Re:[gmx-users] Carbohydrate MD Simulation

[fufengliu]

Hi Nancy,
   I think that the atom C1 in residue TRP 1 does not exist in rtp entry. In 
other words, atom C1 is not understood by the software. You should change the 
atom type in order to be understood. I have a question, how do you obtain the 
URL about trehalose. Because I want to some polyols from PDB. Can you tell me 
how to obtain the pdb files about orginic molecules? Thanks a lot!
Good luck!
   
Fufeng Liu



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Re: [gmx-users] GROMACS parameterization

[Justin A. Lemkul]

rams rams wrote:

Hello users,
I have a question about the Gromacs parameterization. 
By using which water model (SPC / SPC/E / TIP3P etc) and their variants, 
the protein force field parameters in GROMACS were optimized ? 


This information can be found in the primary literature for each force field. 
Further comparative studies can also be found that compare different water 
models with different force fields.


-Justin

Since a few of the properties of proteins depends upon the water models 
we employ (for instance, SPC water model over estimates the 
diffusion properties of the proteins by a factor of approx. 2). it is 
necessary to know which water model needs to be used in the simulation.

Thanks in advance.
Ram. 





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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] GROMACS parameterization

[rams rams]

Hello users,
I have a question about the Gromacs parameterization.
By using which water model (SPC / SPC/E / TIP3P etc) and their variants, the
protein force field parameters in GROMACS were optimized ?
Since a few of the properties of proteins depends upon the water models we
employ (for instance, SPC water model over estimates the
diffusion properties of the proteins by a factor of approx. 2). it is
necessary to know which water model needs to be used in the simulation.
Thanks in advance.
Ram.
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Re: [gmx-users] Carbohydrate MD Simulation

[Justin A. Lemkul]

Nancy wrote:
High-throughput "in silico" screening (e.g. for ligand-protein binding) 
has been performed on a number of systems.  How are such automated 
simulations performed (I assume they utilize molecular dynamics)?




I doubt that large classes of ligands have been done effectively with MD. 
Docking is better suited to finding initial bound configurations, after which MD 
can be useful in analyzing interactions over time.


Assumptions can be cleared up by reading Methods sections.  If anyone has a 
method for using unbiased MD to demonstrate ligand binding in large classes of 
ligands, I'd love to know about it.


-Justin





On Fri, Jul 31, 2009 at 5:47 PM, Justin A. Lemkul > wrote:




Nancy wrote:

If it necessary to manually create force field parameters for
each molecule, then how can one run a simulation involving a
number of arbitrary molecules (e.g. a set of mono and
disaccharides) for which there are no existing force fields?

Do you know of any other MD software package that is capable of
running simulations on arbitrary molecules without having to
"piece together" a force field for each molecule?


Indeed it would be nice if there was a software package that would
parameterize your molecule, validate said parameters, then run a
meaningful simulation with all the proper conditions.  Maybe it
could even make coffee...

All kidding aside, the answer is no.  It is the job of the user to
generate and validate parameters when none are available.  A proper
topology is perhaps the most important part of setting up a simulation!

There are some methods for doing some of this in an automated
fashion (i.e., RESP charge derivation, antechamber with GAFF, etc).
 But the hard truth comes down to one simple fact - if no parameters
are already available, you must do that work.  It is hard, but
necessary.  Have a look at the Gromos96 force fields; they contain
some monosaccharide building blocks that should give you a
reasonable starting point.

-Justin

Thanks,

Nancy





On Fri, Jul 31, 2009 at 4:53 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   Nancy wrote:

   Hello,

   I am trying to run a MD simulation on trehalose (glucose
   disaccharide) in water.  I obtained the PDB file from the
URL:
   http://www.rcsb.org/pdb/files/ligand/TRE_model.pdb .
 When I run
   pdb2gmx on the PDB file:

   pdb2gmx -f TRE_model.pdb -o TRE_model.gro -v

   I chose force field 5 (OPLS) from the list:

   Select the Force Field:
0: GROMOS96 43a1 force field
1: GROMOS96 43a2 force field (improved alkane dihedrals)
2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
6: [DEPRECATED] Gromacs force field (see manual)
7: [DEPRECATED] Gromacs force field with hydrogens for NMR
8: Encad all-atom force field, using scaled-down vacuum
charges
9: Encad all-atom force field, using full solvent charges

   And I received the following error message:

   ---
   Program pdb2gmx, VERSION 4.0.5
   Source code file: pdb2gmx.c, line: 429

   Fatal error:
   Atom C1 in residue TRP 1 not found in rtp entry with 24 atoms
   while sorting atoms
   ---


   Well, pdb2gmx thinks that TRE is tryptophan, so it's looking to
   complete a TRP building block.  Furthermore, your procedure is
   undoubtedly going to fail. Force fields and pdb2gmx are not
magic;
   they are not equipped to handle any arbitrary molecule you
may want
   to simulate.  None of the force fields provided with Gromacs will
   contain information for trehalose by default.  There is
information
   for glucose in some of the force fields (check the .rtp
files), and
   you may be able to piece trehalose together from that
information.

   Otherwise, you will have to go through the *very difficult and
   time-consuming* process of parameterization:

   http://oldwiki.gromacs.org/index.php/Parameterization

   -Justin

   Please help.


   Thank you,

   Nancy







 
 ---

Re: [gmx-users] Carbohydrate MD Simulation

[Nancy]

High-throughput "in silico" screening (e.g. for ligand-protein binding) has
been performed on a number of systems.  How are such automated simulations
performed (I assume they utilize molecular dynamics)?




