[gmx-users] lipid_posre.itp file

[nitu sharma]

Dear all

  I need lipid_posre.itp file  can anyone suggest me from
where I can find it ?or If I have to make it by my own then please  let me
know how can I make it.
If anyone can suggest me I really will be thankful for him.

Nitu Sharma
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Re: [gmx-users] No default Angle types

[darrellk]

Hi Justin,
Thanks for the quick reply.

Yes, I was also thinking about using a different atom type such as the
alkane types you mentioned below. However, when I thought about how I
can include these atom types in my .n2t file, I recognized that this
might cause a potential problem since now I would have two definitions
for an H atom, as I would then have one definition for an H atom
attached to a C atom within a benzene ring and another definition for an
H atom attached to a C atom that is not on a benzene ring. Thus, my .n2t
file would then look as follows:

Copls_1450  12.011  3C 0.140   C 0.140   C 0.140
Copls_145-0.06  12.011  3C 0.140   C 0.140   H 0.108
Hopls_1460.061.008  1C 0.108 (H attached to benzene ring)
Copls_136-0.12  12.011  3C 0.140   H 0.108   H 0.108
Hopls_1400.061.008  1C 0.108 (H not attached to benzene
ring)

Would this dual definition of the H atom confuse GROMACS? Would GROMACS
know when to use the opls_146 definition and when to use the opls_140
definition?

Much thanks in advance.

Darrell

>Date: Mon, 11 May 2009 18:23:30 -0400
>From: "Justin A. Lemkul" 
>Subject: Re: [gmx-users] No default Angle types
>To: Discussion list for GROMACS users 
>Message-ID: <4a08a562.5020...@vt.edu>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
>darre...@ece.ubc.ca wrote:
>> Dear All,
>> I ran grompp and was presented with the following error:
>> ERROR 0 [file "graphene_nm_test.top", line 51217]:
>>   No default Angle types
>>
>> Line 51217 of the topology file is:
>>  5116 5115 5117 1
>>
>> and atoms 5115 to 5117 are defined in the topology file as:
>>   5115 opls_145 1 Grph C 4859 -0.12 12.011 ;
>> qtot -0.12
>>   5116 opls_146 1 Grph H 4859 0.06 1.008 ;
>> qtot -0.06
>>   5117 opls_146 1 Grph H 4859 0.06 1.008 ;
>> qtot 0
>>
>> My assumption is that this error means that there does not exist an
>> angletype for this threesome of atoms in the ffolpsaabon.itp file.
>>
>
>You are correct.  Take a closer look at the atom types:
>
>opls_145   12.01100  ; Benzene C - 12 site JACS,112,4768-90. Use #145B for 
>biphenyl
>
>opls_1461.00800  ; Benzene H - 12 site.
>
>Both atom types correspond to benzene/aromatic sites.  So, in these aromatic
>species, there is no such thing as a ring CH2.
>
>Maybe you want something more like:
>
>opls_136   12.01100  ; alkane CH2
>
>opls_1401.00800  ; alkane H.
>
>-Justin
>
>> I looked within the ffoplsaabon.itp file for an entry of the form:
>> HA CA HA
>>
>> and, as expected, "pattern not found" was returned as the response.
>>
>> So, I copied over the ffoplsaabon.itp file to my home (working) directory
>> and added the following test entry:
>>   HA CA HA  1   107.000276.000   ; TEST PARAMETERS *
>> NOT VALID *** ONLY FOR TESTING
>>
>> I expected that the ERROR O message above would disappear. But the error
>> was still present. Could you please tell me what I need to do in order
>> to resolve this error?
>>
>> Much thanks in advance.
>>
>> Darrell
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>
>
>Justin A. Lemkul
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>Department of Biochemistry
>Virginia Tech
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>jalemkul[at]vt.edu | (540) 231-9080
>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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Re: [gmx-users] Re: Problem with protein in lipid bilayer simulation

[Pawan Kumar]

Hi Anirban,

I have also followed Justin sir's tutorial.
You should not remove the OW entries.
You can remove the HW entries for sure and then this will work.

Regards,
Pawan

On Tue, May 12, 2009 at 9:45 AM, Anirban Ghosh wrote:

> Hello Justin,
>
> Thanks a lot for the reply. Your tutorial is indeed very good.
> I followed your tutorial on protein-lipid simulation. I added the
> non-bonded parameters from the lipid.itp file to the ffG53a6nb_lipid.itp
> file. You have told to either delete the atom-type HW entries having zero
> values in the non-bonded section or replace them with H. But the HW values
> are not zero. And they are also present in the "pairlist" section. So should
> I change in this section also? And when I am running the grompp command I am
> getting the error "Atom-type OW not found". So should I also delete the OW
> entries or should I replace them? If replace, then with what? Should I
> replace all the OW and HW entries throughout the ffG53a6nb_lipid.itp file?
> Please advice.
>
> Regards,
>
>
> *Anirban Ghosh*
> *Grade Based Engineer
> Bioinformatics Team
> Centre for Development of Advanced Computing (C-DAC)
> Pune, India
> *
>
> --
> Cricket on your mind? Visit the ultimate cricket website. Enter 
> now!
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Re: [gmx-users] protein falls apart in energy minimization

[Pawan Kumar]

hi,

Defining a specific box size with -d option in editconf will help to
overcome this problem...

Regards,
Pawan

On Tue, May 12, 2009 at 8:05 AM, Zhong Zheng  wrote:

> hi all
>
> I am running Gromacs on a protein consisted of three chains. But no matter
> how I tried, the protein always falls into three parts (corresponding to
> each chain) after a simple 2000 steps energy minimization. Can anyone help
> me please? Thanks.
>
> Zhong Zheng
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Re: [gmx-users] protein falls apart in energy minimization

[Mark Abraham]

Zhong Zheng wrote:

hi all

I am running Gromacs on a protein consisted of three chains. But no 
matter how I tried, the protein always falls into three parts 
(corresponding to each chain) after a simple 2000 steps energy 
minimization. Can anyone help me please? Thanks.


Are you seeing a visualization artefact caused by periodic boundary 
conditions? You can play with trjconv on your output file to see.


Mark
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Re: [gmx-users] Coordinate covalent bond

[Mark Abraham]

Zhanglin Ni wrote:

Dear all,
In pdb file. the metal ion form a coordinate covalent bond with SG of 
cystine. but seems pdb2gmx ignored CONNECT in pdb file. how to modify 
the .top or .itp to include the bond and parameterize the bond. I tried 
to find some tutorial for some special case like this. But I couldnot. 
Could someone provide the knowledge or source to learn it. Thanks


http://wiki.gromacs.org/index.php/specbond.dat

Mark
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Re: [gmx-users] TestBed in MPI not working

[Mark Abraham]

Jones de Andrade wrote:

Hi Justin.

Well, bothering again. Good and bad news.

The good news: I found a strange "work-around" for my problems here. For 
some reason, the perl script updates the path, environments and 
everything else when runs. So, the variables I placed on the script I 
was using where simply lost. Workaround here was, then, to just include 
those in the .tcshrc file and log again.


Neither perl nor gmxtest.pl "update" the environment variables. That 
will be determined by the shell from which you call your script (and/or 
your queueing system), and what your script does. See my earlier reply 
for how to set the PATH correctly.


The problem is that it's not pratical. I'm trying a lot of different 
MPIs and libraries compilations, and having to edit that file, and or 
logou/login or source it, is not pratical at all. Is there any other 
way, so that the perl script will be happy with the variables it has 
when its called, instead of initializing all them again?


If you have a normal system, the environment variables from your shell 
are propagated to your script after being modified by your .tcshrc, and 
then passed to the perl script. You may get some ideas here 
http://hell.org.ua/Docs/oreilly/perl2/prog/ch19_02.htm


If you haven't got a normal system, finding out how it works is not 
really a problem for the GROMACS mailing list :-)


Mark


Second, here comes the real bad news: Lots of erros.

Without MPI, in single precision, 4 complex and 16 kernel tests fail.

Without MPI, but in double precision, "just" the 16 kernel tests fail.

With MPI, in single precision, it fails on 1 simple, 9 complex and 16 
kernel tests!


And with MPI and double precision, 1 simple, 7 complex and 16 kernel 
tests fails. :P


Edit: Just received your message. Well, it seems that I've done a 
mistake on my script, but since at least part of the tests worked, it 
means that it's not the MPI that is, at least, missconfigured.


I will look deeper into the erros above, and tell you later.

Thanks a lot,

Jones

On Mon, May 11, 2009 at 9:41 PM, Jones de Andrade > wrote:


Hi Justin.

Thanks a lot for that. It helped, but enough yet. :(  Just made
4.0.4 tests reach the same "range of errors" that I'm getting with
3.3.3. :P

Using openMPI, it just complains that it can't find orted. That
would mean that the paths are not in there, BUT they are. :P If I
just try to run orted from the command line without any arguments:

*
/gmxtest404 196% orted
[palpatine:28366] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in
file runtime/orte_init.c at line 125
--
It looks like orte_init failed for some reason; your parallel process is
likely to abort.  There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems.  This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):

  orte_ess_base_select failed
  --> Returned value Not found (-13) instead of ORTE_SUCCESS
--
[palpatine:28366] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in
file orted/orted_main.c at line 323
/*

So, the shell IS finding the file. But when I do it not from the
script anymore (I was already thinking in something on the
"it-else-end" stack), all mpi tests fail with the following message
on mdrun.out file:

**
/orted: Command not found.
--
A daemon (pid 27972) died unexpectedly with status 1 while attempting
to launch so we are aborting.

There may be more information reported by the environment (see above).

This may be because the daemon was unable to find all the needed shared
libraries on the remote node. You may set your LD_LIBRARY_PATH to
have the
location of the shared libraries on the remote nodes and this will
automatically be forwarded to the remote nodes.
--
--
mpirun noticed that the job aborted, but has no info as to the process
that caused that situation.
--
mpirun: clean termination accomplished
/**

What is going on? Next thing I think about doing is to execute a
full command line from one of the tests directly, to see that it
works...  :(  :P

Now I'm absolutelly lost. Any ideas, please?

Thanks a lot,

Jones


On Mon, May 11, 2009 at 9:07 PM, Justin A

[gmx-users] Coordinate covalent bond

[Zhanglin Ni]

Dear all,
In pdb file. the metal ion form a coordinate covalent bond with SG of 
cystine. but seems pdb2gmx ignored CONNECT in pdb file. how to modify 
the .top or .itp to include the bond and parameterize the bond. I tried 
to find some tutorial for some special case like this. But I couldnot. 
Could someone provide the knowledge or source to learn it. Thanks

Johnny

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[gmx-users] Re: Problem with protein in lipid bilayer simulation

[Anirban Ghosh]

Hello Justin,

Thanks a lot for the reply. Your tutorial is indeed very good.
I followed your
tutorial on protein-lipid simulation. I added the non-bonded parameters
from the lipid.itp file to the ffG53a6nb_lipid.itp file. You have told
to either delete the atom-type HW entries having zero values in the
non-bonded section or replace them with H. But the HW values are not
zero. And they are also present in the "pairlist" section. So should I
change in this section also? And when I am running the grompp command I
am getting the error "Atom-type OW not found". So should I also delete
the OW entries or should I replace them? If replace, then with what?
Should I replace all the OW and HW entries throughout the
ffG53a6nb_lipid.itp file? Please advice.

Regards,

 Anirban GhoshGrade Based Engineer
Bioinformatics Team
Centre for Development of Advanced Computing (C-DAC)
Pune, India



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[gmx-users] protein falls apart in energy minimization

[Zhong Zheng]

hi all

I am running Gromacs on a protein consisted of three chains. But no  
matter how I tried, the protein always falls into three parts  
(corresponding to each chain) after a simple 2000 steps energy  
minimization. Can anyone help me please? Thanks.


Zhong Zheng
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Re: [gmx-users] TestBed in MPI not working

[Jones de Andrade]

Hi Justin.

On Mon, May 11, 2009 at 11:10 PM, Justin A. Lemkul  wrote:

>  All of the above can be fixed by changing the appropriate .mdp option.


Yes, I agree. I'll try that. Probably that's what will solve that problem.
If that's ok, I'll send to the site a "revised" version of the test set. :)


> Known issue:
>
> http://bugzilla.gromacs.org/show_bug.cgi?id=313
>

Ok, this one I would never expect coming. Since 1-4 nonbonded interations
are pretty important (specially) on our studies here, does this error means
that I should get back to 4.0.3 version (which is reported to NOT yeld those
errors), or perharps even back to 3.3.3?


> Someone else just experienced this problem as well.  Probably needs to be
> looked into.  Look into thee contents of checkpot.out and checkvir.out to
> see if the results are similar to:
>
> http://www.gromacs.org/pipermail/gmx-users/2009-May/041696.html
>
> The problem there appeared to be a missing energy term (Vir-XX).


Again here: how to deal with this issue? Go back one revision in gromacs for
now, and report to bugzilla with all files this one? :)

Thanks a lot for all help. Looking forward for your answer.

Jones
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Re: [gmx-users] TestBed in MPI not working

[Justin A. Lemkul]

Jones de Andrade wrote:

Ok, summary of errors begin here.

First, errors with MPI in double precision:

1 Simple Test:
bham: ns type Simple is not supported with domain decomposition, use 
particle decomposition: mdrun -pd


7 Complex Tests:
acetonitrilRF: ns type Simple is not supported with domain 
decomposition, use particle decomposition: mdrun -pd
aminoacids: ns type Simple is not supported with domain decomposition, 
use particle decomposition: mdrun -pd
argon: ns type Simple is not supported with domain decomposition, use 
particle decomposition: mdrun -pd
sw: ns type Simple is not supported with domain decomposition, use 
particle decomposition: mdrun -pd
tip4p: ns type Simple is not supported with domain decomposition, use 
particle decomposition: mdrun -pd
urea: ns type Simple is not supported with domain decomposition, use 
particle decomposition: mdrun -pd
water: ns type Simple is not supported with domain decomposition, use 
particle decomposition: mdrun -pd




All of the above can be fixed by changing the appropriate .mdp option.

