I have a *pdb file for a polymer box which I want to use. I defined the 
residues (the first, the last and the inner monomers).
Pdb2gmx runs, but I obtain a "soup" of monomers instead of N chains a M 
monomers each.
My problem now is how to connect the monomers. What is the best way to 
do so?


We can't tell yet. You might have a PDB file with each residue in its 
own chain. You might have defined residue topologies without suitable 
connectors. You might be observing a visualization artefact. You might 
have some warnings from pdb2gmx you haven't observed yet.


Mark
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Re: [gmx-users] modify bondfree.c and recompile

[Mark Abraham]

He, Yang wrote:

Hi David,


Thank you for your reply. As for the new non-bond potential, if I want to use 
the gromacs to deal with them, what should i do in the gromacs? Do you have any 
suggestions about that? Change the source code?



You can use tables for bonded potentials as well, without changing any code.


You can use tables for *non*-nbonded potentials as well, without 
changing any code. :-)


Mark
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[gmx-users] how to use the new potential

[He, Yang]

Hi all users,

I am engaged in deal with the course grain model,in which the potential 
functions are not the same as in gromacs.Hence, If I want to use the new 
potentials , I guess I can change the source code or use the table. But I never 
have this experience about  that.Can anyone of you give me some suggestions or 
examples?

Thank you in advance.

Yang
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[gmx-users] monomer's conectivity

[Andrea Muntean]

I have a *pdb file for a polymer box which I want to use. I defined the
residues (the first, the last and the inner monomers).
Pdb2gmx runs, but I obtain a "soup" of monomers instead of N chains a M
monomers each.
My problem now is how to connect the monomers. What is the best way to do
so?

Regards,
Andrea
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RE: [gmx-users] Re: modify bondfree.c and recompile

[Berk Hess]

Hi,

In the Makefiles in kernel, tools and ngmx you will see that all binaries
depend on gmxlib and mdlib.
So if you type make in the top level directory or in src/kernel,
first bondfree.c will be compiled and put into the gmxlib library,
in kernel make will then notice that gmxlib is new and relink everything.

If you only type make (mdrun) in kernel, you new potential will not be in there.
Typing make in src or the top level dir is always safe.