On Fri, Jul 31, 2009 at 5:47 PM, Justin A. Lemkul  wrote:

>
>
> Nancy wrote:
>
>> If it necessary to manually create force field parameters for each
>> molecule, then how can one run a simulation involving a number of arbitrary
>> molecules (e.g. a set of mono and disaccharides) for which there are no
>> existing force fields?
>>
>> Do you know of any other MD software package that is capable of running
>> simulations on arbitrary molecules without having to "piece together" a
>> force field for each molecule?
>>
>>
> Indeed it would be nice if there was a software package that would
> parameterize your molecule, validate said parameters, then run a meaningful
> simulation with all the proper conditions.  Maybe it could even make
> coffee...
>
> All kidding aside, the answer is no.  It is the job of the user to generate
> and validate parameters when none are available.  A proper topology is
> perhaps the most important part of setting up a simulation!
>
> There are some methods for doing some of this in an automated fashion
> (i.e., RESP charge derivation, antechamber with GAFF, etc).  But the hard
> truth comes down to one simple fact - if no parameters are already
> available, you must do that work.  It is hard, but necessary.  Have a look
> at the Gromos96 force fields; they contain some monosaccharide building
> blocks that should give you a reasonable starting point.
>
> -Justin
>
>  Thanks,
>>
>> Nancy
>>
>>
>>
>>
>>
>> On Fri, Jul 31, 2009 at 4:53 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Nancy wrote:
>>
>>Hello,
>>
>>I am trying to run a MD simulation on trehalose (glucose
>>disaccharide) in water.  I obtained the PDB file from the URL:
>>http://www.rcsb.org/pdb/files/ligand/TRE_model.pdb .  When I run
>>pdb2gmx on the PDB file:
>>
>>pdb2gmx -f TRE_model.pdb -o TRE_model.gro -v
>>
>>I chose force field 5 (OPLS) from the list:
>>
>>Select the Force Field:
>> 0: GROMOS96 43a1 force field
>> 1: GROMOS96 43a2 force field (improved alkane dihedrals)
>> 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
>> 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
>> 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
>> 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
>> 6: [DEPRECATED] Gromacs force field (see manual)
>> 7: [DEPRECATED] Gromacs force field with hydrogens for NMR
>> 8: Encad all-atom force field, using scaled-down vacuum charges
>> 9: Encad all-atom force field, using full solvent charges
>>
>>And I received the following error message:
>>
>>---
>>Program pdb2gmx, VERSION 4.0.5
>>Source code file: pdb2gmx.c, line: 429
>>
>>Fatal error:
>>Atom C1 in residue TRP 1 not found in rtp entry with 24 atoms
>>while sorting atoms
>>---
>>
>>
>>Well, pdb2gmx thinks that TRE is tryptophan, so it's looking to
>>complete a TRP building block.  Furthermore, your procedure is
>>undoubtedly going to fail. Force fields and pdb2gmx are not magic;
>>they are not equipped to handle any arbitrary molecule you may want
>>to simulate.  None of the force fields provided with Gromacs will
>>contain information for trehalose by default.  There is information
>>for glucose in some of the force fields (check the .rtp files), and
>>you may be able to piece trehalose together from that information.
>>
>>Otherwise, you will have to go through the *very difficult and
>>time-consuming* process of parameterization:
>>
>>http://oldwiki.gromacs.org/index.php/Parameterization
>>
>>-Justin
>>
>>Please help.
>>
>>
>>Thank you,
>>
>>Nancy
>>
>>
>>
>>
>>
>>
>>
>>
>>  
>>
>>___
>>gmx-users mailing listgmx-users@gromacs.org
>>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/search
>>before posting!
>>Please don't post (un)subscribe requests to the list. Use the
>>www interface or send it to gmx-users-requ...@gromacs.org
>>.
>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>--
>>
>>Justin A. Lemkul
>>Ph.D. Candidate
>>ICTAS Doctoral Scholar
>>Department of Biochemistry
>>Virginia Tech

Re: [gmx-users] Carbohydrate MD Simulation

[Justin A. Lemkul]

Nancy wrote:
If it necessary to manually create force field parameters for each 
molecule, then how can one run a simulation involving a number of 
arbitrary molecules (e.g. a set of mono and disaccharides) for which 
there are no existing force fields?


Do you know of any other MD software package that is capable of running 
simulations on arbitrary molecules without having to "piece together" a 
force field for each molecule?




Indeed it would be nice if there was a software package that would parameterize 
your molecule, validate said parameters, then run a meaningful simulation with 
all the proper conditions.  Maybe it could even make coffee...


All kidding aside, the answer is no.  It is the job of the user to generate and 
validate parameters when none are available.  A proper topology is perhaps the 
most important part of setting up a simulation!


There are some methods for doing some of this in an automated fashion (i.e., 
RESP charge derivation, antechamber with GAFF, etc).  But the hard truth comes 
down to one simple fact - if no parameters are already available, you must do 
that work.  It is hard, but necessary.  Have a look at the Gromos96 force 
fields; they contain some monosaccharide building blocks that should give you a 
reasonable starting point.


-Justin


Thanks,

Nancy




On Fri, Jul 31, 2009 at 4:53 PM, Justin A. Lemkul > wrote:




Nancy wrote:

Hello,

I am trying to run a MD simulation on trehalose (glucose
disaccharide) in water.  I obtained the PDB file from the URL:
http://www.rcsb.org/pdb/files/ligand/TRE_model.pdb .  When I run
pdb2gmx on the PDB file:

pdb2gmx -f TRE_model.pdb -o TRE_model.gro -v

I chose force field 5 (OPLS) from the list:

Select the Force Field:
 0: GROMOS96 43a1 force field
 1: GROMOS96 43a2 force field (improved alkane dihedrals)
 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
 6: [DEPRECATED] Gromacs force field (see manual)
 7: [DEPRECATED] Gromacs force field with hydrogens for NMR
 8: Encad all-atom force field, using scaled-down vacuum charges
 9: Encad all-atom force field, using full solvent charges

And I received the following error message:

---
Program pdb2gmx, VERSION 4.0.5
Source code file: pdb2gmx.c, line: 429

Fatal error:
Atom C1 in residue TRP 1 not found in rtp entry with 24 atoms
while sorting atoms
---


Well, pdb2gmx thinks that TRE is tryptophan, so it's looking to
complete a TRP building block.  Furthermore, your procedure is
undoubtedly going to fail. Force fields and pdb2gmx are not magic;
they are not equipped to handle any arbitrary molecule you may want
to simulate.  None of the force fields provided with Gromacs will
contain information for trehalose by default.  There is information
for glucose in some of the force fields (check the .rtp files), and
you may be able to piece trehalose together from that information.