16 Kernel Tests: 0 computation time. Something gone REALLY bad on 
those...  :(




Known issue:

http://bugzilla.gromacs.org/show_bug.cgi?id=313

Except for the kernel tests, (seems that) in all I'm getting that same 
error message (still looking at it). Are those expected to appear? And 
the kernel ones? Am I wrong, or that means compilation problems 
(specially because they appear in all tests, single and double 
precision, with and withou MPI).


Also getting error in serial in single precision in 4 complex tests. 
Those seems to have run, but yelded wrong results?




Someone else just experienced this problem as well.  Probably needs to be looked 
into.  Look into thee contents of checkpot.out and checkvir.out to see if the 
results are similar to:


http://www.gromacs.org/pipermail/gmx-users/2009-May/041696.html

The problem there appeared to be a missing energy term (Vir-XX).

-Justin

Does anybody has any clue, please? Shall I go straight to recompilation, 
despite there is no reason for failure here?


Thanks a lot!

Jones

On Mon, May 11, 2009 at 10:42 PM, Jones de Andrade > wrote:


Hi Justin.

Well, bothering again. Good and bad news.

The good news: I found a strange "work-around" for my problems here.
For some reason, the perl script updates the path, environments and
everything else when runs. So, the variables I placed on the script
I was using where simply lost. Workaround here was, then, to just
include those in the .tcshrc file and log again.

The problem is that it's not pratical. I'm trying a lot of different
MPIs and libraries compilations, and having to edit that file, and
or logou/login or source it, is not pratical at all. Is there any
other way, so that the perl script will be happy with the variables
it has when its called, instead of initializing all them again?

Second, here comes the real bad news: Lots of erros.

Without MPI, in single precision, 4 complex and 16 kernel tests fail.

Without MPI, but in double precision, "just" the 16 kernel tests fail.

With MPI, in single precision, it fails on 1 simple, 9 complex and
16 kernel tests!

And with MPI and double precision, 1 simple, 7 complex and 16 kernel
tests fails. :P

Edit: Just received your message. Well, it seems that I've done a
mistake on my script, but since at least part of the tests worked,
it means that it's not the MPI that is, at least, missconfigured.

I will look deeper into the erros above, and tell you later.

Thanks a lot,

Jones


On Mon, May 11, 2009 at 9:41 PM, Jones de Andrade
mailto:johanne...@gmail.com>> wrote:

Hi Justin.

Thanks a lot for that. It helped, but enough yet. :(  Just made
4.0.4 tests reach the same "range of errors" that I'm getting
with 3.3.3. :P

Using openMPI, it just complains that it can't find orted. That
would mean that the paths are not in there, BUT they are. :P If
I just try to run orted from the command line without any arguments:

*
/gmxtest404 196% orted
[palpatine:28366] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found
in file runtime/orte_init.c at line 125

--
It looks like orte_init failed for some reason; your parallel
process is
likely to abort.  There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems.  This failure appears to be an internal
failure;
here's some additional information (which may only be relevant to an
Open MPI developer):

  orte_ess_base_select failed
  --> Returned value Not found (-13) instead of ORTE_SUCCESS

--

Re: [gmx-users] TestBed in MPI not working

[Jones de Andrade]

Ok, summary of errors begin here.

First, errors with MPI in double precision:

1 Simple Test:
bham: ns type Simple is not supported with domain decomposition, use
particle decomposition: mdrun -pd

7 Complex Tests:
acetonitrilRF: ns type Simple is not supported with domain decomposition,
use particle decomposition: mdrun -pd
aminoacids: ns type Simple is not supported with domain decomposition, use
particle decomposition: mdrun -pd
argon: ns type Simple is not supported with domain decomposition, use
particle decomposition: mdrun -pd
sw: ns type Simple is not supported with domain decomposition, use particle
decomposition: mdrun -pd
tip4p: ns type Simple is not supported with domain decomposition, use
particle decomposition: mdrun -pd
urea: ns type Simple is not supported with domain decomposition, use
particle decomposition: mdrun -pd
water: ns type Simple is not supported with domain decomposition, use
particle decomposition: mdrun -pd

16 Kernel Tests: 0 computation time. Something gone REALLY bad on those...
:(

Except for the kernel tests, (seems that) in all I'm getting that same error
message (still looking at it). Are those expected to appear? And the kernel
ones? Am I wrong, or that means compilation problems (specially because they
appear in all tests, single and double precision, with and withou MPI).

Also getting error in serial in single precision in 4 complex tests. Those
seems to have run, but yelded wrong results?

Does anybody has any clue, please? Shall I go straight to recompilation,
despite there is no reason for failure here?

Thanks a lot!

Jones

On Mon, May 11, 2009 at 10:42 PM, Jones de Andrade wrote:

> Hi Justin.
>
> Well, bothering again. Good and bad news.
>
> The good news: I found a strange "work-around" for my problems here. For
> some reason, the perl script updates the path, environments and everything
> else when runs. So, the variables I placed on the script I was using where
> simply lost. Workaround here was, then, to just include those in the .tcshrc
> file and log again.
>
> The problem is that it's not pratical. I'm trying a lot of different MPIs
> and libraries compilations, and having to edit that file, and or logou/login
> or source it, is not pratical at all. Is there any other way, so that the
> perl script will be happy with the variables it has when its called, instead
> of initializing all them again?
>
> Second, here comes the real bad news: Lots of erros.
>
> Without MPI, in single precision, 4 complex and 16 kernel tests fail.
>
> Without MPI, but in double precision, "just" the 16 kernel tests fail.
>
> With MPI, in single precision, it fails on 1 simple, 9 complex and 16
> kernel tests!
>
> And with MPI and double precision, 1 simple, 7 complex and 16 kernel tests
> fails. :P
>
> Edit: Just received your message. Well, it seems that I've done a mistake
> on my script, but since at least part of the tests worked, it means that
> it's not the MPI that is, at least, missconfigured.
>
> I will look deeper into the erros above, and tell you later.
>
> Thanks a lot,
>
> Jones
>
>
> On Mon, May 11, 2009 at 9:41 PM, Jones de Andrade wrote:
>
>> Hi Justin.
>>
>> Thanks a lot for that. It helped, but enough yet. :(  Just made 4.0.4
>> tests reach the same "range of errors" that I'm getting with 3.3.3. :P
>>
>> Using openMPI, it just complains that it can't find orted. That would mean
>> that the paths are not in there, BUT they are. :P If I just try to run orted
>> from the command line without any arguments:
>>
>> *
>> *gmxtest404 196% orted
>> [palpatine:28366] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file
>> runtime/orte_init.c at line 125
>> --
>> It looks like orte_init failed for some reason; your parallel process is
>> likely to abort.  There are many reasons that a parallel process can
>> fail during orte_init; some of which are due to configuration or
>> environment problems.  This failure appears to be an internal failure;
>> here's some additional information (which may only be relevant to an
>> Open MPI developer):
>>
>>   orte_ess_base_select failed
>>   --> Returned value Not found (-13) instead of ORTE_SUCCESS
>> --
>> [palpatine:28366] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file
>> orted/orted_main.c at line 323
>> **
>>
>> So, the shell IS finding the file. But when I do it not from the script
>> anymore (I was already thinking in something on the "it-else-end" stack),
>> all mpi tests fail with the following message on mdrun.out file:
>>
>> **
>> *orted: Command not found.
>> --
>> A daemon (pid 27972) died unexpectedly with status 1 while attempting
>> to launch so we are aborting.
>>
>> There may be more information reported by the environment (see above).
>>
>

Re: [gmx-users] how to use atom2cg.awk

[Justin A. Lemkul]

I have discovered two other potential errors in the script:

1. Coordinates are not processed quite right; this leads to a molecule with the 
correct shape, but some residues are scrambled.

2. ILE residues are not handled correctly (only a backbone particle is 
generated)

I modified the script, and it is working in my own internal tests.  I would 
suggest using the script below.


-Justin

---

#!/usr/bin/awk -f
#Converts Atomic PDB file to Coarse-grain PDB file
#The atom types are default values - BN0, SC1, SC2
#Should be corrected by using correct itp file
#if columns are not separate (e.g. x or y or z > 99) the script doesnt work
#in that case insert an empty column or use PDBCat to separate columns
#d! groningen   29.01.08

{if 
($1=="HEADER"||$1=="REMARK"||$1=="CRYST1"||$1=="MODEL"||$1=="TER"||$1=="ENDMDL"||$1=="END")

print $0
if($1=="ATOM" && $4=="ARG" && $3=="CA")
printf("%4s  %5i %4s %3s  %4i%8.3f%8.3f%8.3f%6.2f%6.2f\n",$1, $2, "BN0", 
$4, $5, $6, $7, $8, $9,$10,$11);

else if($1=="ATOM" && $4=="ARG" && $3=="CG")
printf("%4s  %5i %4s %3s  %4i%8.3f%8.3f%8.3f%6.2f%6.2f\n",$1, $2, "SC1", 
$4, $5, $6, $7, $8, $9,$10,$11);

else if($1=="ATOM" && $4=="ARG" && $3=="NE")
printf("%4s  %5i %4s %3s  %4i%8.3f%8.3f%8.3f%6.2f%6.2f\n",$1, $2, "SC2", 
$4, $5, $6, $7, $8, $9,$10,$11);

else if ($1=="ATOM" && $4=="ALA" && $3=="CA")
printf("%4s  %5i %4s %3s  %4i%8.3f%8.3f%8.3f%6.2f%6.2f\n",$1, $2, "BN0", 
$4, $5, $6, $7, $8, $9,$10,$11);

else if ($1=="ATOM" && $4=="ASN" && $3=="CA" )
printf("%4s  %5i %4s %3s  %4i%8.3f%8.3f%8.3f%6.2f%6.2f\n",$1, $2, "BN0", 
$4, $5, $6, $7, $8, $9,$10,$11);

else if ($1=="ATOM" && $4=="ASN" && $3=="CG")
printf("%4s  %5i %4s %3s  %4i%8.3f%8.3f%8.3f%6.2f%6.2f\n",$1, $2, "SC1", 
$4, $5, $6, $7, $8, $9,$10,$11);

else if ($1=="ATOM" && $4=="ASP" && $3=="CA")
printf("%4s  %5i %4s %3s  %4i%8.3f%8.3f%8.3f%6.2f%6.2f\n",$1, $2, "BN0", 
$4, $5, $6, $7, $8, $9,$10,$11);

else if ($1=="ATOM" && $4=="ASP" && $3=="CG")
printf("%4s  %5i %4s %3s  %4i%8.3f%8.3f%8.3f%6.2f%6.2f\n",$1, $2, "SC1", 
$4, $5, $6, $7, $8, $9,$10,$11);

else if ($1=="ATOM" && $4=="CYS" && $3=="CA")
printf("%4s  %5i %4s %3s  %4i%8.3f%8.3f%8.3f%6.2f%6.2f\n",$1, $2, "BN0", 
$4, $5, $6, $7, $8, $9,$10,$11);

else if ($1=="ATOM" && $4=="CYS" && $3=="SG")
printf("%4s  %5i %4s %3s  %4i%8.3f%8.3f%8.3f%6.2f%6.2f\n",$1, $2, "SC1", 
$4, $5, $6, $7, $8, $9,$10,$11);

else if ($1=="ATOM" && $4=="GLN" && $3=="CA" )
printf("%4s  %5i %4s %3s  %4i%8.3f%8.3f%8.3f%6.2f%6.2f\n",$1, $2, "BN0", 
$4, $5, $6, $7, $8, $9,$10,$11);

else if ($1=="ATOM" && $4=="GLN" && $3=="CB")
printf("%4s  %5i %4s %3s  %4i%8.3f%8.3f%8.3f%6.2f%6.2f\n",$1, $2, "SC1", 
$4, $5, $6, $7, $8, $9,$10,$11);

else if ($1=="ATOM" && $4=="GLU" && $3=="CA")
printf("%4s  %5i %4s %3s  %4i%8.3f%8.3f%8.3f%6.2f%6.2f\n",$1, $2, "BN0", 
$4, $5, $6, $7, $8, $9,$10,$11);

else if ($1=="ATOM" && $4=="GLU" && $3=="CB")
printf("%4s  %5i %4s %3s  %4i%8.3f%8.3f%8.3f%6.2f%6.2f\n",$1, $2, "SC1", 
$4, $5, $6, $7, $8, $9,$10,$11);

else if ($1=="ATOM" && $4=="GLY" && $3=="CA")
printf("%4s  %5i %4s %3s  %4i%8.3f%8.3f%8.3f%6.2f%6.2f\n",$1, $2, "BN0", 
$4, $5, $6, $7, $8, $9,$10,$11);

else if ($1=="ATOM" && $4=="HIS" && $3=="CA")
printf("%4s  %5i %4s %3s  %4i%8.3f%8.3f%8.3f%6.2f%6.2f\n",$1, $2, "BN0", 
$4, $5, $6, $7, $8, $9,$10,$11);

else if ($1=="ATOM" && $4=="HIS" && $3=="CB")
printf("%4s  %5i %4s %3s  %4i%8.3f%8.3f%8.3f%6.2f%6.2f\n",$1, $2, "SC1", 
$4, $5, $6, $7, $8, $9,$10,$11);

else if ($1=="ATOM" && $4=="HIS" && $3=="ND1")
printf("%4s  %5i %4s %3s  %4i%8.3f%8.3f%8.3f%6.2f%6.2f\n",$1, $2, "SC2", 
$4, $5, $6, $7, $8, $9,$10,$11);