Berk


> Date: Wed, 22 Oct 2008 10:06:44 -0400
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Re: modify bondfree.c and recompile
> 
> Hi Mark, David and Bess,
> 
> Thank you all for the suggestions.
> 
> 
> I know the dependency has to be somewhere in the Makefiles or the
> files they include but I cannot find it. What I am doing is simply
> "make" under top-level source directory followed by make install. In
> this case, the content of all the files (except the RC files) under
> bin and lib will be rebuild and differ from the previous build, even
> from the same source.
> 
> Berk told me to do "make" in src/gmxlib. I checked the top-level
> Makefile and the the rules for "make mdrun" is "make" under
> src/gmxlib, src/mdlib and src/kernel, so it seems for my case "make
> mdrun" then "make install-mdrun" should be enough to update the
> binary, but how about the library?
> 
> The potential I am working is 1D only instead of 3D, therefore the
> tabulated bonded/nonbond potential may not apply to my problem.
> "Walls" with wall_type=table in gmx4 could be a solution. But  I do
> not find the implementation details like Chapter 6.7 for tabulated
> nonbond interaction, and therefore do not know how to make
> interactions of each atomtype with the wall different.
> 
> 
> Hi Yang He,
> 
> I started from Appendix B.4, where the files to be modified for bonded
> potential are listed (Files No.6 and No.12 are the same). You may also
> have a look at include/physics.h and include/vec.h.
> 
> 
> Regards,
> 
> Jian
> 
> On Wed, Oct 22, 2008 at 3:40 AM,  <[EMAIL PROTECTED]> wrote:
> >
> > Message: 1
> > Date: Wed, 22 Oct 2008 11:57:46 +1100
> > From: Mark Abraham <[EMAIL PROTECTED]>
> > Subject: Re: [gmx-users] modify bondfree.c and recompile
> > To: Discussion list for GROMACS users 
> > Message-ID: <[EMAIL PROTECTED]>
> > Content-Type: text/plain; charset=UTF-8; format=flowed
> >
> > Jian Zou wrote:
> >> Hi,
> >>
> >> If I only change some functional form in bondfree.c (the number of
> >> parameters are kept the same), can I just do "make mdrun" and "make
> >> install-mdrun" to recompile from the source?
> >>
> >> I cannot find the dependency between the source files and the Gromacs
> >> utilities (grompp and mdrun).
> >
> > It's there in the Makefiles, but you don't need to know about it. Just
> > use make (or just make mdrun) from the top-level source directory.
> >
> >> I compare the tpr file generated before and after the change and they
> >> are the same. Therefore it seems to me that grompp does not read the
> >> formulation of bonded interactions, am I right?
> >
> > grompp isn't changing, so its output is the same. All it does is
> > interpret the contents of your .top file and tell mdrun which function
> > to use.
> >
> > Mark
> 
> 
> > Message: 5
> > Date: Wed, 22 Oct 2008 08:09:17 +0200
> > From: David van der Spoel <[EMAIL PROTECTED]>
> > Subject: Re: [gmx-users] modify bondfree.c and recompile
> > To: Discussion list for GROMACS users 
> > Message-ID: <[EMAIL PROTECTED]>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> > He, Yang wrote:
> >> Hi Jian,
> >>
> >> Do you also need to change the source code to get a new potential 
> >> function? I am also engaged in this job. DO you have any experience about 
> >> this job?
> >>
> >>
> > You can use tables for bonded potentials as well, without changing any code.
> >
> >> Regards,
> >>
> >> Yang
> >> 
> >> From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Jian Zou [EMAIL 
> >> PROTECTED]
> >> Sent: Tuesday, October 21, 2008 7:24 AM
> >> To: [EMAIL PROTECTED]; gmx-users@gromacs.org
> >> Subject: [gmx-users] modify bondfree.c and recompile
> >>
> >> Hi,
> >>
> >> If I only change some functional form in bondfree.c (the number of
> >> parameters are kept the same), can I just do "make mdrun" and "make
> >> install-mdrun" to recompile from the source?
> >>
> >> I cannot find the dependency between the source files and the Gromacs
> >> utilities (grompp and mdrun).
> >>
> >> I compare the tpr file generated before and after the change and they
> >> are the same. Therefore it seems to me that grompp does not read the
> >> formulation of bonded interactions, am I right?
> >>
> >> Thank you very much for the reply.
> >>
> >>
> >> Regards,
> >>
> >> Jian
> >> ___
> >> gmx-users mailing listgmx-users@gromacs.org
> >> http://www.gromacs.org/mailman/listinfo/gmx-users
> >> Please search

[gmx-users] Re: modify bondfree.c and recompile

[Jian Zou]

Hi Mark, David and Bess,

Thank you all for the suggestions.


I know the dependency has to be somewhere in the Makefiles or the
files they include but I cannot find it. What I am doing is simply
"make" under top-level source directory followed by make install. In
this case, the content of all the files (except the RC files) under
bin and lib will be rebuild and differ from the previous build, even
from the same source.

Berk told me to do "make" in src/gmxlib. I checked the top-level
Makefile and the the rules for "make mdrun" is "make" under
src/gmxlib, src/mdlib and src/kernel, so it seems for my case "make
mdrun" then "make install-mdrun" should be enough to update the
binary, but how about the library?

The potential I am working is 1D only instead of 3D, therefore the
tabulated bonded/nonbond potential may not apply to my problem.
"Walls" with wall_type=table in gmx4 could be a solution. But  I do
not find the implementation details like Chapter 6.7 for tabulated
nonbond interaction, and therefore do not know how to make
interactions of each atomtype with the wall different.


Hi Yang He,

I started from Appendix B.4, where the files to be modified for bonded
potential are listed (Files No.6 and No.12 are the same). You may also
have a look at include/physics.h and include/vec.h.