Otherwise, you will have to go through the *very difficult and
time-consuming* process of parameterization:

http://oldwiki.gromacs.org/index.php/Parameterization

-Justin

Please help.


Thank you,

Nancy









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-- 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] Carbohydrate MD Simulation

[Nancy]

If it necessary to manually create force field parameters for each molecule,
then how can one run a simulation involving a number of arbitrary molecules
(e.g. a set of mono and disaccharides) for which there are no existing force
fields?

Do you know of any other MD software package that is capable of running
simulations on arbitrary molecules without having to "piece together" a
force field for each molecule?

Thanks,

Nancy




On Fri, Jul 31, 2009 at 4:53 PM, Justin A. Lemkul  wrote:

>
>
> Nancy wrote:
>
>> Hello,
>>
>> I am trying to run a MD simulation on trehalose (glucose disaccharide) in
>> water.  I obtained the PDB file from the URL:
>> http://www.rcsb.org/pdb/files/ligand/TRE_model.pdb .  When I run pdb2gmx
>> on the PDB file:
>>
>> pdb2gmx -f TRE_model.pdb -o TRE_model.gro -v
>>
>> I chose force field 5 (OPLS) from the list:
>>
>> Select the Force Field:
>>  0: GROMOS96 43a1 force field
>>  1: GROMOS96 43a2 force field (improved alkane dihedrals)
>>  2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
>>  3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
>>  4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
>>  5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
>>  6: [DEPRECATED] Gromacs force field (see manual)
>>  7: [DEPRECATED] Gromacs force field with hydrogens for NMR
>>  8: Encad all-atom force field, using scaled-down vacuum charges
>>  9: Encad all-atom force field, using full solvent charges
>>
>> And I received the following error message:
>>
>> ---
>> Program pdb2gmx, VERSION 4.0.5
>> Source code file: pdb2gmx.c, line: 429
>>
>> Fatal error:
>> Atom C1 in residue TRP 1 not found in rtp entry with 24 atoms
>> while sorting atoms
>> ---
>>
>>
> Well, pdb2gmx thinks that TRE is tryptophan, so it's looking to complete a
> TRP building block.  Furthermore, your procedure is undoubtedly going to
> fail. Force fields and pdb2gmx are not magic; they are not equipped to
> handle any arbitrary molecule you may want to simulate.  None of the force
> fields provided with Gromacs will contain information for trehalose by
> default.  There is information for glucose in some of the force fields
> (check the .rtp files), and you may be able to piece trehalose together from
> that information.
>
> Otherwise, you will have to go through the *very difficult and
> time-consuming* process of parameterization:
>
> http://oldwiki.gromacs.org/index.php/Parameterization
>
> -Justin
>
>  Please help.
>>
>>
>> Thank you,
>>
>> Nancy
>>
>>
>>
>>
>>
>>
>>
>> 
>>
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] Carbohydrate MD Simulation

[Justin A. Lemkul]

Nancy wrote:

Hello,

I am trying to run a MD simulation on trehalose (glucose disaccharide) 
in water.  I obtained the PDB file from the URL: 
http://www.rcsb.org/pdb/files/ligand/TRE_model.pdb .  When I run pdb2gmx 
on the PDB file:


pdb2gmx -f TRE_model.pdb -o TRE_model.gro -v

I chose force field 5 (OPLS) from the list:

Select the Force Field:
 0: GROMOS96 43a1 force field
 1: GROMOS96 43a2 force field (improved alkane dihedrals)
 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
 6: [DEPRECATED] Gromacs force field (see manual)
 7: [DEPRECATED] Gromacs force field with hydrogens for NMR
 8: Encad all-atom force field, using scaled-down vacuum charges
 9: Encad all-atom force field, using full solvent charges

And I received the following error message:

---
Program pdb2gmx, VERSION 4.0.5
Source code file: pdb2gmx.c, line: 429

Fatal error:
Atom C1 in residue TRP 1 not found in rtp entry with 24 atoms
 while sorting atoms
---



Well, pdb2gmx thinks that TRE is tryptophan, so it's looking to complete a TRP 
building block.  Furthermore, your procedure is undoubtedly going to fail. 
Force fields and pdb2gmx are not magic; they are not equipped to handle any 
arbitrary molecule you may want to simulate.  None of the force fields provided 
with Gromacs will contain information for trehalose by default.  There is 
information for glucose in some of the force fields (check the .rtp files), and 
you may be able to piece trehalose together from that information.


Otherwise, you will have to go through the *very difficult and time-consuming* 
process of parameterization:


http://oldwiki.gromacs.org/index.php/Parameterization

-Justin


Please help.


Thank you,

Nancy









___
gmx-users mailing listgmx-users@gromacs.org
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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] Carbohydrate MD Simulation

[Nancy]

Hello,

I am trying to run a MD simulation on trehalose (glucose disaccharide) in
water.  I obtained the PDB file from the URL:
http://www.rcsb.org/pdb/files/ligand/TRE_model.pdb .  When I run pdb2gmx on
the PDB file:

pdb2gmx -f TRE_model.pdb -o TRE_model.gro -v

I chose force field 5 (OPLS) from the list:

Select the Force Field:
 0: GROMOS96 43a1 force field
 1: GROMOS96 43a2 force field (improved alkane dihedrals)
 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
 6: [DEPRECATED] Gromacs force field (see manual)
 7: [DEPRECATED] Gromacs force field with hydrogens for NMR
 8: Encad all-atom force field, using scaled-down vacuum charges
 9: Encad all-atom force field, using full solvent charges

And I received the following error message:

---
Program pdb2gmx, VERSION 4.0.5
Source code file: pdb2gmx.c, line: 429

Fatal error:
Atom C1 in residue TRP 1 not found in rtp entry with 24 atoms
 while sorting atoms
---

Please help.


Thank you,

Nancy
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RE: [gmx-users] very strange domain composition statistics

[Jennifer Williams]

Quoting Jennifer Williams :



Hi,

Thanks for your input. Sorry I should have mentioned that I am using
the latest version of gromacs (4.0.5).

This morning I noticed that the strange domain decomp statistics are
only produced when my simulations run on certain nodes. Below I have
pasted the domain decomp statistics for the SAME .tpr file run on 2
different nodes (each time using 6 nodes)- the first looks ok to me
while the second produces crazy numbers.