else if ($1=="ATOM" && $4=="HIS" && $3=="NE2")
printf("%4s  %5i %4s %3s  %4i%8.3f%8.3f%8.3f%6.2f%6.2f\n",$1, $2, "SC3", 
$4, $5, $6, $7, $8, $9,$10,$11);

else if ($1=="ATOM" && $4=="ILE" && $3=="CA")
printf("%4s  %5i %4s %3s  %4i%8.3f%8.3f%8.3f%6.2f%6.2f\n",$1, $2, "BN0", 
$4, $5, $6, $7, $8, $9,$10,$11);

else if ($1=="ATOM" && $4=="ILE" && ($3=="CD" || $3=="CD1"))
printf("%4s  %5i %4s %3s  %4i%8.3f%8.3f%8.3f%6.2f%6.2f\n",$1, $2, "SC1", 
$4, $5, $6, $7, $8, $9,$10,$11);

else if ($1=="ATOM" && $4=="LEU" && $3=="CA" )
printf("%4s  %5i %4s %3s  %4i%8.3f%8.3f%8.3f%6.2f%6.2f\n",$1, $2, "BN0", 
$4, $5, $6, $7, $8, $9,$10,$11);

else if ($1=="ATOM" && $4=="LEU" && $3=="CG")
printf("%4s  %5i %4s %3s  %4i%8.3f%8.3f%8.3f%6.2f%6.2f\n",$1, $2, "SC1", 
$4, $5, $6, $7, $8, $9,$10,$11);

else if ($1=="ATOM" && $4=="LYS" && $3=="CA")
printf("%4s  %5i %4s %3s  %4i%8.3f%8.3f%8.3f%6.2f%6.2f\n",$1, $2, "BN0", 
$4, $5, $6, $7, $8, $9,$10,$11);

else if ($1=="ATOM" && $4=="LYS" && $3=="CG")
printf("%4s  %5i %4s %3s  %4i%8.3f%8.3f%8.3f%6.2f%6.2f\n",$1, $2, "SC1", 
$4, $5, $6, $7, $8, $9,$10,$11);

else if ($1=="ATOM" && $4=="LYS" && $3=="CE")
printf("%4s  %5i %4s %3s  %4i%8.3f

Re: [gmx-users] TestBed in MPI not working

[Jones de Andrade]

Hi Justin.

Well, bothering again. Good and bad news.

The good news: I found a strange "work-around" for my problems here. For
some reason, the perl script updates the path, environments and everything
else when runs. So, the variables I placed on the script I was using where
simply lost. Workaround here was, then, to just include those in the .tcshrc
file and log again.

The problem is that it's not pratical. I'm trying a lot of different MPIs
and libraries compilations, and having to edit that file, and or logou/login
or source it, is not pratical at all. Is there any other way, so that the
perl script will be happy with the variables it has when its called, instead
of initializing all them again?

Second, here comes the real bad news: Lots of erros.

Without MPI, in single precision, 4 complex and 16 kernel tests fail.

Without MPI, but in double precision, "just" the 16 kernel tests fail.

With MPI, in single precision, it fails on 1 simple, 9 complex and 16 kernel
tests!

And with MPI and double precision, 1 simple, 7 complex and 16 kernel tests
fails. :P

Edit: Just received your message. Well, it seems that I've done a mistake on
my script, but since at least part of the tests worked, it means that it's
not the MPI that is, at least, missconfigured.

I will look deeper into the erros above, and tell you later.

Thanks a lot,

Jones

On Mon, May 11, 2009 at 9:41 PM, Jones de Andrade wrote:

> Hi Justin.
>
> Thanks a lot for that. It helped, but enough yet. :(  Just made 4.0.4 tests
> reach the same "range of errors" that I'm getting with 3.3.3. :P
>
> Using openMPI, it just complains that it can't find orted. That would mean
> that the paths are not in there, BUT they are. :P If I just try to run orted
> from the command line without any arguments:
>
> *
> *gmxtest404 196% orted
> [palpatine:28366] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file
> runtime/orte_init.c at line 125
> --
> It looks like orte_init failed for some reason; your parallel process is
> likely to abort.  There are many reasons that a parallel process can
> fail during orte_init; some of which are due to configuration or
> environment problems.  This failure appears to be an internal failure;
> here's some additional information (which may only be relevant to an
> Open MPI developer):
>
>   orte_ess_base_select failed
>   --> Returned value Not found (-13) instead of ORTE_SUCCESS
> --
> [palpatine:28366] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file
> orted/orted_main.c at line 323
> **
>
> So, the shell IS finding the file. But when I do it not from the script
> anymore (I was already thinking in something on the "it-else-end" stack),
> all mpi tests fail with the following message on mdrun.out file:
>
> **
> *orted: Command not found.
> --
> A daemon (pid 27972) died unexpectedly with status 1 while attempting
> to launch so we are aborting.
>
> There may be more information reported by the environment (see above).
>
> This may be because the daemon was unable to find all the needed shared
> libraries on the remote node. You may set your LD_LIBRARY_PATH to have the
> location of the shared libraries on the remote nodes and this will
> automatically be forwarded to the remote nodes.
> --
> --
> mpirun noticed that the job aborted, but has no info as to the process
> that caused that situation.
> --
> mpirun: clean termination accomplished
> ***
>
> What is going on? Next thing I think about doing is to execute a full
> command line from one of the tests directly, to see that it works...  :(  :P
>
> Now I'm absolutelly lost. Any ideas, please?
>
> Thanks a lot,
>
> Jones
>
>
> On Mon, May 11, 2009 at 9:07 PM, Justin A. Lemkul  wrote:
>
>>
>>
>> Justin A. Lemkul wrote:
>>
>>>
>>>
>>> Jones de Andrade wrote:
>>>
 Hi Justin

This has been discussed several times on the list.  The -np flag is
no longer necessary with grompp.  You don't get an mdrun.out because
the .tpr file is likely never created, since grompp fails.


 Yes, I know that and that is what I would have expected. But what I'm
 running is the gmxtest.pl script. Even using the 4.0.4 version, it explicit
 states that I must use "-np N" to make parallel works on its own command
 line.

 
 gmxtest.pl
 Usage: ./gmxtest.pl [ -np N ] [-verbose ] [ -double ] [ simple | complex
 | kernel | pdb2gmx | all ]
   or: ./gmxtest.pl clean | refclean | dist
 

 I w

Re: [gmx-users] TestBed in MPI not working

[Mark Abraham]

Jones de Andrade wrote:

Hi Justin.

Thanks a lot for that. It helped, but enough yet. :(  Just made 4.0.4 
tests reach the same "range of errors" that I'm getting with 3.3.3. :P


Using openMPI, it just complains that it can't find orted. That would 
mean that the paths are not in there, BUT they are. :P If I just try to 
run orted from the command line without any arguments:


*
/gmxtest404 196% orted
[palpatine:28366] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file 
runtime/orte_init.c at line 125

--
It looks like orte_init failed for some reason; your parallel process is
likely to abort.  There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems.  This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):

  orte_ess_base_select failed
  --> Returned value Not found (-13) instead of ORTE_SUCCESS
--
[palpatine:28366] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file 
orted/orted_main.c at line 323

/*

So, the shell IS finding the file.


True, but you have a deeper problem that has nothing to do with GROMACS 
or the shell. You need to get your MPI environment working properly 
first. Read its documentation, test and troubleshoot there. Ask its 
mailing list if you can't work it out.


But when I do it not from the script 
anymore (I was already thinking in something on the "it-else-end" 
stack), all mpi tests fail with the following message on mdrun.out file:


**
/orted: Command not found.
--
A daemon (pid 27972) died unexpectedly with status 1 while attempting
to launch so we are aborting.

There may be more information reported by the environment (see above).

This may be because the daemon was unable to find all the needed shared
libraries on the remote node. You may set your LD_LIBRARY_PATH to have the
location of the shared libraries on the remote nodes and this will
automatically be forwarded to the remote nodes.
--
--
mpirun noticed that the job aborted, but has no info as to the process
that caused that situation.
--
mpirun: clean termination accomplished
/**

What is going on? 


Your environment inside your shell is different from your environment 
inside the gmxtest.pl script. If you're running under a queueing system, 
get the environment variables exported to the script. If you're using 
the script you were using earlier, then perhaps you need to learn about 
setting environment variables under different shells. I don't recall 
whether variable names are case-sensitive, but your "set path=(blah)" 
simply won't do the job. Only environment variables get exported to 
child processes (i.e. the gmxtest.pl you spawn later), so you need 
"setenv PATH blah". Under bash, use "export PATH=blah" not "PATH=blah".


Otherwise, change the script to dump the contents of the enviroment PATH 
variable (e.g. print STDERR "$env{'PATH'}\n";) to see if those contents 
clue you in to what is happening.


Next thing I think about doing is to execute a full 
command line from one of the tests directly, to see that it works...  :(  :P


Won't work, because MPI is broken.

Mark
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Re: [gmx-users] TestBed in MPI not working

[Jones de Andrade]

Hi Justin.

Thanks a lot for that. It helped, but enough yet. :(  Just made 4.0.4 tests
reach the same "range of errors" that I'm getting with 3.3.3. :P

Using openMPI, it just complains that it can't find orted. That would mean
that the paths are not in there, BUT they are. :P If I just try to run orted
from the command line without any arguments:

*
*gmxtest404 196% orted
[palpatine:28366] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file
runtime/orte_init.c at line 125
--
It looks like orte_init failed for some reason; your parallel process is
likely to abort.  There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems.  This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):

  orte_ess_base_select failed
  --> Returned value Not found (-13) instead of ORTE_SUCCESS
--
[palpatine:28366] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file
orted/orted_main.c at line 323
**

So, the shell IS finding the file. But when I do it not from the script
anymore (I was already thinking in something on the "it-else-end" stack),
all mpi tests fail with the following message on mdrun.out file:

**
*orted: Command not found.
--
A daemon (pid 27972) died unexpectedly with status 1 while attempting
to launch so we are aborting.

There may be more information reported by the environment (see above).

This may be because the daemon was unable to find all the needed shared
libraries on the remote node. You may set your LD_LIBRARY_PATH to have the
location of the shared libraries on the remote nodes and this will
automatically be forwarded to the remote nodes.
--
--
mpirun noticed that the job aborted, but has no info as to the process
that caused that situation.
--
mpirun: clean termination accomplished
***

What is going on? Next thing I think about doing is to execute a full
command line from one of the tests directly, to see that it works...  :(  :P

Now I'm absolutelly lost. Any ideas, please?

Thanks a lot,

Jones

On Mon, May 11, 2009 at 9:07 PM, Justin A. Lemkul  wrote:

>
>
> Justin A. Lemkul wrote:
>
>>
>>
>> Jones de Andrade wrote:
>>
>>> Hi Justin
>>>
>>>This has been discussed several times on the list.  The -np flag is
>>>no longer necessary with grompp.  You don't get an mdrun.out because
>>>the .tpr file is likely never created, since grompp fails.
>>>
>>>
>>> Yes, I know that and that is what I would have expected. But what I'm
>>> running is the gmxtest.pl script. Even using the 4.0.4 version, it explicit
>>> states that I must use "-np N" to make parallel works on its own command
>>> line.
>>>
>>> 
>>> gmxtest.pl
>>> Usage: ./gmxtest.pl [ -np N ] [-verbose ] [ -double ] [ simple | complex
>>> | kernel | pdb2gmx | all ]
>>>   or: ./gmxtest.pl clean | refclean | dist
>>> 
>>>
>>> I would expect that the script would use it only for mdrun and not for
>>> grompp, but it seems to try to use on both. What becomes really strange it
>>> the testbed really works. So, gmxtest.pl has a bug on 4.0.4? Or how should I
>>> really tell gmxtest.pl to test in a growing number of cores?
>>>
>>>
>>
>> Ah, sorry for the mis-read :)  There is a simple fix that you can apply to
>> the gmxtest.pl script:
>>
>> % diff gmxtest.pl gmxtest_orig.pl
>> 161c161
>> < system("$grompp -maxwarn 10 $ndx > grompp.out 2>&1");
>> ---
>>  > system("$grompp -maxwarn 10 $ndx $par > grompp.out 2>&1");
>>
>> -Justin
>>
>>
>>>
>>>Version 3.3.3 on the other hand already failed in so many
>>>different places that I'm really thinking IF I'll make it
>>>available in the new cluster. :P
>>>
>>>
>>>What messages are you getting from 3.3.3?  I thought you said the
>>>3.3.x series worked fine.
>>>
>>>
>>> I'll login for those and try to get any reproducible error here. ;) As
>>> soon as I have these, I post back in this thread.
>>>
>>> Thanks a lot again,
>>>
>>> Jones
>>>
>>
>>
> --
> 
>
> 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://www.gromacs.org/mailman

Re: [gmx-users] TestBed in MPI not working

[Justin A. Lemkul]

Justin A. Lemkul wrote:



Jones de Andrade wrote:

Hi Justin

This has been discussed several times on the list.  The -np flag is
no longer necessary with grompp.  You don't get an mdrun.out because
the .tpr file is likely never created, since grompp fails.


Yes, I know that and that is what I would have expected. But what I'm 
running is the gmxtest.pl script. Even using the 4.0.4 version, it 
explicit states that I must use "-np N" to make parallel works on its 
own command line.



gmxtest.pl
Usage: ./gmxtest.pl [ -np N ] [-verbose ] [ -double ] [ simple | 
complex | kernel | pdb2gmx | all ]

   or: ./gmxtest.pl clean | refclean | dist


I would expect that the script would use it only for mdrun and not for 
grompp, but it seems to try to use on both. What becomes really 
strange it the testbed really works. So, gmxtest.pl has a bug on 
4.0.4? Or how should I really tell gmxtest.pl to test in a growing 
number of cores?
 



