Re: [gmx-users] Limit on energygrp_table

[Mark Abraham]

On 30/11/2011 5:33 PM, Liu, Liang wrote:
While, is it needed to list all the possible interacting (two) atoms 
in the energygrp_table option? I have more than 3000 possible two-atom 
pairs, corresponding to more than 3000 table_*.xvg files.


Each atomtype probably doesn't need its own energy group. I'm busy and 
am going to stop making guesses based on incomplete descriptions of what 
you are trying to do and how you are doing it. :-)


Mark




On Wed, Nov 30, 2011 at 12:29 AM, Mark Abraham 
mailto:mark.abra...@anu.edu.au>> wrote:


On 30/11/2011 5:25 PM, Liu, Liang wrote:

The error shows as "An input file contains a line longer than
4095 characters, while the buffer passed to fgets2 has size 4095."


No text table file needs a line this long. We still don't have
information from you, but I expect you have a malformed file.

Mark




On Wed, Nov 30, 2011 at 12:22 AM, Mark Abraham
mailto:mark.abra...@anu.edu.au>> wrote:

On 30/11/2011 5:09 PM, Liu, Liang wrote:

Dear all,

I am trying to use tabulated potentials in my simulation.
However, there is a limit on energygrp_table and the grompp
reports error.


What error?



The interaction happens between any two of atoms, and their
might be more than 3000 possible couples.
What should I do to remove the limit? Thanks.


We don't know what limit you are observing.

Mark

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Liang Liu





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Re: [gmx-users] Limit on energygrp_table

[Liu, Liang]

While, is it needed to list all the possible interacting (two) atoms
in the energygrp_table
option? I have more than 3000 possible two-atom pairs, corresponding to
more than 3000 table_*.xvg files.


On Wed, Nov 30, 2011 at 12:29 AM, Mark Abraham wrote:

>  On 30/11/2011 5:25 PM, Liu, Liang wrote:
>
> The error shows as "An input file contains a line longer than 4095
> characters, while the buffer passed to fgets2 has size 4095."
>
>
> No text table file needs a line this long. We still don't have information
> from you, but I expect you have a malformed file.
>
> Mark
>
>
>
>  On Wed, Nov 30, 2011 at 12:22 AM, Mark Abraham 
> wrote:
>
>>  On 30/11/2011 5:09 PM, Liu, Liang wrote:
>>
>> Dear all,
>>
>>  I am trying to use tabulated potentials in my simulation. However,
>> there is a limit on energygrp_table and the grompp reports error.
>>
>>
>>  What error?
>>
>>
>>  The interaction happens between any two of atoms, and their might be
>> more than 3000 possible couples.
>> What should I do to remove the limit? Thanks.
>>
>>
>>  We don't know what limit you are observing.
>>
>> Mark
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
>  --
> Best,
> Liang Liu
>
>
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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-- 
Best,
Liang Liu
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Re: [gmx-users] Limit on energygrp_table

[Mark Abraham]

On 30/11/2011 5:25 PM, Liu, Liang wrote:
The error shows as "An input file contains a line longer than 4095 
characters, while the buffer passed to fgets2 has size 4095."


No text table file needs a line this long. We still don't have 
information from you, but I expect you have a malformed file.


Mark



On Wed, Nov 30, 2011 at 12:22 AM, Mark Abraham 
mailto:mark.abra...@anu.edu.au>> wrote:


On 30/11/2011 5:09 PM, Liu, Liang wrote:

Dear all,

I am trying to use tabulated potentials in my simulation.
However, there is a limit on energygrp_table and the grompp
reports error.


What error?



The interaction happens between any two of atoms, and their might
be more than 3000 possible couples.
What should I do to remove the limit? Thanks.


We don't know what limit you are observing.

Mark

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--
Best,
Liang Liu




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Re: [gmx-users] Limit on energygrp_table

[Liu, Liang]

The error shows as "An input file contains a line longer than 4095
characters, while the buffer passed to fgets2 has size 4095."