I have opened a call to computer support at my Uni to ask if there is
some difference between the nodes and for now I specify that my
simulations should run on certain nodes which I have checked are ok.

I don't know if this is something to do with the way I compiled
gromacs or the architecture. I did a standard installation and it
seemed to run smoothly-no error messages. I have attached my config.log.

If you have any ideas please let me know,

Thanks



D O M A I N   D E C O M P O S I T I O N   S T A T I S T I C S

 av. #atoms communicated per step for force:  2 x 1967.2
 av. #atoms communicated per step for LINCS:  2 x 20.4

 Average load imbalance: 30.3 %
 Part of the total run time spent waiting due to load imbalance: 5.8 %
 Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 9 %

NOTE: 5.8 % performance was lost due to load imbalance
  in the domain decomposition.

 R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G

 Computing: Nodes Number G-CyclesSeconds %
---
 Domain decomp. 6 11  852.216  341.9 3.0
 Comm. coord.   6101  594.411  238.5 2.1
 Neighbor search6 11 2271.294  911.2 7.9
 Force  6101 5560.129 2230.519.3
 Wait + Comm. F 6101 1216.171  487.9 4.2
 PME mesh   610115071.432 6046.152.2
 Write traj.6   10012.5771.0 0.0
 Update 6101  264.545  106.1 0.9
 Constraints6101  923.418  370.4 3.2
 Comm. energies 6101  942.036  377.9 3.3
 Rest   61167.866  468.5 4.0
---
 Total  6   28866.09611580.0   100.0
---

Parallel run - timing based on wallclock.

   NODE (s)   Real (s)  (%)
   Time:   1930.000   1930.000100.0
   32:10
   (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
Performance: 51.737  6.922 44.767  0.536
Finished mdrun on node 0 Fri Jul 31 13:05:01 2009


D O M A I N   D E C O M P O S I T I O N   S T A T I S T I C S

 av. #atoms communicated per step for force:  2 x 1969.0
 av. #atoms communicated per step for LINCS:  2 x 15.7

 Average load imbalance: 500.0 %
 Part of the total run time spent waiting due to load imbalance:
5822746112.0 %
 Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 9 %

NOTE: 5822746112.0 % performance was lost due to load imbalance
  in the domain decomposition.

 R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G

 Computing: Nodes Number G-CyclesSeconds %
---
 Write traj.6   1001 18443320128.89043061.8   100.0
 Update 6101  314.1750.0 0.0
 Rest   69223372036.85521534.950.0
---
 Total  618443397799.33643062.0   100.0
---

NOTE: 306 % of the run time was spent communicating energies,
  you might want to use the -nosum option of mdrun

Parallel run - timing based on wallclock.

   NODE (s)   Real (s)  (%)
   Time:   7177.000   7177.000100.0
   1h59:37
   (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
Performance: 13.907  1.861 12.038  1.994
Finished mdrun on node 0 Thu Jul 30 01:47:05 2009










Quoting Berk Hess :






Date: Fri, 31 Jul 2009 07:49:49 +0200
From: sp...@xray.bmc.uu.se
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] very strange domain composition statistics

Mark Abraham wrote:

Jennifer Williams wrote:

Hi ,

I am having some problems when running in parallel. Although my jobs
run to completion I am getting some worrying domain decomposition
statistics in particular the average load imbalance and the
performance loss due to load imbalance see below:


Please report your GROMACS version number. If it's not th

[gmx-users] reg mopac gromacs installation

[vidhya sankar]

dear gmx user , 
i am doing QM/MM using MOPAC/GROMACS when i configure mopac7-1.10 the software 
using for the interface with gromacs by 
../configure command i got error as follows 
configure error: f2c or g2c library cannot be found . 
solution for the above error would be  appericiated 
reply please thanks in advance 
c.text+0x160): undefined reference to `__ctype_b' 
/usr/lib/gcc/i386-redhat-linux/4.3.0/../../../libmopac.a(lread.o): In function 
`e_rsle': 
(.text+0x21f): undefined reference to `__ctype_b' 
/usr/lib/gcc/i386-redhat-linux/4.3.0/../../../libmopac.a(lread.o): In function 
`e_rsle': 
(.text+0x296): undefined reference to `__ctype_b' 
/usr/lib/gcc/i386-redhat-linux/4.3.0/../../../libmopac.a(lread.o): In function 
`e_rsle': 
(.text+0x2d0): undefined reference to `__ctype_b' 
/usr/lib/gcc/i386-redhat-linux/4.3.0/../../../libmopac.a(lread.o): In function 
`e_rsle': 
(.text+0x8b2): undefined reference to `__ctype_b' 
/usr/lib/gcc/i386-redhat-linux/4.3.0/../../../libmopac.a(lread.o):(.text+0xb05):
 more undefined references to `__ctype_b' follow 
collect2: ld returned 1 exit status 
make[3]: *** [grompp] Error 1 
make[3]: Leaving directory `/root/gromacs-4.0.5/src/kernel' 
make[2]: *** [all-recursive] Error 1 
make[2]: Leaving directory `/root/gromacs-4.0.5/src' 
make[1]: *** [all] Error 2 
make[1]: Leaving directory `/root/gromacs-4.0.5/src' 
make: *** [all-recursive] Error 1


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RE: [gmx-users] Re: pulling

[Berk Hess]

gt;>> Thx,
> >>>> Alex
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[gmx-users] Re: pulling

[Thomas Schlesier]

---
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RE: [gmx-users] pulling

[Berk Hess]

Ah, then you could have a pbc problem for determining the COM of the slab,
since you slab is thicker than half the box.
You have to set pull_pbcatom0 to an atom in the middle of the slab.

pull_init1 doesn't change.
The only thing the geometry change affects is the direction you pull in.
With distance you could be unlucky that it takes the distance
in the opposite direction.