Regards,

Jian

On Wed, Oct 22, 2008 at 3:40 AM,  <[EMAIL PROTECTED]> wrote:
>
> Message: 1
> Date: Wed, 22 Oct 2008 11:57:46 +1100
> From: Mark Abraham <[EMAIL PROTECTED]>
> Subject: Re: [gmx-users] modify bondfree.c and recompile
> To: Discussion list for GROMACS users 
> Message-ID: <[EMAIL PROTECTED]>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> Jian Zou wrote:
>> Hi,
>>
>> If I only change some functional form in bondfree.c (the number of
>> parameters are kept the same), can I just do "make mdrun" and "make
>> install-mdrun" to recompile from the source?
>>
>> I cannot find the dependency between the source files and the Gromacs
>> utilities (grompp and mdrun).
>
> It's there in the Makefiles, but you don't need to know about it. Just
> use make (or just make mdrun) from the top-level source directory.
>
>> I compare the tpr file generated before and after the change and they
>> are the same. Therefore it seems to me that grompp does not read the
>> formulation of bonded interactions, am I right?
>
> grompp isn't changing, so its output is the same. All it does is
> interpret the contents of your .top file and tell mdrun which function
> to use.
>
> Mark


> Message: 5
> Date: Wed, 22 Oct 2008 08:09:17 +0200
> From: David van der Spoel <[EMAIL PROTECTED]>
> Subject: Re: [gmx-users] modify bondfree.c and recompile
> To: Discussion list for GROMACS users 
> Message-ID: <[EMAIL PROTECTED]>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> He, Yang wrote:
>> Hi Jian,
>>
>> Do you also need to change the source code to get a new potential function? 
>> I am also engaged in this job. DO you have any experience about this job?
>>
>>
> You can use tables for bonded potentials as well, without changing any code.
>
>> Regards,
>>
>> Yang
>> 
>> From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Jian Zou [EMAIL 
>> PROTECTED]
>> Sent: Tuesday, October 21, 2008 7:24 AM
>> To: [EMAIL PROTECTED]; gmx-users@gromacs.org
>> Subject: [gmx-users] modify bondfree.c and recompile
>>
>> Hi,
>>
>> If I only change some functional form in bondfree.c (the number of
>> parameters are kept the same), can I just do "make mdrun" and "make
>> install-mdrun" to recompile from the source?
>>
>> I cannot find the dependency between the source files and the Gromacs
>> utilities (grompp and mdrun).
>>
>> I compare the tpr file generated before and after the change and they
>> are the same. Therefore it seems to me that grompp does not read the
>> formulation of bonded interactions, am I right?
>>
>> Thank you very much for the reply.
>>
>>
>> Regards,
>>
>> Jian
>> ___
>> 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!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to [EMAIL PROTECTED]
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>> ___
>> 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!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to [EMAIL PROTECTED]
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
> --
> David.
> 
> David van der Spoel, PhD, Professor of Biology
> Dept. of Cell and Molecular Biology, Uppsala University.
> Hus

Re: [gmx-users] How to make a pdb file for methane pair?

[xianghong qi]

Thanks so much , Justin. I will try.
-Xianghong Qi

On Wed, Oct 22, 2008 at 7:41 AM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:

>
>
> xianghong qi wrote:
>
>> Thanks, so how to edit  a residue name ? I am confused.  sorry about such
>> simple question.
>>
>
> Use a text editor.  Be sure to keep the formatting right when doing so:
>
> http://www.wwpdb.org/documentation/format32/sect9.html
>
> -Justin
>
>  -Xianghong Qi
>>
>> On Tue, Oct 21, 2008 at 9:01 PM, Mark Abraham <[EMAIL PROTECTED]> [EMAIL PROTECTED]>> wrote:
>>
>>xianghong qi wrote:
>>
>>Hello, everyone,
>>I want to create a pdb file for methane pair . I can make
>>methane pair from MOE and then save to pdb file format without
>>any residue name there.
>>The question is that I can't convert pdb file to .gro file from
>>gromacs without residue name.  Anyone has any idea about this
>>question. I appreciate
>>your help.
>>
>>
>>You don't need a .gro file for itself.. see
>>
>> http://wiki.gromacs.org/index.php/Coordinate_File#On_the_need_for_a_.gro_file
>>
>>You'll need a residue name to get a topology defined, so edit one in.
>>
>>Mark
>>___
>>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!
>>Please don't post (un)subscribe requests to the list. Use the www
>>interface or send it to [EMAIL PROTECTED]
>>.
>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
>>
>> --
>> Some people make the world more special just by being in it.
>>
>>
>> 
>>
>> ___
>> 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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>> interface or send it to [EMAIL PROTECTED]
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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
>
> 
>
> ___
> 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!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to [EMAIL PROTECTED]
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>



-- 
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RE: [gmx-users] modify bondfree.c and recompile

[He, Yang]

Hi David,


Thank you for your reply. As for the new non-bond potential, if I want to use 
the gromacs to deal with them, what should i do in the gromacs? Do you have any 
suggestions about that? Change the source code?