On Wed, Nov 30, 2011 at 12:22 AM, Mark Abraham wrote:

>  On 30/11/2011 5:09 PM, Liu, Liang wrote:
>
> Dear all,
>
>  I am trying to use tabulated potentials in my simulation. However, there
> is a limit on energygrp_table and the grompp reports error.
>
>
> What error?
>
>
>  The interaction happens between any two of atoms, and their might be
> more than 3000 possible couples.
> What should I do to remove the limit? Thanks.
>
>
> We don't know what limit you are observing.
>
> Mark
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Best,
Liang Liu
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Re: [gmx-users] Limit on energygrp_table

[Mark Abraham]

On 30/11/2011 5:09 PM, Liu, Liang wrote:

Dear all,

I am trying to use tabulated potentials in my simulation. However, 
there is a limit on energygrp_table and the grompp reports error.


What error?

The interaction happens between any two of atoms, and their might be 
more than 3000 possible couples.

What should I do to remove the limit? Thanks.


We don't know what limit you are observing.

Mark
-- 
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Re: [gmx-users] limit on energygrp_table

[Adrien Leygue]

Thanks for your suggestions,

I have gone for the solution where I change the type of group numbers
from uchars to unsigned short.

It seems however that this solution is not very elegant:

I fail to understand the logic of limiting the number of groups in the
energygrp_table field to 254. Indeed the energygrp_table field is made
of pairs of groups. So if the group numbers are stored as uchar the
number of possible pairwise interactions between those groups is much
greater than 254 (of the order of 2^16 and not 2^8).

I am actually in that case: I have not too many groups (~20) so I can
store all the numbers in a uchar but when I generate all possible
pairwise interactions I have to input something like 400 group names
under energygrp_table and then grompp complains.

> >-Is there a way to increase this limit (by changing a constant and
> >then recompile) ? or is it more complicated (from the value 254 one
> >could guess that there is some one one-byte optimization)
> >
>
> This is indeed a on-byte optimization.
> The group numbers are stored as uchars (include/types/atoms.h).
> You could change this, then you also have to change 2 or more other files
> for the io and communication of these numbers.
>

I have modified include/types/atoms.h
Then it seemed logical to also change the following lines in src/kernel/readir.c
#define MAXPTR 65534
#define NOGID  65535
to account for the new limits.

I can compile the modified code and run grompp without a warning on my
system. The only strange thing is that grompp complains if I do not
provide tablep*.xvg files even though I want to use the same tabulated
potentials for my inter and intra (defined through some pairs)
molecular non-bonded potentials.

Nevertheless when I try to run some energy minimization it directly
complains that my first 1-4 interaction is beyond table range of 0
nm,... and will ignore all 1-4 (i assume it means pairs).
This message seems really odd,... especially the 0nm part.

I have probably to propagate the change of type to more files. I
welcome all suggestions.

Adrien.

-- 
Adrien Leygue

Department of Materials Science and Engineering
School of Chemical Engineering
National Technical University of Athens
9 Heroon Polytechniou Street
Zografou Campus, Athens 157 80,
GREECE
Tel/Fax: +30210 772-3112
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RE: [gmx-users] limit on energygrp_table

[Berk Hess]

From: "Adrien Leygue" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users 
To: gmx-users@gromacs.org
Subject: [gmx-users] limit on energygrp_table
Date: Tue, 9 Oct 2007 18:13:21 +0300

Dear Gromacs users (and developpers)

I need to use a force field, derived from ab initio methods, for which
the non-bonded interactions between the different atom types is a
modified 3-parameters LJ potential.

As this kind of potential is not implemented within Gromacs I am using
fully tabulated user defined potentials V_i_j for the non bonded
interactions between atom types i and j. The problem is that I have
many different atomtypes (on the order of 20) and therefore I have to
input many groups in the energygrp_table field of my mdp file.

When I run grompp I have a message saying that there is a limit on the
(254 if I remember correctly) on the number of groups that I can have
in  the energygrp_table field.

-Is there a way to increase this limit (by changing a constant and
then recompile) ? or is it more complicated (from the value 254 one
could guess that there is some one one-byte optimization)



This is indeed a on-byte optimization.
The group numbers are stored as uchars (include/types/atoms.h).
You could change this, then you also have to change 2 or more other files
for the io and communication of these numbers.


-If the above solution is not an option, is there a "simple" way to
modify the Gromacs source code to use these more advanced potentials
while keeping good performances.


This depends on what combination rules you have for your parameters.
If you are lucky, you can use the buckingham 3-parameter setup
and modify the plain C buckingham innerloops to calculate your functional 
form.


Berk.

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