Berk

> Date: Fri, 31 Jul 2009 12:32:13 +0200
> From: alexander.h...@mytum.de
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] pulling
> 
> Thx for the quick reply!
> 
> I use 4.0.5, pbc z=yes
> Box height = 17.5nm
> gld slab is from z=0 to z= 9.5;
> So distance=5.5 should give 1.0nm above surface right?
> 
> What do I have to put for pull_init1 if i use direction??
> 
> Thx,
> Alex
> 
> Berk Hess schrieb:
> > Hi,
> >
> > I hope you are using 4.0.5, I fixed several bug in the pull code for
> > older 4.0 versions.
> >
> > The problems you are seing could be due to  pbc.
> > Do you have pbc in Z, and what is the height of your box?
> >
> > A safer setup is:
> > pull_geometry = direction
> > pull_vec1 = 0 0 1
> > But they should give the same answers if you do not have pbc issues.
> >
> > Berk
> >
> > > Date: Fri, 31 Jul 2009 12:13:07 +0200
> > > From: alexander.h...@mytum.de
> > > To: gmx-users@gromacs.org
> > > Subject: [gmx-users] pulling
> > >
> > > Hey,
> > >
> > > I appear to have serious trouble understanding how to set up the pulling
> > > properly.
> > >
> > > I have many configurations of a protein partially adsorbed to a froozen
> > > surface (the configs differ
> > > in the amount of the protein that has been desorbed).
> > > Now I want the pulling to keep the distance of the desorbed end of the
> > > protein to the surface using the harmonic pot.
> > > Now the documentation is not very clear how this all works so I ran
> > > several experiments to figure it out but I failed.
> > > I use the following options:
> > >
> > > ;PULLING
> > > pull = umbrella
> > > pull_geometry = distance
> > > pull_dim = N N Y
> > > pull_nstxout = 1000
> > > pull_nstfout = 1000
> > > pull_ngroups = 1
> > > pull_group0 = GLD
> > > pull_group1 = ASN
> > > pull_vec1 = 0.0 0.0 0.0
> > > pull_init1 = 5.27778
> > > pull_rate1 = 0.0
> > > pull_k1 = 100
> > >
> > >
> > > where gld is the surface and asn is the end residue of the protein and
> > > pull_init1 is set to the desired COM distance of the two
> > > groups (gld is froozen). I use the same settings for all runs, only
> > > changing pull_init1 to get the desired distance.
> > > Now for some reason using this setup either pulls the ASN end of the
> > > protein completely onto the surface or very far away from it depending
> > > on the value I use for pull_init1.
> > > So the distance between what and what shall I put for pull_init1? What
> > > else is wrong?
> > >
> > > Thx,
> > > Alex
> > > ___
> > > gmx-users mailing list gmx-users@gromacs.org
> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
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> > posting!
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Re: [gmx-users] pulling

[aherz]

Thx for the quick reply!

I use 4.0.5, pbc z=yes
Box height = 17.5nm
gld slab is from z=0 to z= 9.5;
So distance=5.5 should give 1.0nm above surface right?

What do I have to put for pull_init1 if i use direction??

Thx,
Alex

Berk Hess schrieb:
> Hi,
>
> I hope you are using 4.0.5, I fixed several bug in the pull code for
> older 4.0 versions.
>
> The problems you are seing could be due to  pbc.
> Do you have pbc in Z, and what is the height of your box?
>
> A safer setup is:
> pull_geometry = direction
> pull_vec1 = 0 0 1
> But they should give the same answers if you do not have pbc issues.
>
> Berk
>
> > Date: Fri, 31 Jul 2009 12:13:07 +0200
> > From: alexander.h...@mytum.de
> > To: gmx-users@gromacs.org
> > Subject: [gmx-users] pulling
> >
> > Hey,
> >
> > I appear to have serious trouble understanding how to set up the pulling
> > properly.
> >
> > I have many configurations of a protein partially adsorbed to a froozen
> > surface (the configs differ
> > in the amount of the protein that has been desorbed).
> > Now I want the pulling to keep the distance of the desorbed end of the
> > protein to the surface using the harmonic pot.
> > Now the documentation is not very clear how this all works so I ran
> > several experiments to figure it out but I failed.
> > I use the following options:
> >
> > ;PULLING
> > pull = umbrella
> > pull_geometry = distance
> > pull_dim = N N Y
> > pull_nstxout = 1000
> > pull_nstfout = 1000
> > pull_ngroups = 1
> > pull_group0 = GLD
> > pull_group1 = ASN
> > pull_vec1 = 0.0 0.0 0.0
> > pull_init1 = 5.27778
> > pull_rate1 = 0.0
> > pull_k1 = 100
> >
> >
> > where gld is the surface and asn is the end residue of the protein and
> > pull_init1 is set to the desired COM distance of the two
> > groups (gld is froozen). I use the same settings for all runs, only
> > changing pull_init1 to get the desired distance.
> > Now for some reason using this setup either pulls the ASN end of the
> > protein completely onto the surface or very far away from it depending
> > on the value I use for pull_init1.
> > So the distance between what and what shall I put for pull_init1? What
> > else is wrong?
> >
> > Thx,
> > Alex
> > ___
> > gmx-users mailing list gmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
> 
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> 
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[gmx-users] mdrun_make_hole installation

[Moutusi Manna]

Dear Ansgar Esztermann,

                   
Thanks for your kind help. With fftw-2.1.5.tar.gz i can successfully install 
gromacs-3.1.4.

With regards,
Moutan>usi Manna





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RE: [gmx-users] pulling

[Berk Hess]

Hi,

I hope you are using 4.0.5, I fixed several bug in the pull code for older 4.0 
versions.

The problems you are seing could be due to  pbc.
Do you have pbc in Z, and what is the height of your box?

A safer setup is:
pull_geometry = direction
pull_vec1 = 0 0 1
But they should give the same answers if you do not have pbc issues.