Thank you for your help.

Regard,

Yang

From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of David van der Spoel 
[EMAIL PROTECTED]
Sent: Tuesday, October 21, 2008 11:09 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] modify bondfree.c and recompile

He, Yang wrote:
> Hi Jian,
>
> Do you also need to change the source code to get a new potential function? I 
> am also engaged in this job. DO you have any experience about this job?
>
>
You can use tables for bonded potentials as well, without changing any code.

> Regards,
>
> Yang
> 
> From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Jian Zou [EMAIL 
> PROTECTED]
> Sent: Tuesday, October 21, 2008 7:24 AM
> To: [EMAIL PROTECTED]; gmx-users@gromacs.org
> Subject: [gmx-users] modify bondfree.c and recompile
>
> Hi,
>
> If I only change some functional form in bondfree.c (the number of
> parameters are kept the same), can I just do "make mdrun" and "make
> install-mdrun" to recompile from the source?
>
> I cannot find the dependency between the source files and the Gromacs
> utilities (grompp and mdrun).
>
> I compare the tpr file generated before and after the change and they
> are the same. Therefore it seems to me that grompp does not read the
> formulation of bonded interactions, am I right?
>
> Thank you very much for the reply.
>
>
> Regards,
>
> Jian
> ___
> 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!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to [EMAIL PROTECTED]
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> ___
> 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!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to [EMAIL PROTECTED]
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--
David.

David van der Spoel, PhD, Professor of Biology
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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Re: [gmx-users] spliting clusters.pdb

[Justin A. Lemkul]

Abu Naser wrote:
Thanks Justin. I did try and did not work. trajconv is more of 
controlled by time step.
 


It works just fine for me when I've got a clusters.pdb file; what command did 
you try?


-Justin


With regards,
 
Abu



 



 > Date: Wed, 22 Oct 2008 08:59:39 -0400
 > From: [EMAIL PROTECTED]
 > To: gmx-users@gromacs.org
 > Subject: Re: [gmx-users] spliting clusters.pdb
 >
 >
 >
 > Abu Naser wrote:
 > > Hi All,
 > >
 > > I have been wondering whether there is any tools for spliting
 > > clusters.pdb file into individual snapshots.
 > >
 >
 > Try: trjconv -sep
 >
 > -Justin
 >
 > > With regards,
 > >
 > > Abu
 > >
 > >
 > >
 > >
 > > 


 > > Read amazing stories to your kids on Messenger Try it Now!
 > > 
 > >
 > >
 > > 


 > >
 > > ___
 > > gmx-users mailing list gmx-users@gromacs.org
 > > http://www.gromacs.org/mailman/listinfo/gmx-users
 > > Please search the archive at http://www.gromacs.org/search before 
posting!

 > > Please don't post (un)subscribe requests to the list. Use the
 > > www interface or send it to [EMAIL PROTECTED]
 > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
 >
 > --
 > 
 >
 > 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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Justin A. Lemkul
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Department of Biochemistry
Virginia Tech
Blacksburg, VA
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http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] spliting clusters.pdb

[Justin A. Lemkul]

Abu Naser wrote:

Hi All,
 
I have been wondering whether there is any tools for spliting 
clusters.pdb file into individual snapshots.
 


Try: trjconv -sep

-Justin


With regards,
 
Abu



 



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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] spliting clusters.pdb

[Abu Naser]

Hi All,
 
I have been wondering whether there is any tools for spliting clusters.pdb file 
into individual snapshots.
 
With regards,
 
Abu






 
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Re: [gmx-users] How to make a pdb file for methane pair?