Ah, sorry for the mis-read :)  There is a simple fix that you can apply 
to the gmxtest.pl script:


% diff gmxtest.pl gmxtest_orig.pl
161c161
< system("$grompp -maxwarn 10 $ndx > grompp.out 2>&1");
---
 > system("$grompp -maxwarn 10 $ndx $par > grompp.out 2>&1");

-Justin




Version 3.3.3 on the other hand already failed in so many
different places that I'm really thinking IF I'll make it
available in the new cluster. :P


What messages are you getting from 3.3.3?  I thought you said the
3.3.x series worked fine.


I'll login for those and try to get any reproducible error here. ;) As 
soon as I have these, I post back in this thread.


Thanks a lot again,

Jones




--


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] TestBed in MPI not working

[Jones de Andrade]

Hi Justin

This has been discussed several times on the list.  The -np flag is no
> longer necessary with grompp.  You don't get an mdrun.out because the .tpr
> file is likely never created, since grompp fails.


Yes, I know that and that is what I would have expected. But what I'm
running is the gmxtest.pl script. Even using the 4.0.4 version, it explicit
states that I must use "-np N" to make parallel works on its own command
line.


gmxtest.pl
Usage: ./gmxtest.pl [ -np N ] [-verbose ] [ -double ] [ simple | complex |
kernel | pdb2gmx | all ]
   or: ./gmxtest.pl clean | refclean | dist


I would expect that the script would use it only for mdrun and not for
grompp, but it seems to try to use on both. What becomes really strange it
the testbed really works. So, gmxtest.pl has a bug on 4.0.4? Or how should I
really tell gmxtest.pl to test in a growing number of cores?


>
>
>  Version 3.3.3 on the other hand already failed in so many different places
>> that I'm really thinking IF I'll make it available in the new cluster. :P
>>
>>
> What messages are you getting from 3.3.3?  I thought you said the 3.3.x
> series worked fine.


I'll login for those and try to get any reproducible error here. ;) As soon
as I have these, I post back in this thread.

Thanks a lot again,

Jones
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Re: [gmx-users] TestBed in MPI not working

[Justin A. Lemkul]

Jones de Andrade wrote:



Using just the "simple" tests now to try to find out where is the error. 
Since the error goes everywhere, it just simplify things.
It outputs everything ok with the serial part, but it all gets really 
messy in the mpi section.


In version 4.0.4, it's complaining that the grompp is not understanding 
the "-np" flag (Invalid command line argument). Then, it doesn't even 
create a mdrun.out file. I tried to google this error, but basically 
nothing was found. It also can't be a mixing of compilations, since 
everything is done in completelly different and independent directories.




This has been discussed several times on the list.  The -np flag is no longer 
necessary with grompp.  You don't get an mdrun.out because the .tpr file is 
likely never created, since grompp fails.


Version 3.3.3 on the other hand already failed in so many different 
places that I'm really thinking IF I'll make it available in the new 
cluster. :P




What messages are you getting from 3.3.3?  I thought you said the 3.3.x series 
worked fine.


-Justin

This has to be any sort of pretty stupid mistake so. But I'm clueless 
this time. :( Any ideas?


Thanks a lot in advance! :)

Jones

On Mon, May 11, 2009 at 7:53 PM, Justin A. Lemkul > wrote:




Jones de Andrade wrote:

Hi everyone.

Well, lets go straight to the point: last time I've installed
gromacs, it was still 3.3.x and there was no testbed available
yet. I've done some tests of my own and everything gone fine.

I'm doing some new installations now, both gmx3.3.3 and
gmx4.0.4. They weem to work pretty well in serial, but
absolutelly not with mpi. A whole "plethora" of different errors
appear.

Before bothering the list with error messages, my question is:
someone has successfully used it with OpenMPI or MPIch? Before
questions arise, I have different test users for each, and
absolutelly independent compilations.


Every installation (serial and MPI) that I have installed worked
flawlessly. Our cluster uses mpich, and our local machines
(dual-core) use OpenMPI.

Can you provide some of the error messages?  Are the reported from
Gromacs, or from the MPI implementations?

-Justin

Thanks a lot for any answer in advance.

Sincerally yours,

Jones




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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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--


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] TestBed in MPI not working

[Jones de Andrade]

Thanks Justin. ;)

Well, I'm using a simple script to run the tests. The script follows:

**
#!/bin/tcsh
source ../../tcshrc
source /opt/chemistry/gmx404.ompi/bin/GMXRC.csh
set path=( $path /opt/mpi/ompi131/bin )
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/opt/mpi/ompi131/lib

set NCPUS = 2

set i = 1
while ($i <= $NCPUS)
  if ($i == 1) then
echo Single Precision Tests:
./gmxtest.pl simple #all
./gmxtest.pl clean >& /dev/null
echo Double Precision Tests:
./gmxtest.pl -double simple #all
./gmxtest.pl clean >& /dev/null
  else
echo Single Precision Tests - Parallel in $i
./gmxtest.pl -np $i simple #all
./gmxtest.pl clean >& /dev/null
echo Double Precision Tests - Parallel in $i
./gmxtest.pl -np $i -double simple #all
#./gmxtest.pl clean >& /dev/null
  endif
  @ i++
end
**

Using just the "simple" tests now to try to find out where is the error.
Since the error goes everywhere, it just simplify things.
It outputs everything ok with the serial part, but it all gets really messy
in the mpi section.

In version 4.0.4, it's complaining that the grompp is not understanding the
"-np" flag (Invalid command line argument). Then, it doesn't even create a
mdrun.out file. I tried to google this error, but basically nothing was
found. It also can't be a mixing of compilations, since everything is done
in completelly different and independent directories.

Version 3.3.3 on the other hand already failed in so many different places
that I'm really thinking IF I'll make it available in the new cluster. :P

This has to be any sort of pretty stupid mistake so. But I'm clueless this
time. :( Any ideas?

Thanks a lot in advance! :)

Jones

On Mon, May 11, 2009 at 7:53 PM, Justin A. Lemkul  wrote:

>
>
> Jones de Andrade wrote:
>
>> Hi everyone.
>>
>> Well, lets go straight to the point: last time I've installed gromacs, it
>> was still 3.3.x and there was no testbed available yet. I've done some tests
>> of my own and everything gone fine.
>>
>> I'm doing some new installations now, both gmx3.3.3 and gmx4.0.4. They
>> weem to work pretty well in serial, but absolutelly not with mpi. A whole
>> "plethora" of different errors appear.
>>
>> Before bothering the list with error messages, my question is: someone has
>> successfully used it with OpenMPI or MPIch? Before questions arise, I have
>> different test users for each, and absolutelly independent compilations.
>>
>>
> Every installation (serial and MPI) that I have installed worked
> flawlessly. Our cluster uses mpich, and our local machines (dual-core) use
> OpenMPI.
>
> Can you provide some of the error messages?  Are the reported from Gromacs,
> or from the MPI implementations?
>
> -Justin
>
>  Thanks a lot for any answer in advance.
>>
>> Sincerally yours,
>>
>> Jones
>>
>>
>> 
>>
>> ___
>> 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
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>> 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
>
> 
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RE: [gmx-users] Protein-Ligand Docking?

[Dallas B. Warren]

First step, define what you mean by being "DOCKed".

 

Second step, determine if those conditions are meet by your protein and
ligand.

 

Catch ya,

Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only tool you own is a hammer, every problem begins to resemble
a nail. 

From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Chih-Ying Lin
Sent: Tuesday, 12 May 2009 7:37 AM
To: gmx-users@gromacs.org
Subject: [gmx-users] Protein-Ligand Docking?

 

HI
When i visualize the MD trajectory, the protein and ligand are closed
by.
But, I don't know if ligand really DOCK on the protein.

Please tell me how to define the successful docking.
Thank you
Lin

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Re: [gmx-users] TestBed in MPI not working

[Justin A. Lemkul]

Jones de Andrade wrote:

Hi everyone.

Well, lets go straight to the point: last time I've installed gromacs, 
it was still 3.3.x and there was no testbed available yet. I've done 
some tests of my own and everything gone fine.


I'm doing some new installations now, both gmx3.3.3 and gmx4.0.4. They 
weem to work pretty well in serial, but absolutelly not with mpi. A 
whole "plethora" of different errors appear.


Before bothering the list with error messages, my question is: someone 
has successfully used it with OpenMPI or MPIch? Before questions arise, 
I have different test users for each, and absolutelly independent 
compilations.




Every installation (serial and MPI) that I have installed worked flawlessly. 
Our cluster uses mpich, and our local machines (dual-core) use OpenMPI.


Can you provide some of the error messages?  Are the reported from Gromacs, or 
from the MPI implementations?


-Justin


Thanks a lot for any answer in advance.

Sincerally yours,

Jones




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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] TestBed in MPI not working

[Jones de Andrade]

Hi everyone.

Well, lets go straight to the point: last time I've installed gromacs, it
was still 3.3.x and there was no testbed available yet. I've done some tests
of my own and everything gone fine.

I'm doing some new installations now, both gmx3.3.3 and gmx4.0.4. They weem
to work pretty well in serial, but absolutelly not with mpi. A whole
"plethora" of different errors appear.

Before bothering the list with error messages, my question is: someone has
successfully used it with OpenMPI or MPIch? Before questions arise, I have
different test users for each, and absolutelly independent compilations.

Thanks a lot for any answer in advance.

Sincerally yours,

Jones
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Re: [gmx-users] No default Angle types

[Justin A. Lemkul]

darre...@ece.ubc.ca wrote:

Dear All,
I ran grompp and was presented with the following error:
ERROR 0 [file "graphene_nm_test.top", line 51217]:
  No default Angle types

Line 51217 of the topology file is:
 5116 5115 5117 1

and atoms 5115 to 5117 are defined in the topology file as:
  5115 opls_145 1 Grph C 4859 -0.12 12.011 ;
qtot -0.12
  5116 opls_146 1 Grph H 4859 0.06 1.008 ;
qtot -0.06
  5117 opls_146 1 Grph H 4859 0.06 1.008 ;
qtot 0

My assumption is that this error means that there does not exist an
angletype for this threesome of atoms in the ffolpsaabon.itp file.



You are correct.  Take a closer look at the atom types:

opls_145   12.01100  ; Benzene C - 12 site JACS,112,4768-90. Use #145B for 
biphenyl

opls_1461.00800  ; Benzene H - 12 site.

Both atom types correspond to benzene/aromatic sites.  So, in these aromatic 
species, there is no such thing as a ring CH2.


Maybe you want something more like:

opls_136   12.01100  ; alkane CH2

opls_1401.00800  ; alkane H.

-Justin


I looked within the ffoplsaabon.itp file for an entry of the form:
HA CA HA

and, as expected, "pattern not found" was returned as the response.

So, I copied over the ffoplsaabon.itp file to my home (working) directory
and added the following test entry:
  HA CA HA  1   107.000276.000   ; TEST PARAMETERS *
NOT VALID *** ONLY FOR TESTING

I expected that the ERROR O message above would disappear. But the error
was still present. Could you please tell me what I need to do in order
to resolve this error?

Much thanks in advance.

Darrell
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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] RE: RE: RDF in GMX 4 (Justin)

[Justin A. Lemkul]

Eudes Fileti wrote:

Thanks for reply Justin.
I had already read this part of the manual but I can´t understood it well. 
How can I take account the mentioned input file run? Would it be a kind 
of index file? 


http://wiki.gromacs.org/index.php/.tpr_File

http://wiki.gromacs.org/index.php/.ndx_file

-Justin


Could you provide me an example?
Bests
eef
___
Eudes Eterno Fileti
Centro de Ciências Naturais e Humanas
Universidade Federal do ABC — CCNH
Av. dos Estados, 5001
Santo André - SP - Brasil
CEP 09210-971
+55.11.4437-0196
skype: eefileti
http://fileti.ufabc.edu.br




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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] Protein-Ligand Docking?

[Justin A. Lemkul]

Chih-Ying Lin wrote:

HI
When i visualize the MD trajectory, the protein and ligand are closed by.
But, I don't know if ligand really DOCK on the protein.



"Docking" cannot be accomplished by Gromacs.  If you wish to determine whether 
or not your ligand or protein are favorably associated, it is up to you to 
quantify whatever is important in your system (distances, hydrogen bonds, etc).


-Justin


Please tell me how to define the successful docking.
Thank you
Lin




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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] RE: RE: RDF in GMX 4 (Justin)

[Dallas B. Warren]

Run input file = .tpr

 

Catch ya,

Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only tool you own is a hammer, every problem begins to resemble a 
nail. 

From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of Eudes Fileti
Sent: Tuesday, 12 May 2009 6:33 AM
To: gmx-users@gromacs.org
Subject: [gmx-users] RE: RE: RDF in GMX 4 (Justin)

 

Thanks for reply Justin.

I had already read this part of the manual but I can´t understood it well. 

How can I take account the mentioned input file run? Would it be a kind of 
index file? 

Could you provide me an example?

Bests

eef

___
Eudes Eterno Fileti
Centro de Ciências Naturais e Humanas
Universidade Federal do ABC - CCNH
Av. dos Estados, 5001
Santo André - SP - Brasil
CEP 09210-971
+55.11.4437-0196
skype: eefileti
http://fileti.ufabc.edu.br

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[gmx-users] No default Angle types

[darrellk]

Dear All,
I ran grompp and was presented with the following error:
ERROR 0 [file "graphene_nm_test.top", line 51217]:
  No default Angle types

Line 51217 of the topology file is:
 5116 5115 5117 1

and atoms 5115 to 5117 are defined in the topology file as:
  5115 opls_145 1 Grph C 4859 -0.12 12.011 ;
qtot -0.12
  5116 opls_146 1 Grph H 4859 0.06 1.008 ;
qtot -0.06
  5117 opls_146 1 Grph H 4859 0.06 1.008 ;
qtot 0

My assumption is that this error means that there does not exist an
angletype for this threesome of atoms in the ffolpsaabon.itp file.