Berk

> Date: Fri, 31 Jul 2009 12:13:07 +0200
> From: alexander.h...@mytum.de
> To: gmx-users@gromacs.org
> Subject: [gmx-users] pulling
> 
> Hey,
> 
> I appear to have serious trouble understanding how to set up the pulling
> properly.
> 
> I have many configurations of a protein partially adsorbed to a froozen
> surface (the configs differ
> in the amount of the protein that has been desorbed).
> Now I want the pulling to keep the distance of the desorbed end of the
> protein to the surface using the harmonic pot.
> Now the documentation is not very clear how this all works so I ran
> several experiments to figure it out but I failed.
> I use the following options:
> 
> ;PULLING
> pull = umbrella
> pull_geometry= distance
> pull_dim = N N Y
> pull_nstxout = 1000
> pull_nstfout = 1000
> pull_ngroups = 1
> pull_group0  = GLD
> pull_group1  = ASN
> pull_vec1= 0.0 0.0 0.0
> pull_init1   =   5.27778
> pull_rate1   = 0.0
> pull_k1  = 100
> 
> 
> where gld is the surface and asn is the end residue of the protein and
> pull_init1 is set to the desired COM distance of the two
> groups (gld is froozen). I use the same settings for all runs, only
> changing pull_init1 to get the desired distance.
> Now for some reason using this setup either pulls the ASN end of the
> protein completely onto the surface or very far away from it depending
> on the value I use for pull_init1.
> So the distance between what and what shall I put for pull_init1? What
> else is wrong?
> 
> Thx,
> Alex
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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[gmx-users] pulling

[aherz]

Hey,

I appear to have serious trouble understanding how to set up the pulling
properly.

I have many configurations of a protein partially adsorbed to a froozen
surface (the configs differ
in the amount of the protein that has been desorbed).
Now I want the pulling to keep the distance of the desorbed end of the
protein to the surface using the harmonic pot.
Now the documentation is not very clear how this all works so I ran
several experiments to figure it out but I failed.
I use the following options:

;PULLING
pull = umbrella
pull_geometry= distance
pull_dim = N N Y
pull_nstxout = 1000
pull_nstfout = 1000
pull_ngroups = 1
pull_group0  = GLD
pull_group1  = ASN
pull_vec1= 0.0 0.0 0.0
pull_init1   =   5.27778
pull_rate1   = 0.0
pull_k1  = 100


where gld is the surface and asn is the end residue of the protein and
pull_init1 is set to the desired COM distance of the two
groups (gld is froozen). I use the same settings for all runs, only
changing pull_init1 to get the desired distance.
Now for some reason using this setup either pulls the ASN end of the
protein completely onto the surface or very far away from it depending
on the value I use for pull_init1.
So the distance between what and what shall I put for pull_init1? What
else is wrong?

Thx,
Alex
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Re: [gmx-users] mdrun_make_hole installation

[Ansgar Esztermann]

On Jul 30, 2009, at 12:08 , Moutusi Manna wrote:


Dear Ansgar Esztermann,
   Thanks for your reply. I have source .bashrc  
after adding the environment variables as follows..

 "source .bashrc" and then run
./configure --enable-float --prefix=/home/cm/install --program- 
suffix=_h

The same problem arise again.


OK, I did not spot the real error the first time, but here it is  
(quoting from your original mail):


after that the files generated in /home/cm/install/fftw-3.2.1/ 
include are.

fftw3.f  fftw3.h


And then the configure script says:


checking for sfftw.h... no
checking for fftw.h... no
configure: error: Cannot find any single precision sfftw.h or fftw.h


... it cannot find fftw.h because the header is called fftw3.h.  
Looking through git/CVS history, fftw3 seems to be supported by  
gromacs only from v3.3 on. You should install fftw2 instead.



Regards,

A.

--
Ansgar Esztermann
DV-Systemadministration
Max-Planck-Institut für biophysikalische Chemie, Abteilung 105

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RE: [gmx-users] Re: Pulling a CG protein

[Berk Hess]

Hi,

The suggested pull parameters below are correct,
except that you should not use pull_geometry=position,
since that will only make group1 move, not group0.
You should use pull_geometry=distance,
pull_vec1 is that no longer required, since distance
will move the two groups away along the vector
between the two COM's.