[Justin A. Lemkul]

xianghong qi wrote:
Thanks, so how to edit  a residue name ? I am confused.  sorry about 
such simple question. 


Use a text editor.  Be sure to keep the formatting right when doing so:

http://www.wwpdb.org/documentation/format32/sect9.html

-Justin


-Xianghong Qi

On Tue, Oct 21, 2008 at 9:01 PM, Mark Abraham <[EMAIL PROTECTED] 
> wrote:


xianghong qi wrote:

Hello, everyone,
I want to create a pdb file for methane pair . I can make
methane pair from MOE and then save to pdb file format without
any residue name there.
The question is that I can't convert pdb file to .gro file from
gromacs without residue name.  Anyone has any idea about this
question. I appreciate
your help.


You don't need a .gro file for itself.. see

http://wiki.gromacs.org/index.php/Coordinate_File#On_the_need_for_a_.gro_file

You'll need a residue name to get a topology defined, so edit one in.

Mark
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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] How to make a pdb file for methane pair?

[xianghong qi]

Thanks, so how to edit  a residue name ? I am confused.  sorry about such
simple question.
-Xianghong Qi

On Tue, Oct 21, 2008 at 9:01 PM, Mark Abraham <[EMAIL PROTECTED]>wrote:

> xianghong qi wrote:
>
>> Hello, everyone,
>> I want to create a pdb file for methane pair . I can make methane pair
>> from MOE and then save to pdb file format without any residue name there.
>> The question is that I can't convert pdb file to .gro file from gromacs
>> without residue name.  Anyone has any idea about this question. I appreciate
>> your help.
>>
>
> You don't need a .gro file for itself.. see
> http://wiki.gromacs.org/index.php/Coordinate_File#On_the_need_for_a_.gro_file
>
> You'll need a residue name to get a topology defined, so edit one in.
>
> Mark
> ___
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RE: [gmx-users] Walls & user defined potential

[Berk Hess]

Date: Wed, 22 Oct 2008 05:55:16 +0800
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject: [gmx-users] Walls & user defined potential

Hi gmx-users and developers,
 
I met a strange error when using wall function combined with user defined 
potential. Following is a part of the mdp:
 

vdw-type = user
energygrps  = Surf   SOL
 
; WALLS
; Number of walls, type, atom types, densities and box-z scale factor for Ewald
nwall  = 2
wall_type= table
wall_r_linpot= -1
wall_atomtype = W1  W2

wall_density= 1.5  1.5
wall_ewald_zfac   = 2
energygrp_table   = Surf  wall0  Surf  wall1  SOL  wall0  SOL  wall1 
table-extension=  1.0

1) With the command bellow,
 
mdrun -table table_Surf_wall0.xvg table_Surf_wall1.xvg table_SOL_wall0.xvg 
table_SOL_wall1.xvg -deffnm prod
 
A fatal error was generated: Library file table_Surf_wall0_Surf_wall0.xvg not 
found in current dir nor in default directories.
 
Then I copy the table6-12.xvg from the top dir, rename it by table.xvg and add 
it in the command line,
 
mdrun -table table6-12.xvg table_Surf_wall0.xvg table_Surf_wall1.xvg 
table_SOL_wall0.xvg table_SOL_wall1.xvg -deffnm prod
 
Am I right? It seems to be ok now. BTW, only the parameters in the replusive 
colunm in table_SOL_wall1.xvg are none zero (when z>1, these values are aslo 
set to zero.)


This table should not be necessary.
I can see if I can modify the code such that it does not ask for this 
combination.


Note that you can use wall_type=table together will normal non-user vdw and 
Coulomb.




2) But when I make a parallel run, a crash was found: 
 
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 5798 failed on node n0 (127.0.0.1) due to signal 11.
-
mpirun failed with exit status 11
 

Can you send me the input for this (or file a bugzilla)?



3) Moreover, if table-extension set to 0.0, a fatal error was caught: 
'An atom is beyond the wall: coordinates -5371173273600.00 
-20382570512384.00 2778490208256.00, distance -1.00
You might want to use the mdp option wall_r_linpot'

 
I have tested several values, crash is found only when this value is less than 
0.2.