I looked within the ffoplsaabon.itp file for an entry of the form:
HA CA HA

and, as expected, "pattern not found" was returned as the response.

So, I copied over the ffoplsaabon.itp file to my home (working) directory
and added the following test entry:
  HA CA HA  1   107.000276.000   ; TEST PARAMETERS *
NOT VALID *** ONLY FOR TESTING

I expected that the ERROR O message above would disappear. But the error
was still present. Could you please tell me what I need to do in order
to resolve this error?

Much thanks in advance.

Darrell
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[gmx-users] Protein-Ligand Docking?

[Chih-Ying Lin]

HI
When i visualize the MD trajectory, the protein and ligand are closed by.
But, I don't know if ligand really DOCK on the protein.

Please tell me how to define the successful docking.
Thank you
Lin
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[gmx-users] RE: RE: RDF in GMX 4 (Justin)

[Eudes Fileti]

Thanks for reply Justin.
I had already read this part of the manual but I can´t understood it well.
How can I take account the mentioned input file run? Would it be a kind of
index file?
Could you provide me an example?
Bests
eef
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Re: [gmx-users] Some molecules disconnected into many parts after EM

[Justin A. Lemkul]

Yanmei Song wrote:

Dear Justin:

-
Program mdrun_d, VERSION 4.0.4
Source code file: gmx_fft_mkl.c, line: 825

Fatal error:
Error executing Intel MKL FFT.
---

I really could not find out what is the reason for the error above. Do 
you mean something is wrong with the installation. if this is the case 
then should I re-install it?


This morning I did the same procedure with the same input file using 
gromacs-3.3.3 ( which means I did all the editconf, genbox EM, and mdrun 
in 3.3.3) and the mdrun works well. So I think there must be something 
wrong with the 4.0.4. How can I fix this?


Anyone had the same problem before?




By default, your system configuration probably located Intel's MKL FFT package. 
 Likely your 3.3.3 installation was installed using something else, like FFTW. 
 I would recommend re-installing 4.0.4, using FFTW (if you have it), paying 
attention to the information that the ./configure step prints to the screen, and 
trying again.


-Justin



On Fri, May 8, 2009 at 1:04 PM, Justin A. Lemkul > wrote:




Yanmei Song wrote:

Dear Justin:

Sorry to bother so many times. After EM everything looks fine.
However the mdrun died with the error:

---
Program mdrun_d, VERSION 4.0.4
Source code file: gmx_fft_mkl.c, line: 825

Fatal error:
Error executing Intel MKL FFT.
---

what is the problem coming from?


It looks like you have Intel MKL for your FFT package, but mdrun
can't find it (or it otherwise failed for some reason).  Make sure
your environment can find the location of all necessary binaries or
libraries and try again.

-Justin

On Fri, May 8, 2009 at 11:28 AM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:


   VMD guesses bonds based on distances, so it is not
necessarily very
   smart.

   I have no idea why increasing the box causes the molecules to be
   displayed correctly, other than that VMD cannot deal with the
   periodicity correctly, as I implied before.  Causing all of the
   molecules to be within the unit cell may lead VMD to induce the
   desired visualization.

   But in any case, bonds aren't broken and/or formed in
classical MD
   so there is likely nothing to be concerned about.

   -Justin

   Yanmei Song wrote:

   Dear Justin:

   Thanks for your message.

   When I open the gro file using VMD it shows:

   atom:1950
   bonds 1907
   residue:43

   I was thinking the problem may not come from the artifact of
   visualization. Since if the gro file is fine it should be
like:

   atom:1950
   bonds 1944
   residue:6

   because I have 6 chains in the box.

   This morning I found that it seems the problem was
resolved by
   increasing the box size. Why is that?


   On Thu, May 7, 2009 at 5:10 PM, Justin A. Lemkul
   mailto:jalem...@vt.edu>
>
   

Re: [gmx-users] Some molecules disconnected into many parts after EM

[Yanmei Song]

Dear Justin:

-
Program mdrun_d, VERSION 4.0.4
Source code file: gmx_fft_mkl.c, line: 825

Fatal error:
Error executing Intel MKL FFT.
---

I really could not find out what is the reason for the error above. Do you
mean something is wrong with the installation. if this is the case then
should I re-install it?

This morning I did the same procedure with the same input file using
gromacs-3.3.3 ( which means I did all the editconf, genbox EM, and mdrun in
3.3.3) and the mdrun works well. So I think there must be something wrong
with the 4.0.4. How can I fix this?

Anyone had the same problem before?



On Fri, May 8, 2009 at 1:04 PM, Justin A. Lemkul  wrote:

>
>
> Yanmei Song wrote:
>
>> Dear Justin:
>>
>> Sorry to bother so many times. After EM everything looks fine. However the
>> mdrun died with the error:
>>
>> ---
>> Program mdrun_d, VERSION 4.0.4
>> Source code file: gmx_fft_mkl.c, line: 825
>>
>> Fatal error:
>> Error executing Intel MKL FFT.
>> ---
>>
>> what is the problem coming from?
>>
>>
> It looks like you have Intel MKL for your FFT package, but mdrun can't find
> it (or it otherwise failed for some reason).  Make sure your environment can
> find the location of all necessary binaries or libraries and try again.
>
> -Justin
>
>  On Fri, May 8, 2009 at 11:28 AM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>VMD guesses bonds based on distances, so it is not necessarily very
>>smart.
>>
>>I have no idea why increasing the box causes the molecules to be
>>displayed correctly, other than that VMD cannot deal with the
>>periodicity correctly, as I implied before.  Causing all of the
>>molecules to be within the unit cell may lead VMD to induce the
>>desired visualization.
>>
>>But in any case, bonds aren't broken and/or formed in classical MD
>>so there is likely nothing to be concerned about.
>>
>>-Justin
>>
>>Yanmei Song wrote:
>>
>>Dear Justin:
>>
>>Thanks for your message.
>>
>>When I open the gro file using VMD it shows:
>>
>>atom:1950
>>bonds 1907
>>residue:43
>>
>>I was thinking the problem may not come from the artifact of
>>visualization. Since if the gro file is fine it should be like:
>>
>>atom:1950
>>bonds 1944
>>residue:6
>>
>>because I have 6 chains in the box.
>>
>>This morning I found that it seems the problem was resolved by
>>increasing the box size. Why is that?
>>
>>
>>On Thu, May 7, 2009 at 5:10 PM, Justin A. Lemkul
>>mailto:jalem...@vt.edu>
>>>> wrote:
>>
>>
>>
>>   Yanmei Song wrote:
>>
>>   Dear users:
>>
>>   I set up a 8nm cubic box with 6 long chain molecules.
>>After EM,
>>   there is no error message. However I found that in the
>>gro file
>>   by visualization, 2 of the chains has been split in many
>>parts,
>>   which means many bonds in the molecules disconnected. And
>>also
>>   the other 4 are good. I checked em.log and eveyting looks
>>fine.
>>
>>   Steepest Descents converged to machine precision in 1545
>>steps,
>>   but did not reach the requested Fmax < 10.
>>   Potential Energy  = -7.51461594735782e+03
>>   Maximum force =  2.66505909651672e+02 on atom 1256
>>   Norm of force =  9.84300153087768e+00
>>
>>   Anyone knows how to solve the problem? Thanks in advance!
>>
>>
>>   Probably an artifact of visualization, or otherwise periodic
>>   boundary conditions:
>>
>>   http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions
>>
>>   -Justin
>>
>>   --Yanmei Song
>>   Department of Chemical Engineering
>>   ASU
>>
>>
>>
>> 
>>
>>   ___
>>   gmx-users mailing listgmx-users@gromacs.org
>>
>>   > >>
>>
>>   http://www.gromacs.org/mailman/listinfo/gmx-users
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>>

Re: [gmx-users] How to create .pdb files?

[Justin A. Lemkul]

Justin A. Lemkul wrote:



Joseph Johnson wrote:
I have tried to export .pdb files from ChemBio3D Ultra but it does not 
do a very good job.  What is the best or simply a good, reliable 
method of generating a .pdb file?


If it is simply a formatting issue, you can fix it yourself using the 
PDB format guidelines:


http://www.wwpdb.org/docs.html

If the software just isn't well-suited to this purpose, I find that the 
PRODRG server is useful for such purposes.




I forgot to ask - what kind of structures are you trying to export?  Small 
molecules can be handled by PRODRG, but proteins/lipid membranes/nucleic acids 
and such are too large to be supported.


-Justin


-Justin



Thanks for your help :)
Casey


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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] How to create .pdb files?

[Justin A. Lemkul]

Joseph Johnson wrote:
I have tried to export .pdb files from ChemBio3D Ultra but it does not 
do a very good job.  What is the best or simply a good, reliable method 
of generating a .pdb file?


If it is simply a formatting issue, you can fix it yourself using the PDB format 
guidelines:


http://www.wwpdb.org/docs.html

If the software just isn't well-suited to this purpose, I find that the PRODRG 
server is useful for such purposes.


-Justin



Thanks for your help :)
Casey


Insert movie times and more without leaving Hotmail®. See how. 






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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] How to create .pdb files?

[Joseph Johnson]

I have tried to export .pdb files from ChemBio3D Ultra but it does not do a 
very good job.  What is the best or simply a good, reliable method of 
generating a .pdb file?

Thanks for your help :)
Casey

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Re: [gmx-users] RDF in GMX 4

[Justin A. Lemkul]

Eudes Fileti wrote:

Hello, everyone, in earlier versions of the Gromacs
the option to calculate rdf between center of mass (com-com) was not 
implemented.

Is this option implemented in version 4.0? If no, someone would have
suggestion to calculate the RDF com-com for liquid benzene?


From g_rdf -h:

"The option -rdf sets the type of rdf to be computed. Default is for atoms or
particles, but one can also select center of mass or geometry of molecules or
residues. In all cases only the atoms in the index groups are taken into
account. For molecules and/or the center of mass option a run input file is
required. Other weighting than COM or COG can currently only be achieved by
providing a run input file with different masses. Option -com also works in
conjunction with -rdf."

-Justin


thanks
EEF
___
Eudes Eterno Fileti
Centro de Ciências Naturais e Humanas
Universidade Federal do ABC — CCNH
Av. dos Estados, 5001
Santo André - SP - Brasil
CEP 09210-971
+55.11.4437-0196
skype: eefileti
http://fileti.ufabc.edu.br




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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] restraining ligand for position restraint simulation

[Justin A. Lemkul]

Halie Shah wrote:

I am trying to do what Hitesh tried to do..get a pos restraint on both 
my protein and ligandI found that -DPOSRES only takes into account 1 
posre.itp file...so I appended the atom numbers of my ligand (2519-2531) 
to the end of the posre file for my protein (1-2518). Then I tried 
running grompp on this and it gave me the error


---
Program grompp, VERSION 3.3.3
Source code file: ../../../src/kernel/toppush.c, line: 1193

Fatal error:
[ file "posre.itp", line 2015 ]:
Atom index (2519) in position_restraints out of bounds (1-2518).
This probably means that you have inserted topology section 
"position_restraints"

in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right molecule.
---

Also, fyi, earlier for energy minimization, I had included the ff for 
the itp file in [forcefield] section and included HSL (my ligand) in the 
[molecule] section after putting the coords for the HSL into my protein 
pdb file. See parts of the top file below:




Position restraints sections must be placed within the same [ moleculetype ] 
definition.  So, you can't include all of the position restraint information in 
one file, since that file is part of the Protein [ moleculetype ] definition. 
The ligand should be placed in its own posre.itp file and included in the topology.


These lines must be placed *outside* of the [ moleculetype ] directive of any 
other molecule(s) in the system.  For consistency, whenever I have ligands, I 
place them immediately after the protein [ moleculetype ] and water topology, i.e.:


#ifdef POSRES
#include "posre.itp"
#endif

#include "ligand.itp"

#ifdef POSRES_LIGAND
#include "ligand_posre.itp"
#endif

#include "spc.itp"

(etc).

That way, the protein [ moleculetype ] ends with the #ifdef POSRES, the ligand 
section begins with #include "ligand.itp", ends with the POSRES_LIGAND section, 
and then the topology reads the water topology, etc.


-Justin

P.S. ffgmx is deprecated; you should probably be using a more modern Gromos96 
variant.  Topologies compatible with ffG43a1 can be produced from the PRODRG 
beta server.  These can also be modified to correspond with newer (i.e, ffG53a6) 
force fields.



;   File 'BR6.top' was generated
;   By user: onbekend (0)
;   On host: onbekend
;   At date: Wed Apr 29 11:35:48 2009
;
;   This is your topology file
;   "I'll Match Your DNA" (Red Hot Chili Peppers)
;
; Include forcefield parameters
#include "ffgmx.itp"
#include "C4AHLdbMarc.itp"

[ moleculetype ]
; Namenrexcl
Protein_A   3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass  
typeBchargeB  massB
 1 NL  1MET  N  1  0.12914.0067   ; 
qtot 0.129
 2  H  1MET H1  1  0.248  1.008   ; 
qtot 0.377
 3  H  1MET H2  1  0.248  1.008   ; 
qtot 0.625
 4  H  1MET H3  1  0.248  1.008   ; 
qtot 0.873
 5CH1  1MET CA  1  0.127 13.019   ; 
qtot 1
 6CH2  1MET CB  2  0 14.027   ; 
qtot 1
 7CH2  1MET CG  3  0 14.027   ; 
qtot 1
 8  S


;etcend of file below

2509  2507  2514  2510 2
2509  2512  2511  2510 2
2509  2516  2515  2514 2

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Include water topology
#include "spc.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound#mols
Protein_A   1
HSL 1
SOL 1
SOL 12480
Na 11


So, is it not possible in GROMACS to restrain multiple molecules 
together? If it is, how do you do this?