Berk

> Date: Fri, 31 Jul 2009 09:58:56 +0200
> From: schl...@uni-mainz.de
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Re: Pulling a CG protein
> 
> Hi Johnny,
> i replied something to the pull-code of your question. But problem was,
> i didn't edited the subject line...
> So here is my answer (see below) with the right subject line (so that
> you hopefully find it).
> Hope it helps you.
> Thomas
> 
> > 
> > Message: 3
> > Date: Thu, 30 Jul 2009 12:08:40 -0700 (PDT)
> > From: "Johnny Lam" 
> > Subject: Re: [gmx-users] Pulling a CG protein
> > To: gmx-users@gromacs.org
> > Cc: baa...@smplinux.de
> > Message-ID:
> > <56441.128.32.142.53.1248980920.squir...@calmail.berkeley.edu>
> > Content-Type: text/plain;charset=iso-8859-1
> > 
> > Hi XAvier, Marc, and David,
> > 
> > Thank you so much for the reply and encouragement ;-). Please forgive me
> > as I am trying to learn how to reply to the thread that I started. With
> > regards to the fun discussion, it was my original intent to compare the
> > results of pulling with the MARTINI forcefield (if the pull code was
> > correct) with already published works on MD (using all-atomistic modeling
> > of course :-)). I just wanted to know whether the pull code that I am
> > using will be valid at all. If you guys can verify that would be awesome!
> > Otherwise, I'd be happy to share the results with you guys if you wish.
> > Again, thanks!
> > 
> > --Johnny
> > 
> > 
> > -
> > Johnny Lam
> > ISPE Berkeley Chapter External Vice President
> > Department of Bioengineering
> > College of Engineering
> > University of California, Berkeley
> > Tel: (408) 655- 6829
> > Email: john...@berkeley.edu
> > 
> > 
> > --
> > >
> > > Message: 1
> > > Date: Wed, 29 Jul 2009 16:04:54 -0700 (PDT)
> > > From: "Johnny Lam" 
> > > Subject: [gmx-users] Pulling a CG protein
> > > To: gmx-users@gromacs.org
> > > Message-ID:
> > > <55658.128.32.142.63.1248908694.squir...@calmail.berkeley.edu>
> > > Content-Type: text/plain;charset=iso-8859-1
> > >
> > > Dear gromacs users,
> > >
> > > Hi, I am trying to pull apart a relatively large protein (CG using the
> > > martini force field) by pulling on two groups in opposite directions. To
> > > do this, I will be using the following .mdp file. However, I am almost
> > > certain that it contains errors:
> > >
> 
> -snip
> 
> > >
> > > ; Pulling
> > > pull=  afm
> > > pull_geometry   =  direction
> > > pull_start  =  no
> > > pull_nstxout=  10
> > > pull_nstfout=  10
> > > pull_ngroups=  2
> > > pull_group0 =
> > > pull_group1 =  pull
> > > pull_vec1   =  -0.1764 -0.9823 -0.0625
> > > pull_init1  =  -0.1764 -0.9823 -0.0625
> > > pull_rate1  =  0.0001
> > > pull_k1 =  1000
> > > pull_group2 =  freeze
> > > pull_vec2   =  0.1764 0.9823 0.0625
> > > pull_init2  =  0.1764 0.9823 0.0625
> > > pull_rate2  =  0.01
> > > pull_k2 =  5000
> > >
> > >
> 
> Think the first problem is the:
> pull = afm
> In the manual there is no more a 'afm' option, but as far as i know
> 'umbrella' should be the same (don't ask me why there was no error
> message about this). If you have no pull_group0 you could get problem
> with the com-motion.
> If you want to pull 'pull' away from 'freeze', i would do the following:
> 
> pull = umbrella
> pull_geometry = position
> pull_start = yes  (we don't want to calculate the initial distance
> between 'pull' and 'freeze' by hand)
> pull_ngroups = 1 (because the reference group doesn't count to this value)
> pull_dim = Y Y Y (because we want to pull in 3D)
> pull_group0 = freeze
> pull_group1 = pull
> pull_vec1 = vector from 'freeze' to 'pull'
> pull_init1 = 0.0 0.0 0.0
> 
> Now you are pulling 'pull' away from 'freeze' and and you should have no
> problem with com-motion.
> If you want to fix the position of 'freeze' i would use position_restraints.
> One thing: once i had problems with the 'pull_weightsX', i got (with one
> system) every time error messages (i had only 1atom in each group and
> tried the values 0 and 1 both, but didn't work). So i left these to
> values blank and GROMACS selected them, and it worked. In other
> simulations with a similar setup i had no problems with 'pull_weightsX'.
> 
> 
> > > The reason why group 2 has such a high force constant and low pull
> rate is
> > > because I wanted to simulate putting a harmonic constraint on the freeze
> > > group. However, when I process this .mdp with grompp, I ge

RE: [gmx-users] very strange domain composition statistics

[Berk Hess]

> Date: Fri, 31 Jul 2009 07:49:49 +0200
> From: sp...@xray.bmc.uu.se
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] very strange domain composition statistics
> 
> Mark Abraham wrote:
> > Jennifer Williams wrote:
> >> Hi ,
> >>
> >> I am having some problems when running in parallel. Although my jobs 
> >> run to completion I am getting some worrying domain decomposition 
> >> statistics in particular the average load imbalance and the 
> >> performance loss due to load imbalance see below:
> > 
> > Please report your GROMACS version number. If it's not the latest 
> > (4.0.5), then you should probably update and see if it's a problem that 
> > may have been fixed between those releases. You might also try it 
> > without your freeze groups, especially if they dominate the system.
> 
> In addition, you do not specify how may processors you used, nor the 
> division over processors that mdrun makes and not the expected 
> performance either. From the numbers below it seems like you used 1 or 2 
> processors at most. The large number is definitely erroneous though.
> 

For the cycle count table the number of processors seems to be 6.

It seems that the cycle counters have overflowed.
On what kind of architecture with what kind of compilers are you running this?

Berk

> > 
> >> D O M A I N   D E C O M P O S I T I O N   S T A T I S T I C S
> >>
> >>  av. #atoms communicated per step for force:  2 x 1974.8
> >>  av. #atoms communicated per step for LINCS:  2 x 15.2
> >>
> >>  Average load imbalance: 500.0 %
> >>  Part of the total run time spent waiting due to load imbalance: 
> >> 4246403072.0 %
> >>  Steps where the load balancing was limited by -rdd, -rcon and/or 
> >> -dds: X 9 %
> >>
> >> NOTE: 4246403072.0 % performance was lost due to load imbalance
> >>   in the domain decomposition.
> >>
> >>  R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G
> >>
> >>  Computing: Nodes Number G-CyclesSeconds %
> >> ---
> >>  Write traj.6   1001 18443320139.16442130.9   100.0
> >>  Update 6101 18442922984.49142130.0   100.0
> >>  Rest   69223372036.85521069.450.0
> >> ---
> >>  Total  618446422611.66942138.0   100.0
> >> ---
> >>
> >> NOTE: 305 % of the run time was spent communicating energies,
> >>   you might want to use the -nosum option of mdrun
> >>
> >> Parallel run - timing based on wallclock.
> >>
> >>NODE (s)   Real (s)  (%)
> >>Time:   7023.000   7023.000100.0
> >>1h57:03
> >>(Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
> >> Performance: 14.214  1.902 12.302  1.951
> >> Finished mdrun on node 0 Wed Jul 29 23:47:18 2009
> >>
> >>
> >>
> >> Below is my .mdp file: I am using the PME but not having much of a 
> >> feel for how to set the options under  Spacing for the PME/PPPM FFT 
> >> grid, I left these as the default values. Could this be where the 
> >> trouble lies?
> >>
> >> My cut-off cannot be larger than 0.9 as my unit cell is only 18.2A in 
> >> one direction.
> >>
> >> How do I choose values for PME/PPPM? Ie what kind of values to use for 
> >> nx, ny and nz ?
> > 
> > See manual section 3.17.5
> > 
> >> I read that they should be divisible by npme to get the best 
> >> performance. Is npme the pme_order in the .mdp file? If not where do I 
> >> set this parameter?
> > 
> > No, -npme is a command line parameter to mdrun. Roughly speaking, things 
> > that have a material effect on the physics are specified in the .mdp 
> > file, and things that either require external file(names) to be supplied 
> > or which only affect the implementation of the physics are specified on 
> > the command line.
> > 
> > Mark
> > 
> >> Much appreciated,
> >>
> >> Jenny
> >>
> >>
> >>
> >> ; VARIOUS PREPROCESSING OPTIONS
> >> ; Preprocessor information: use cpp syntax.
> >> ; e.g.: -I/home/joe/doe -I/home/mary/hoe
> >> include  = -I../top
> >> ; e.g.: -DI_Want_Cookies -DMe_Too
> >> define   =
> >>
> >> ; RUN CONTROL PARAMETERS
> >> integrator   = md
> >> ; Start time and timestep in ps
> >> tinit= 0
> >> dt   = 0.001
> >> nsteps   = 100
> >> ; For exact run continuation or redoing part of a run
> >> ; Part index is updated automatically on checkpointing (keeps files 
> >> separate)
> >> simulation_part  = 1
> >> init_step= 0
> >> ; mode for center of mass motion removal
> >> comm-mode= linear
> >> ; number of steps for center of mass motion removal
> >> nstcomm  = 1
> >> ; group(s) for center of mass mo