You should never set table-extension to 0.
You need a certain extension for charge group size and atom diffusion with 
nstlist steps.

Berk

 
If you have any suggestions, that would be much appreciated. Thanks in
advance.


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[gmx-users] RE: How can I generate a Input *.gro file of coarse grain(xuji)

[xuji]

Hi Yang:
I checked the potential fnctions the Martini force field used in Gromacs. 
The bond and angle potential funtions are g96 harmonic potential functions.
The VDW and COULOMB potential functions are in nb_kernel330_x86_64_sse.s file 
in my workstation's environment.

>Hi ,
>
>I was also engaged in dealing with the problem about the course grain model . 
>I find that in this CG force field , the potential functions almost don't 
>correspond to that in the gromacs.
>
>Hence, I wonder whether you know to how to define these new potential 
>functions.
>
>Thank you in advance.
>
>Yang

And Hi all gromacs users:
These two days, I choose one CG molecule of DPPC of the exmple "Solvated DPPC 
and POPE vesicles"
in http://md.chem.rug.nl/~marrink/MARTINI/Coordinates.html. And I translate the 
DPPC meloclue to fill
the box as three dimensional arrays. And then I fill the system with CG waters. 
In this method the 
whole system is absolutely not equilibrium. And I always get "segment fault" 
when I run this system 
with GROMACS 4.0.
And I also try to simulate this type of system with "GROMACS 3.3.3", but I get 

Program grompp, VERSION 3.3.3
Source code file: grompp.c, line: 469
 
Fatal error:
number of coordinates in coordinate file (dppc_vesicle.gro, 72076)
 does not match topology (dppc_vesicle.top, 0)

when I use grompp to generate the input file of mdrun.
How can I solve these two problems?
Appreciate any help in advance!

xuji
[EMAIL PROTECTED]
　　2008-10-22

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RE: [gmx-users] How to make a soft repulsive potential wall

[Berk Hess]

Date: Wed, 22 Oct 2008 01:22:09 +0800
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject: [gmx-users] How to make a soft repulsive potential wall

Hi gmx-users,
 
I was simulating a water-surface system recently. The water molecules will 
escape from the solid surface, evaporate into the vacuum space above the 
surface, probably never come back and be trapped into the underpart of the 
surface for periodicity. I want to prevent the evaporating water molecules to 
be trapped by the lower part of the surface, and my thought is putting a soft 
repulsive potential wall just below the z_box. For clarity, the schematic is 
showed as follows,

——
|  vacuum|
| |
|×× wall  ×× | (a soft repulsive potential wall )
| |
| |
| |
|  vacuum|
|.|
|water.|
|.|
|-|
|-solid-|
——
My questions are:
 
1) Note that wall function was is available in gmx4 now, I wonder which 
wall_type I should choose. I do not understand the phrase 'LJ integrated over 
the volume behind the wall' and 'LJ integrated over the wall surface, could you 
give me a little more explanation?

Integrate over the volume (for 9-3) means that you have a uniform 3D LJ 
"particle" density beyond the wall.
Integrate over the wall surface (for 10-4) means that you have a uniform 2D LJ 
density on the wall surface.
 

 
2) I test the both wall_types and each of them works fine (both walls are 
uncharged). I find that the LJ interation between the wall and the solid 
surface would not be cut-offed when the distance between them is beyond the vdw 
cutoff. I wonder if it is feasible that the water molecules will feel the 
repulsive force from the wall only within the cufoff distance around the wall. 
It would somewhat the same as the distance restraint, but the latter is hard to 
implement in intermolecular case. 

 
No, for the walls there is not cut-off. The walls work on all the particles.
You have to make a table to get this to work.
Having a plain LJ cut-off on the wall is nasty. The attractive potential is 
effectively r^-3 or r^4,
so relatively long ranged and the cut-off would be on a perfect flat plane 
which would probably
introduce some nasty artifacts (although for a near vacuum the effect would be 
small).


3) If wall_type = table is used, could I set the dispersion columns to zero? 
Does rvdw work in this case?

Yes, you can do anything you like with the tables.
rvdw does not work, but you can of course put any functional form in the table 
that you want.

Berk
 
If you have any suggestions, that would be much appreciated. Thanks in advance.

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