Thanks in advance,
Halie Shah
U of H Briggs Lab




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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

[gmx-users] RDF in GMX 4

[Eudes Fileti]

Hello, everyone, in earlier versions of the Gromacs
the option to calculate rdf between center of mass (com-com) was not
implemented.
Is this option implemented in version 4.0? If no, someone would have
suggestion to calculate the RDF com-com for liquid benzene?
thanks
EEF
___
Eudes Eterno Fileti
Centro de Ciências Naturais e Humanas
Universidade Federal do ABC — CCNH
Av. dos Estados, 5001
Santo André - SP - Brasil
CEP 09210-971
+55.11.4437-0196
skype: eefileti
http://fileti.ufabc.edu.br
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[gmx-users] restraining ligand for position restraint simulation

[Halie Shah]

Hi,

I think this was answered earlier but I didn't quite understand the answer
given.

Hi Hitesh,

The posre.itp file only contains a header [ position_restraints ]
followed by a list of atom numbers and restraint force constants.

Check chapter 5 of the manual for how and what. For a ligand it's
probably best to directly add the [ position_restraints  ] section in
the file with the [ molecule_type ] definition, possibly enclosed by
the statements #ifdef POSRES and #endif. Mind that the aom numbers

need to refer to the atom numbers within the molecule_type definition
and are not related to the atom numbers in the coordinate file.

Cheers,

Tsjerk

On Wed, Apr 15, 2009 at 9:05 AM, Hitesh singla

http://www.gromacs.org/mailman/listinfo/gmx-users>> wrote:
>* Dear all,
*>*
*>* I have generated .itp file for ligand using PRODRG server which i included
*>* in topology file. Now for position restrained dynamics, i wanted to restrain
*>* atom positions for ligand and protein . But porse.itp which generated using
*>* pdb2gmx contain restraints for protein only. Kindly provide me the solution
*>* to restrain ligand atoms.
*>*
*>* Thanks,
*>* Hitesh Singla
*


I am trying to do what Hitesh tried to do..get a pos restraint on both my
protein and ligandI found that -DPOSRES only takes into account 1
posre.itp file...so I appended the atom numbers of my ligand (2519-2531) to
the end of the posre file for my protein (1-2518). Then I tried running
grompp on this and it gave me the error

---
Program grompp, VERSION 3.3.3
Source code file: ../../../src/kernel/toppush.c, line: 1193

Fatal error:
[ file "posre.itp", line 2015 ]:
Atom index (2519) in position_restraints out of bounds (1-2518).
This probably means that you have inserted topology section
"position_restraints"
in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right molecule.
---

Also, fyi, earlier for energy minimization, I had included the ff for the
itp file in [forcefield] section and included HSL (my ligand) in the
[molecule] section after putting the coords for the HSL into my protein pdb
file. See parts of the top file below:

;   File 'BR6.top' was generated
;   By user: onbekend (0)
;   On host: onbekend
;   At date: Wed Apr 29 11:35:48 2009
;
;   This is your topology file
;   "I'll Match Your DNA" (Red Hot Chili Peppers)
;
; Include forcefield parameters
#include "ffgmx.itp"
#include "C4AHLdbMarc.itp"

[ moleculetype ]
; Namenrexcl
Protein_A   3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass
typeBchargeB  massB
 1 NL  1MET  N  1  0.12914.0067   ; qtot
0.129
 2  H  1MET H1  1  0.248  1.008   ; qtot
0.377
 3  H  1MET H2  1  0.248  1.008   ; qtot
0.625
 4  H  1MET H3  1  0.248  1.008   ; qtot
0.873
 5CH1  1MET CA  1  0.127 13.019   ; qtot
1
 6CH2  1MET CB  2  0 14.027   ; qtot
1
 7CH2  1MET CG  3  0 14.027   ; qtot
1
 8  S

;etcend of file below

2509  2507  2514  2510 2
2509  2512  2511  2510 2
2509  2516  2515  2514 2

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Include water topology
#include "spc.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound#mols
Protein_A   1
HSL 1
SOL 1
SOL 12480
Na 11


So, is it not possible in GROMACS to restrain multiple molecules together?
If it is, how do you do this?

Thanks in advance,
Halie Shah
U of H Briggs Lab
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RE: [gmx-users] where is the normalization direction in radial axial g_densmap plots?

[Berk Hess]

Hi,

Well, there is axial, radial and angular (angle of rotation around the axial 
direction).
Averaging happens over the radial coordinate.

Berk

Date: Mon, 11 May 2009 18:27:07 +0200
From: mariagorano...@gmail.com
To: gmx-users@gromacs.org
Subject: [gmx-users] where is the normalization direction in radial axial   
g_densmap plots?

I made a radial-axial density plot using g_densmap. What one gets out is a 3-D 
number density as a function of radial and axial distance from the defined 
axis. So which is the third direction, and how is it averaged out? Sorry if 
this is a very elementary question


g_densmap -f protein.xtc -s protein.tpr -n proteinndx -o protein.xpm -b 1 
-e 3 -bin 0.01 -amax 2 -rmax 2 -dmax 40


-- 
Maria G.
Technical University of Denmark
Copenhagen

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[gmx-users] where is the normalization direction in radial axial g_densmap plots?

[maria goranovic]

I made a radial-axial density plot using g_densmap. What one gets out is a
3-D number density as a function of radial and axial distance from the
defined axis. So which is the third direction, and how is it averaged out?
Sorry if this is a very elementary question

g_densmap -f protein.xtc -s protein.tpr -n proteinndx -o protein.xpm -b
1 -e 3 -bin 0.01 -amax 2 -rmax 2 -dmax 40



-- 
Maria G.
Technical University of Denmark
Copenhagen
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Re: [gmx-users] Force groups?

[Chze Ling Wee]

Hi Berk - many thanks for your reply and apologies for cross-posting.
Kind Regards
Chze Ling

On Mon, May 11, 2009 at 3:04 PM, Berk Hess  wrote:

>  Hi,
>
> Please do not send the same question to multiple mailing lists,
> (multiple) people might answer the same questions multiple times then.
> Here is my answer on gmx-developers:
>
> You will have to use mdrun -rerun
> with different tpr files where you on switch off all the interactions
> between all energy groups except between the peptide and the group
> you want using the mdp options:
> energygrps
> energygrp_excl
>
> Note that these forces will probably be extremely noisy
> and difficult to make sense of.
>
> Berk
>
>
>
> --
> Date: Mon, 11 May 2009 14:42:58 +0100
> From: chzeling...@gmail.com
> To: gmx-users@gromacs.org; gmx-develop...@gromacs.org
> CC:
> Subject: [gmx-users] Force groups?
>
> Hi - I wonder if it is possible in Gromacs3/4 to write out the forces
> acting on a peptide due to its interaction with different components in the
> system e.g. waters, lipids, etc? If not, could someone comment on how
> difficult to would be to modify the source code to do this?
> Many thanks
> Chze Ling Wee
>
>
>
> --
> Express yourself instantly with MSN Messenger! MSN 
> Messenger
>
> ___
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Re: [gmx-users] grompp in gromacs-4.0.4

[S. Vaitheeswaran]

Thanks!  The problem was indeed the spaces in the group names.

Vaithee
===
S. Vaitheeswaran
Post-doctoral Research Associate
Center for Biotechnology and Interdisciplinary Studies
Rensselaer Polytechnic Institute
110 8th Street, Troy NY 12180
Tel: 518-276-4245
email: vai...@rpi.edu
===


On Fri, May 8, 2009 at 4:53 PM, Justin A. Lemkul  wrote:

>
>
> S. Vaitheeswaran wrote:
>
>> Dear gromacs users,
>>
>> I am trying to calculate the PMF along the end-to-end distance for a short
>> polymer (hexa-ethylene glycol), using the pull code in gromacs-4.0.4.  I run
>> grompp with: grompp_s -v -n OH_ends.ndx -f sd.mdp -c 0.425nm.pdb -p 6EG.top,
>> where sd.mdp is:
>> 
>> title   = cpp  =  /usr/bin/cpp
>> integrator  =  sd
>> dt  =  0.002  ; [ps]
>> nsteps   =  100
>> nstcomm =  10 ; frequency for center of mass motion
>> removal
>> comm_mode   =  Linear ; Remove center of mass translation
>> comm_grps   =  system
>> nstxtcout   =  1  ; frequency to write coordinates to xtc
>> trajectory
>> nstxout =  1  ; frequency to write coordinates to output
>> trajectory file
>> nstvout =  10
>> nstlog  =  1
>> nstenergy   =  1
>> energygrps  =  6EG; group(s) to write to energy file
>> pbc =  no
>> nstlist =  0  ; neighbor list is only constructed once and
>> never updated.
>> ns_type =  simple
>> rlist   =  0  ; cut-off distance for the short-range
>> neighbor list
>> rcoulomb=  0
>> rvdw=  0
>> tc-grps =  6EG
>> tau_t   =  0.1; [ps]
>> ref_t   =  300; [K]
>> pull= umbrella
>> pull_geometry   = distance
>> pull_init1  = 0.425   ; [nm]
>> pull_dim= Y Y Y
>> pull_ngroups= 1
>> pull_group0 = group 1
>> pull_group1 = group 2
>> pull_k1 = 1000
>> 
>> group 1 and group 2 are defined in OH_ends.ndx:
>> 
>> [ group 1 ]
>>  1  2
>> [ group 2 ]
>>  20  21
>> 
>>
>> and 6EG.top is:
>> 
>> #include "ffgmx.itp"
>> #include "6EG.itp"
>> [ system ]
>> Hexa-ethylene glycol: Langevin dynamics
>> [ molecules ]
>> 6EG   1
>> 
>>
>> But, grompp fails with:
>> ---
>> Program grompp_s, VERSION 4.0.4
>> Source code file: readir.c, line: 1013
>>
>> Fatal error:
>> Group 6EG not found in indexfile.
>> Maybe you have non-default goups in your mdp file, while not using the
>> '-n' option of grompp.
>> In that case use the '-n' option.
>> ---
>>
>> But, I *am* using the -n option!  If I include the group 6EG in the index
>> file (I didn't think it was necessary since it is defined in the .top file),
>> grompp chokes with:
>> "Fatal error: Group group 1 not found in indexfile.", even though group 1
>> is defined in the .ndx file.
>>
>
> Perhaps try taking the spaces out of the group names, i.e., group_1 and
> group_2.
>
> -Justin
>
>  It works fine without the pulling options.  I have searched the manual,
>> wiki and mailing list archives for a solution, without success.  This
>> gromacs newbie is out of ideas -- any help is much appreciated.
>>
>> thanks,
>> Vaithee
>>
>>
>> 
>>
>> ___
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>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
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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] Force groups?

[Berk Hess]

Hi,

Please do not send the same question to multiple mailing lists,
(multiple) people might answer the same questions multiple times then.
Here is my answer on gmx-developers:

You will have to use mdrun -rerun
with different tpr files where you on switch off all the interactions
between all energy groups except between the peptide and the group
you want using the mdp options:
energygrps
energygrp_excl

Note that these forces will probably be extremely noisy
and difficult to make sense of.

Berk


Date: Mon, 11 May 2009 14:42:58 +0100
From: chzeling...@gmail.com
To: gmx-users@gromacs.org; gmx-develop...@gromacs.org
CC: 
Subject: [gmx-users] Force groups?

Hi - I wonder if it is possible in Gromacs3/4 to write out the forces acting on 
a peptide due to its interaction with different components in the system e.g. 
waters, lipids, etc? If not, could someone comment on how difficult to would be 
to modify the source code to do this?

Many thanksChze Ling Wee


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Re: [gmx-users] Are Gromos 45a3 and GROMOS 53a6 compatible?

[Tsjerk Wassenaar]

Hi Lin,

Well, actually G53a6 is heavily reparameterized... partly. So your
observation that large portions of the force fields are equal is
correct. That also makes the question of whether or not to mix them
more difficult. It seems implicitly assumed by the authors that the
parts of the force field that weren't reparameterized are still
compatible with the new parameters.
Some of the things you do have to be aware of though is that aromatics
have changed, charges have changed and non-nonded parameters have
changed. If you want to use parameters from 45a3 in 53a6 for aromatic
compounds, you should have a good look at what happened to similar
compounds (residues) which were reparameterized. In summary, the
advice is still: don't do it. First get on terms with force fields and
parameterization. Maybe it's not even a bad idea to use 45a3 in stead.

Cheers,

Tsjerk

On Mon, May 11, 2009 at 3:47 PM, Chih-Ying Lin  wrote:
> Hi
>
> GROMOS 45a3 force field
> GROMOS 53a6 force field
> Are they compatible?
>
> I notice that MOST of the force field parameters sets are THE SAME in the
> GROMOS 45a3 and GROMOS 53a6.
>
> So, I want to ask if GROMOS 53a6 is rectification from GROMOS 45a3.
> I mean if GROMOS 53a6 match more experimental data than GROMOS 45a3.
> But, basically GROMOS 45a3 and GROMOS 53a6 are derived from THE SAME
> METHOD and THE SAME EXPERIMENTAL DATA  SETS ?
>
> Thank you very much
>
> Lin
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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[gmx-users] Are Gromos 45a3 and GROMOS 53a6 compatible?

[Chih-Ying Lin]

Hi

GROMOS 45a3 force field
GROMOS 53a6 force field
Are they compatible?

I notice that MOST of the force field parameters sets are THE SAME in the
GROMOS 45a3 and GROMOS 53a6.

So, I want to ask if GROMOS 53a6 is rectification from GROMOS 45a3.
I mean if GROMOS 53a6 match more experimental data than GROMOS 45a3.
But, basically GROMOS 45a3 and GROMOS 53a6 are derived from THE SAME
METHOD and THE SAME EXPERIMENTAL DATA  SETS ?

Thank you very much

Lin
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[gmx-users] Force groups?