[gmx-users] Re: Pulling a CG protein

[Thomas Schlesier]

Hi Johnny,
i replied something to the pull-code of your question. But problem was,
i didn't edited the subject line...
So here is my answer (see below) with the right subject line (so that
you hopefully find it).
Hope it helps you.
Thomas

> 
> Message: 3
> Date: Thu, 30 Jul 2009 12:08:40 -0700 (PDT)
> From: "Johnny Lam" 
> Subject: Re: [gmx-users] Pulling a CG protein
> To: gmx-users@gromacs.org
> Cc: baa...@smplinux.de
> Message-ID:
> <56441.128.32.142.53.1248980920.squir...@calmail.berkeley.edu>
> Content-Type: text/plain;charset=iso-8859-1
> 
> Hi XAvier, Marc, and David,
> 
> Thank you so much for the reply and encouragement ;-). Please forgive me
> as I am trying to learn how to reply to the thread that I started. With
> regards to the fun discussion, it was my original intent to compare the
> results of pulling with the MARTINI forcefield (if the pull code was
> correct) with already published works on MD (using all-atomistic modeling
> of course :-)). I just wanted to know whether the pull code that I am
> using will be valid at all. If you guys can verify that would be awesome!
> Otherwise, I'd be happy to share the results with you guys if you wish.
> Again, thanks!
> 
> --Johnny
> 
> 
> -
> Johnny Lam
> ISPE Berkeley Chapter External Vice President
> Department of Bioengineering
> College of Engineering
> University of California, Berkeley
> Tel: (408) 655- 6829
> Email: john...@berkeley.edu
> 
> 
> --
> >
> > Message: 1
> > Date: Wed, 29 Jul 2009 16:04:54 -0700 (PDT)
> > From: "Johnny Lam" 
> > Subject: [gmx-users] Pulling a CG protein
> > To: gmx-users@gromacs.org
> > Message-ID:
> > <55658.128.32.142.63.1248908694.squir...@calmail.berkeley.edu>
> > Content-Type: text/plain;charset=iso-8859-1
> >
> > Dear gromacs users,
> >
> > Hi, I am trying to pull apart a relatively large protein (CG using the
> > martini force field) by pulling on two groups in opposite directions. To
> > do this, I will be using the following .mdp file. However, I am almost
> > certain that it contains errors:
> >

-snip

> >
> > ; Pulling
> > pull=  afm
> > pull_geometry   =  direction
> > pull_start  =  no
> > pull_nstxout=  10
> > pull_nstfout=  10
> > pull_ngroups=  2
> > pull_group0 =
> > pull_group1 =  pull
> > pull_vec1   =  -0.1764 -0.9823 -0.0625
> > pull_init1  =  -0.1764 -0.9823 -0.0625
> > pull_rate1  =  0.0001
> > pull_k1 =  1000
> > pull_group2 =  freeze
> > pull_vec2   =  0.1764 0.9823 0.0625
> > pull_init2  =  0.1764 0.9823 0.0625
> > pull_rate2  =  0.01
> > pull_k2 =  5000
> >
> >

Think the first problem is the:
pull = afm
In the manual there is no more a 'afm' option, but as far as i know
'umbrella' should be the same (don't ask me why there was no error
message about this). If you have no pull_group0 you could get problem
with the com-motion.
If you want to pull 'pull' away from 'freeze', i would do the following:

pull = umbrella
pull_geometry = position
pull_start = yes  (we don't want to calculate the initial distance
between 'pull' and 'freeze' by hand)
pull_ngroups = 1 (because the reference group doesn't count to this value)
pull_dim = Y Y Y (because we want to pull in 3D)
pull_group0 = freeze
pull_group1 = pull
pull_vec1 = vector from 'freeze' to 'pull'
pull_init1 = 0.0 0.0 0.0

Now you are pulling 'pull' away from 'freeze' and and you should have no
problem with com-motion.
If you want to fix the position of 'freeze' i would use position_restraints.
One thing: once i had problems with the 'pull_weightsX', i got (with one
system) every time error messages (i had only 1atom in each group and
tried the values 0 and 1 both, but didn't work). So i left these to
values blank and GROMACS selected them, and it worked. In other
simulations with a similar setup i had no problems with 'pull_weightsX'.


> > The reason why group 2 has such a high force constant and low pull
rate is
> > because I wanted to simulate putting a harmonic constraint on the freeze
> > group. However, when I process this .mdp with grompp, I get the
following
> > message:
> >
> > WARNING 1 [file md_vinculin.mdp, line unknown]:
> >   Unknown or double left-hand 'pull_group2' in parameter file

Another thing could be that you have no index group with the name 'freeze'?

But best have also a look in the new (GROMACS 4) manual. COM pulling is
described from page 156 on.

Hope this helps
Thomas

> >
> >
> >
> > WARNING 2 [file md_vinculin.mdp, line unknown]:
> >   Unknown or double left-hand 'pull_vec2' in parameter file
> >
> >
> > The version of gromacs I have running on my powerpc is 4.0.5 so the pull
> > code should be implemented in the .mdp file. I am not sure if I
specified
> > the parameters correctly. Please help! Thanks!
> >
> > --Johnny
> >
>