[Chze Ling Wee]

Hi - I wonder if it is possible in Gromacs3/4 to write out the forces acting
on a peptide due to its interaction with different components in the system
e.g. waters, lipids, etc? If not, could someone comment on how difficult to
would be to modify the source code to do this?
Many thanks
Chze Ling Wee
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Re: [gmx-users] how to use atom2cg.awk

[Justin A. Lemkul]

Justin A. Lemkul wrote:



xi zhao wrote:
But CG structure and native PDB structure is very different, please 
see my attaches.





Remove the chain identifier from the input structure.  You'll note that 
the x-coordinate of each atom in the output is the residue number, so 
the chain identifier is throwing off the awk field count.


-Justin



4 
 



--- *09年5月11日，周一, Justin A. Lemkul //* 写道：


发件人: Justin A. Lemkul 
主题: Re: [gmx-users] how to use atom2cg.awk
收件人: "Gromacs Users' List" 
日期: 2009年5月11日,周一,下午8:33



xi zhao wrote:
 > Dear sir:
 > This is my modified script, please see it! I take CG 
simulations according to  
http://md.chem.rug.nl/marrink/coarsegrain.html.

 > Thank you !
 >

Then your structure should be built appropriately.

-Justin

 >
 > 4

> 


 >
 > --- *09年5月11日，周一, Justin A. Lemkul />/* 
写道：

 >
 >
 > 发件人: Justin A. Lemkul http://cn.mc151.mail.yahoo.com/mc/compose?to=jalem...@vt.edu>>
 > 主题: Re: [gmx-users] how to use atom2cg.awk
 > 收件人: "Gromacs Users' List" http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org>>
 > 日期: 2009年5月11日,周一,下午6:49
 >
 >
 >
 > xi zhao wrote:
 >  > Dear Sir:
 >  > In fact, I have modified the script as you said, but the CG
 > strucrute produced is not different  in secondary strucure 
with
 > native PDB structure: CG structure became a line strucrue! 
Please

 > help me! Or give me a good script!
 >
 > Visualization is not an appropriate method to use to
determine the
 > validity of your procedure.  The CG model will look a bit 
strange
 > when rendered as "lines" in most visualization software.  
You did
 > modify each line of the script, inserting $5 between every 
$4 and

 > $6, correct?
 >
 > -Justin
 >
 >  > Thank you very much!
 >  > Best regards!>
 >  > 4
 >
 

 >
>> 


 >  >
 >  > --- *09年5月11日，周一, Justin A. Lemkul /http://cn.mc151.mail.yahoo.com/mc/compose?to=jalem...@vt.edu>
 >
>/*

写道：
 >  >
 >  >
 >  > 发件人: Justin A. Lemkul http://cn.mc151.mail.yahoo.com/mc/compose?to=jalem...@vt.edu>
 > 
>

 >  > 主题: Re: [gmx-users] how to use atom2cg.awk
 >  > 收件人: "Gromacs Users' List" http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org>
 >
>

 >  > 日期: 2009年5月11日,周一,上午8:22
 >  >
 >  >
 >  >
 >  > xi zhao wrote:
 >  >  > Dear sir :
 >  >  > how to motify the $5 in details?
 >  >  > Thank you!
 >  >  >
 >  >
 >  > Use a text editor (vi, emacs, gedit, etc), like you
would to
 > create
 >  > any script.
 >  >
 >  > -Justin
 >  >
 >  >  >
 >  >  >
 >  >  > 4
 >  >   
 

 >
> 

 >  >   

Re: [gmx-users] how to use atom2cg.awk

[Justin A. Lemkul]

xi zhao wrote:

Dear sir:
This is my modified script, please see it! I take CG simulations  
according to  http://md.chem.rug.nl/marrink/coarsegrain.html.

Thank you !



Then your structure should be built appropriately.

-Justin



4 



--- *09年5月11日，周一, Justin A. Lemkul //* 写道：


发件人: Justin A. Lemkul 
主题: Re: [gmx-users] how to use atom2cg.awk
收件人: "Gromacs Users' List" 
日期: 2009年5月11日,周一,下午6:49



xi zhao wrote:
 > Dear Sir:
 > In fact, I have modified the script as you said, but the CG
strucrute produced is not different  in secondary strucure with
native PDB structure: CG structure became a line strucrue! Please
help me! Or give me a good script!

Visualization is not an appropriate method to use to determine the
validity of your procedure.  The CG model will look a bit strange
when rendered as "lines" in most visualization software.  You did
modify each line of the script, inserting $5 between every $4 and
$6, correct?

-Justin

 > Thank you very much!
 > Best regards!   
 >

 > 4

>
 >
 > --- *09年5月11日，周一, Justin A. Lemkul /http://cn.mc151.mail.yahoo.com/mc/compose?to=jalem...@vt.edu>>/* 写道：
 >
 >
 > 发件人: Justin A. Lemkul http://cn.mc151.mail.yahoo.com/mc/compose?to=jalem...@vt.edu>>
 > 主题: Re: [gmx-users] how to use atom2cg.awk
 > 收件人: "Gromacs Users' List" http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org>>
 > 日期: 2009年5月11日,周一,上午8:22
 >
 >
 >
 > xi zhao wrote:
 >  > Dear sir :
 >  > how to motify the $5 in details?
 >  > Thank you!
 >  >
 >
 > Use a text editor (vi, emacs, gedit, etc), like you would to
create
 > any script.
 >
 > -Justin
 >
 >  >
 >  >
 >  > 4
 > 
   
 > 
   >>
 >  >
 >  > --- *09年5月8日，周五, Justin A. Lemkul /http://cn.mc151.mail.yahoo.com/mc/compose?to=jalem...@vt.edu>
 > 
   >/*

写道：
 >  >
 >  >
 >  > 发件人: Justin A. Lemkul http://cn.mc151.mail.yahoo.com/mc/compose?to=jalem...@vt.edu>
 > >
 >  > 主题: Re: [gmx-users] how to use atom2cg.awk
 >  > 收件人: "Discussion list for GROMACS users"
 > http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org>
 > 
   >

 >  > 日期: 2009年5月8日,周五,下午6:46
 >  >
 >  >
 >  >
 >  > xi zhao wrote:
 >  >  >
 >  >  >
 >  >  > Dear Sirs:
 >  >  >   I wang to know simulate coarse-graied system using
 > gromacs, but
 >  > I don not know how to use atom2cg.awk to convert CG model!
 >  >  > Thank you very much!
 >  >  >
 >  >
 >  > ./atom2cg_v2.1_tryout.awk my.pdb > out.pdb
 >  >
 >  > Note that the script available online needs to be
modified to
 >  > include a $5 between the $4 and $6 on each line, otherwise
 > you will
 >  > get an incorrectly-formatted .pdb file.
 >  >
 >  > -Justin
 >  >
 >  >  > 4
 >  >   

 > 
   >
 >  >   

Re: [gmx-users] how to use atom2cg.awk

[xi zhao]

Dear sir: 
This is my modified script, please see it! I take CG simulations  according to  
http://md.chem.rug.nl/marrink/coarsegrain.html.
Thank you ! 




--- 09年5月11日，周一, Justin A. Lemkul  写道：


发件人: Justin A. Lemkul 
主题: Re: [gmx-users] how to use atom2cg.awk
收件人: "Gromacs Users' List" 
日期: 2009年5月11日,周一,下午6:49




xi zhao wrote:
> Dear Sir:
> In fact, I have modified the script as you said, but the CG strucrute 
> produced is not different  in secondary strucure with native PDB structure: 
> CG structure became a line strucrue! Please help me! Or give me a good script!

Visualization is not an appropriate method to use to determine the validity of 
your procedure.  The CG model will look a bit strange when rendered as "lines" 
in most visualization software.  You did modify each line of the script, 
inserting $5 between every $4 and $6, correct?

-Justin

> Thank you very much!
> Best regards!   
> 
> 4 
> 
> 
> --- *09年5月11日，周一, Justin A. Lemkul //* 写道：
> 
> 
>     发件人: Justin A. Lemkul 
>     主题: Re: [gmx-users] how to use atom2cg.awk
>     收件人: "Gromacs Users' List" 
>     日期: 2009年5月11日,周一,上午8:22
> 
> 
> 
>     xi zhao wrote:
>      > Dear sir :
>      > how to motify the $5 in details?
>      > Thank you!
>      >
> 
>     Use a text editor (vi, emacs, gedit, etc), like you would to create
>     any script.
> 
>     -Justin
> 
>      >
>      >
>      > 4
>     
>     
>>
>      >
>      > --- *09年5月8日，周五, Justin A. Lemkul /     >/* 写道：
>      >
>      >
>      >     发件人: Justin A. Lemkul      >
>      >     主题: Re: [gmx-users] how to use atom2cg.awk
>      >     收件人: "Discussion list for GROMACS users"
>      >
>      >     日期: 2009年5月8日,周五,下午6:46
>      >
>      >
>      >
>      >     xi zhao wrote:
>      >      >
>      >      >
>      >      > Dear Sirs:
>      >      >   I wang to know simulate coarse-graied system using
>     gromacs, but
>      >     I don not know how to use atom2cg.awk to convert CG model!
>      >      > Thank you very much!
>      >      >
>      >
>      >     ./atom2cg_v2.1_tryout.awk my.pdb > out.pdb
>      >
>      >     Note that the script available online needs to be modified to
>      >     include a $5 between the $4 and $6 on each line, otherwise
>     you will
>      >     get an incorrectly-formatted .pdb file.
>      >
>      >     -Justin
>      >
>      >      > 4
>      >        
>     
>
>      >        
>     
>>>
>      >      >
>      >      >
>      >      >
>      >        
>
>      >      > 好玩贺卡等你发，邮箱贺卡全新上线！
>      >        
>
>      >
>      >      >
>      >      >
>      >      >
>      >        
>
>      >      >
>      >      > ___
>      >      > 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 gmx-users-requ...@gromacs.org
>     
>
>      >        
>.
>      >      > Can't post? Read
>     http://www.gromacs.org/mailing_lists/users.php
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>      >     -- 
>      >
>      >     Justin A. Lemkul
>      >     Ph.D. Candidate
>      >     ICTAS Doctoral Scholar
>      >     Department of Biochemistry
>      

[gmx-users] Re: reg Mopac/gromacs installations reply please

[Justin A. Lemkul]

Please keep all correspondence on the gmx-users list.  I do not have any further 
advice beyond what Mark already told you.  Your shell environment is either 
severely broken, or your system too antiquated to work properly.  IIRC, Red Hat 
5 is from the late 1990's - you should definitely upgrade your system to a more 
modern Linux kernel and try again.


-Justin

vidhya sankar wrote:

Dear sir/Madam *  thanks in Advance*
i Did dos2unixconversions. as u saiid . but 
still i get error when i run the same output configure in command prompt 
of Redhat linux5 as follows

checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
: command not foundissing: line 3: 
: command not foundissing: line 5: 
: command not foundissing: line 9: 
: command not foundissing: line 14: 
: command not foundissing: line 19: 
: command not foundissing: line 24: 
: command not foundissing: line 29: 
'root/mopac7-1.10/missing: line 47: syntax error near unexpected token `in

'root/mopac7-1.10/missing: line 47: `case "$1" in
configure: WARNING: `missing' script is too old or missing
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
can not run ./config/bin/sh  :Error
*Please kindly mail me the error free configure file to My personal 
 Email (scvsankar_...@yahoo.com)  i am expecting your positive reply if 
u send me the the  configure file it will be very very helpful to me 
 thanks in Advance*
** 
 




Now surf faster and smarter ! Check out the new Firefox 3 - Yahoo! 
Edition * Click here! 
 



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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] how to use atom2cg.awk

[Justin A. Lemkul]

xi zhao wrote:

Dear Sir:
In fact, I have modified the script as you said, but the CG strucrute 
produced is not different  in secondary strucure with native PDB 
structure: CG structure became a line strucrue! Please help me! Or give 
me a good script!


Visualization is not an appropriate method to use to determine the validity of 
your procedure.  The CG model will look a bit strange when rendered as "lines" 
in most visualization software.  You did modify each line of the script, 
inserting $5 between every $4 and $6, correct?


-Justin


Thank you very much!
Best regards!   



4 



--- *09年5月11日，周一, Justin A. Lemkul //* 写道：


发件人: Justin A. Lemkul 
主题: Re: [gmx-users] how to use atom2cg.awk
收件人: "Gromacs Users' List" 
日期: 2009年5月11日,周一,上午8:22



xi zhao wrote:
 > Dear sir :
 > how to motify the $5 in details?
 > Thank you!
 >

Use a text editor (vi, emacs, gedit, etc), like you would to create
any script.

-Justin

 >
 >
 > 4

>
 >
 > --- *09年5月8日，周五, Justin A. Lemkul /http://cn.mc151.mail.yahoo.com/mc/compose?to=jalem...@vt.edu>>/* 写道：
 >
 >
 > 发件人: Justin A. Lemkul http://cn.mc151.mail.yahoo.com/mc/compose?to=jalem...@vt.edu>>
 > 主题: Re: [gmx-users] how to use atom2cg.awk
 > 收件人: "Discussion list for GROMACS users"
http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org>>
 > 日期: 2009年5月8日,周五,下午6:46
 >
 >
 >
 > xi zhao wrote:
 >  >
 >  >
 >  > Dear Sirs:
 >  >   I wang to know simulate coarse-graied system using
gromacs, but
 > I don not know how to use atom2cg.awk to convert CG model!
 >  > Thank you very much!
 >  >
 >
 > ./atom2cg_v2.1_tryout.awk my.pdb > out.pdb
 >
 > Note that the script available online needs to be modified to
 > include a $5 between the $4 and $6 on each line, otherwise
you will
 > get an incorrectly-formatted .pdb file.
 >
 > -Justin
 >
 >  > 4
 > 
   
 > 
   >>
 >  >
 >  >
 >  >
 > 
   

 >  > 好玩贺卡等你发，邮箱贺卡全新上线！
 > 
   

 >
 >  >
 >  >
 >  >
 > 
   

 >  >
 >  > ___
 >  > 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 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://www.gromacs.org/mailman/listinfo/gm

[gmx-users] pull code problem solved..

[Andrei Neamtu]

Sorry it appears that something was wrong with my .mdp file .. Idon't
know what ...but I wrote again the pull code lines and the warnings
dissapeared.

Thank you again,
Andrei
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RE: [gmx-users] pull code problem

[Berk Hess]

Hi,

Maybe there is an older grompp in your path.
Type grompp -h to see which version you are using.
And:
which grompp
to see where it comes from.

Berk

> Date: Mon, 11 May 2009 13:03:07 +0300
> From: neamtuand...@gmail.com
> To: gmx-users@gromacs.org
> Subject: [gmx-users] pull code problem
> 
> Hi Berk,
> thank you for the reply
> 
> here is my mdp file:
> 
> ;
> 
> ; User aneamtu
> 
> ; Joi, 7 mai - 2009
> 
> ; Input file
> 
> ;
> 
> title  =  Production_runs
> 
> ;define =  -DPOSRES -DPOSRES_CA2+_IONS
> 
> 
> 
> ;constraints   =  all-bonds
> 
> 
> 
> integrator =  md
> 
> dt =  0.001   
> 
> nsteps =  5   
> 
> 
> 
> nstcomm=  1
> 
> nstxout=  1000
> 
> nstvout=  1000
> 
> nstfout=  1000
> 
> nstlog =  500
> nstxtcout  =  50
> xtc_grps   =  Protein_ions
> 
> 
> nstenergy  =  100
> 
> nstlist=  10
> 
> ns_type=  grid
> 
> 
> coulombtype=  PME
> 
> rlist  =  1.0
> 
> rcoulomb   =  1.0
> 
> rvdw   =  1.0
> optimize_fft   =  yes
> 
> 
> Tcoupl =  v-rescale
> 
> tc-grps  =  Protein   SOL   ions
> 
> tau_t  =  0.1   0.1   0.1
> 
> ref_t  =  310   310   310
> 
> 
> 
> energygrps =  Protein  SOL CA2+ NA+ CL-
> 
> 
> 
> Pcoupl =  berendsen
> 
> Pcoupltype =  isotropic
> 
> tau_p  =  0.5
> 
> compressibility=  4.5e-5
> 
> ref_p  =  1.0
> 
> 
> 
> gen_vel=  no
> 
> gen_temp   =  310.0
> 
> gen_seed   =  173529
> 
> 
> 
> pull   =  constraint
> pull_geometry  =  distance
> pull_dim   =  Y Y Y
> pull_nstxout   =  10
> pull_nstfout   =  10
> pull_ngroups   =  2
> pull_group0=  Protein
> 
> pull_group1=  CA2+1
> pull_rate1 =  0.3
> 
> pull_group2=  CA2+2
> pull_rate2 =  0.3
> 
> 
> I do not understand what I do wrong..
> Should I use a -pi pull.ppa file like in gromacs 3.x ?
> 
> Andrei
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[gmx-users] pull code problem

[Andrei Neamtu]

Hi Berk,
thank you for the reply

here is my mdp file:

;

;   User aneamtu

;   Joi, 7 mai - 2009

;   Input file

;

title  =  Production_runs

;define =  -DPOSRES -DPOSRES_CA2+_IONS



;constraints   =  all-bonds



integrator =  md

dt =  0.001 

nsteps =  5 



nstcomm=  1

nstxout=  1000

nstvout=  1000

nstfout=  1000

nstlog =  500
nstxtcout  =  50
xtc_grps   =  Protein_ions


nstenergy  =  100

nstlist=  10

ns_type=  grid


coulombtype=  PME

rlist  =  1.0

rcoulomb   =  1.0

rvdw   =  1.0
optimize_fft   =  yes


Tcoupl =  v-rescale

tc-grps=  Protein   SOL   ions

tau_t  =  0.1   0.1   0.1

ref_t  =  310   310   310



energygrps =  Protein  SOL CA2+ NA+ CL-



Pcoupl =  berendsen

Pcoupltype =  isotropic

tau_p  =  0.5

compressibility=  4.5e-5

ref_p  =  1.0



gen_vel=  no

gen_temp   =  310.0

gen_seed   =  173529



pull   =  constraint
pull_geometry  =  distance
pull_dim   =  Y Y Y
pull_nstxout   =  10
pull_nstfout   =  10
pull_ngroups   =  2
pull_group0=  Protein

pull_group1=  CA2+1
pull_rate1 =  0.3

pull_group2=  CA2+2
pull_rate2 =  0.3


I do not understand what I do wrong..
Should I use a -pi pull.ppa file like in gromacs 3.x ?

Andrei
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Re: [gmx-users] how to use atom2cg.awk

[xi zhao]

Dear Sir:
In fact, I have modified the script as you said, but the CG strucrute produced 
is not different  in secondary strucure with native PDB structure: CG structure 
became a line strucrue! Please help me! Or give me a good script! 
Thank you very much! 
Best regards!   




--- 09年5月11日，周一, Justin A. Lemkul  写道：


发件人: Justin A. Lemkul 
主题: Re: [gmx-users] how to use atom2cg.awk
收件人: "Gromacs Users' List" 
日期: 2009年5月11日,周一,上午8:22




xi zhao wrote:
> Dear sir :
> how to motify the $5 in details?
> Thank you!
> 

Use a text editor (vi, emacs, gedit, etc), like you would to create any script.

-Justin

> 
> 
> 4 
> 
> 
> --- *09年5月8日，周五, Justin A. Lemkul //* 写道：
> 
> 
>     发件人: Justin A. Lemkul 
>     主题: Re: [gmx-users] how to use atom2cg.awk
>     收件人: "Discussion list for GROMACS users" 
>     日期: 2009年5月8日,周五,下午6:46
> 
> 
> 
>     xi zhao wrote:
>      >
>      >
>      > Dear Sirs:
>      >   I wang to know simulate coarse-graied system using gromacs, but
>     I don not know how to use atom2cg.awk to convert CG model!
>      > Thank you very much!
>      >
> 
>     ./atom2cg_v2.1_tryout.awk my.pdb > out.pdb
> 
>     Note that the script available online needs to be modified to
>     include a $5 between the $4 and $6 on each line, otherwise you will
>     get an incorrectly-formatted .pdb file.
> 
>     -Justin
> 
>      > 4
>     
>     
>>
>      >
>      >
>      >
>     
>      > 好玩贺卡等你发，邮箱贺卡全新上线！
>     
>
> 
>      >
>      >
>      >
>     
>      >
>      > ___
>      > 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 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 list    gmx-users@gromacs.org
>     
>     http://www.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at http://www.gromacs.org/search before
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>     www interface or send it to gmx-users-requ...@gromacs.org
>     
>.
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> 
> 
> 
> 好玩贺卡等你发，邮箱贺卡全新上线！ 
>  

-- 

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] pull code problem

[Berk Hess]

Hi,

Do you have another line with "pull =" somewhere in your mdp file?

PS You should switch to Gromacs 4.0.4, since it contains several small
bug fixes for the pull code.

Berk

> Date: Mon, 11 May 2009 12:38:35 +0300
> From: neamtuand...@gmail.com
> To: gmx-users@gromacs.org
> Subject: [gmx-users] pull code problem
> 
> hello,
> 
> I am trying to do a pulling simulation with gromacs 4.0.2
> 
> I added the following lines to the  .mdp input file for grompp:
> 
> ...
> 
> pull   =  constraint
> pull_geometry  =  distance
> pull_dim   =  Y Y Y
> pull_nstxout   =  10
> pull_nstfout   =  10
> pull_ngroups   =  2
> pull_group0=  Protein
> 
> pull_group1=  CA2+1
> pull_rate1 =  0.3
> 
> pull_group2=  CA2+2
> pull_rate2 =  0.3
> 
> .
> 
> when I run
> > grompp -f production_prm.mdp ...etc.
> 
> it does not recognize the keywords for pulling:
> 
> Ignoring obsolete mdp entry 'title'
> 
> Back Off! I just backed up neutr_RCK_Mthk_solv.04.mdout.mdp to
> ./#neutr_RCK_Mthk_solv.04.mdout.mdp.6#
> 
> WARNING 1 [file production_prm.mdp, line unknown]:
>   Unknown or double left-hand 'pull_geometry' in parameter file
> 
> WARNING 2 [file production_prm.mdp, line unknown]:
>   Unknown or double left-hand 'pull_dim' in parameter file
> 
> WARNING 3 [file production_prm.mdp, line unknown]:
>   Unknown or double left-hand 'pull_nstxout' in parameter file
> 
> WARNING 4 [file production_prm.mdp, line unknown]:
>   Unknown or double left-hand 'pull_nstfout' in parameter file
> 
> WARNING 5 [file production_prm.mdp, line unknown]:
>   Unknown or double left-hand 'pull_ngroups' in parameter file
> 
> WARNING 6 [file production_prm.mdp, line unknown]:
>   Unknown or double left-hand 'pull_group0' in parameter file
> 
> WARNING 7 [file production_prm.mdp, line unknown]:
>   Unknown or double left-hand 'pull_group1' in parameter file
> 
> WARNING 8 [file production_prm.mdp, line unknown]:
>   Unknown or double left-hand 'pull_rate1' in parameter file
> 
> WARNING 9 [file production_prm.mdp, line unknown]:
>   Unknown or double left-hand 'pull_group2' in parameter file
> 
> WARNING 10 [file production_prm.mdp, line unknown]:
>   Unknown or double left-hand 'pull_rate2' in parameter file
> 
> ...
> 
> It appears that grompp doesnot recognize any of these keywords...
> 
> Does anybody can help?
> 
> Thank you
> Andrei
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[gmx-users] pull code problem

[Andrei Neamtu]

hello,

I am trying to do a pulling simulation with gromacs 4.0.2

I added the following lines to the  .mdp input file for grompp:

...

pull   =  constraint
pull_geometry  =  distance
pull_dim   =  Y Y Y
pull_nstxout   =  10
pull_nstfout   =  10
pull_ngroups   =  2
pull_group0=  Protein

pull_group1=  CA2+1
pull_rate1 =  0.3

pull_group2=  CA2+2
pull_rate2 =  0.3

.

when I run
> grompp -f production_prm.mdp ...etc.

it does not recognize the keywords for pulling:

Ignoring obsolete mdp entry 'title'

Back Off! I just backed up neutr_RCK_Mthk_solv.04.mdout.mdp to
./#neutr_RCK_Mthk_solv.04.mdout.mdp.6#

WARNING 1 [file production_prm.mdp, line unknown]:
  Unknown or double left-hand 'pull_geometry' in parameter file

WARNING 2 [file production_prm.mdp, line unknown]:
  Unknown or double left-hand 'pull_dim' in parameter file

WARNING 3 [file production_prm.mdp, line unknown]:
  Unknown or double left-hand 'pull_nstxout' in parameter file

WARNING 4 [file production_prm.mdp, line unknown]:
  Unknown or double left-hand 'pull_nstfout' in parameter file

WARNING 5 [file production_prm.mdp, line unknown]:
  Unknown or double left-hand 'pull_ngroups' in parameter file

WARNING 6 [file production_prm.mdp, line unknown]:
  Unknown or double left-hand 'pull_group0' in parameter file

WARNING 7 [file production_prm.mdp, line unknown]:
  Unknown or double left-hand 'pull_group1' in parameter file

WARNING 8 [file production_prm.mdp, line unknown]:
  Unknown or double left-hand 'pull_rate1' in parameter file

WARNING 9 [file production_prm.mdp, line unknown]:
  Unknown or double left-hand 'pull_group2' in parameter file

WARNING 10 [file production_prm.mdp, line unknown]:
  Unknown or double left-hand 'pull_rate2' in parameter file

...

It appears that grompp doesnot recognize any of these keywords...

Does anybody can help?

Thank you
Andrei
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Re: [gmx-users] Warning: Pressure scaling more than 1%.

[Mark Abraham]

Pawan Kumar wrote:

Hi,

Increasing the tau-p value in the parameter file should help.


... if the problem is that tau-p is too small. If the problem is with 
the model physics or the equilibration, then the above either won't work 
or might mask the problem.


Mark
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Re: [gmx-users] Are Gromos 45a3 and GROMOS 53a6 compatible?

[XAvier Periole]

On May 11, 2009, at 6:18 AM, Chih-Ying Lin wrote:


Hi
GROMOS 45a3 force field
GROMOS 53a6 force field

Are they compatible?

Probably not. They are two different parameterization generations.
The 53a6 being more recent! Mixing them is probably not a good idea!
They have been parameterized differently!



Thank you
Lin
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Re: [gmx-users] Warning: Pressure scaling more than 1%.

[Pawan Kumar]

Hi,

Increasing the tau-p value in the parameter file should help.

Regards,
Pawan

On Mon, May 11, 2009 at 11:06 AM, Zhanglin Ni  wrote:

> Dear all,
> when I run position-restrained simulation (total 15000steps). when it
> reached 740 steps
> Step 741  Warning: Pressure scaling more than 1%.
>
> Step 742  Warning: Pressure scaling more than 1%.
>
> Step 743  Warning: Pressure scaling more than 1%.
>
> Step 744  Warning: Pressure scaling more than 1%.
>
> Step 745  Warning: Pressure scaling more than 1%.
>
> Step 746  Warning: Pressure scaling more than 1%.
>
> Step 747  Warning: Pressure scaling more than 1%.
>
> Step 748  Warning: Pressure scaling more than 1%.
>
> I knew the error was shown in the Gromacs websites. But after I read those,
> I still donot know how to solve it. any one give some clue. Thanks
> Johnny
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