date:20110726




smriti Sebastian wrote:

hi all,
I am new to GROMACS.I would like to know how we will simulate putting 
more than two or more molecules of same proteins inside the box and do 
simulation?Is there any possibility to replace 100 atoms or so of 
solvent with proteins?

Please help.



You received two replies the last time you asked this exact same question:

http://lists.gromacs.org/pipermail/gmx-users/2011-July/063145.html
http://lists.gromacs.org/pipermail/gmx-users/2011-July/063146.html

So what have you done to try to proceed?  If you want free help, you have to be 
willing to use what you're given to make some progress and report back with 
specific issues that arise.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] OPLS for group -N=CH2




bh...@udsu.ru wrote:

Dear users.

Help me.
What parametres of force field OPLS it is necessary to be used
for group -N=CH2 (imine group) ?



Check out the OPLS papers for suitable groups or atom types that are present, 
and if there's nothing already there, then you'll have to parameterize the group 
yourself (not a novice exercise):


http://www.gromacs.org/Documentation/How-tos/Parameterization

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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[gmx-users] genconf and bonded interactions


Hi all,
I used genconf because I wanted to replicate a membrane with ion channel 
on the xy plane:

genconf -f conf.gro -o out.gro -nbox 2 2 1

Then I edited by hand the .top file where I modified the number of 
molecules in the system.


When attempting to run, disregarding the number of processors, the mdrun 
crashes because domain decomposition fails.

Looking with attention to the log I find this:

Initializing Domain Decomposition on 4096 nodes
  Dynamic load balancing: auto
  Will sort the charge groups at every domain (re)decomposition
  Initial maximum inter charge-group distances:
two-body bonded interactions: 30.871 nm, LJ-14, atoms 193657 193660
multi-body bonded interactions: 30.871 nm, Angle, atoms 193656 193659
Minimum cell size due to bonded interactions: 33.959 nm
Maximum distance for 7 constraints, at 120 deg. angles, all-trans: 1.139 nm
Estimated maximum distance required for P-LINCS: 1.139 nm
Guess for relative PME load: 0.44
Will use 2304 particle-particle and 1792 PME only nodes
This is a guess, check the performance at the end of the log file
Using 1792 separate PME nodes
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 2304 cells with a minimum initial size of 42.448 
nm
The maximum allowed number of cells is: X 1 Y 1 Z 0


Now, I'm wondering why do I have such big bond interation length.. 31nm!
I guess that the problems in the DD arises from this.

Can you give me some suggestions?

Thanks in advance,

Fabio

--
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SuperComputing Applications and Innovation Department
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Tel: +39 051 6171794  Fax: +39 051 6132198
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Re: [gmx-users] genconf and bonded interactions




Fabio Affinito wrote:

Hi all,
I used genconf because I wanted to replicate a membrane with ion channel 
on the xy plane:

genconf -f conf.gro -o out.gro -nbox 2 2 1

Then I edited by hand the .top file where I modified the number of 
molecules in the system.


When attempting to run, disregarding the number of processors, the mdrun 
crashes because domain decomposition fails.

Looking with attention to the log I find this:

Initializing Domain Decomposition on 4096 nodes
  Dynamic load balancing: auto
  Will sort the charge groups at every domain (re)decomposition
  Initial maximum inter charge-group distances:
two-body bonded interactions: 30.871 nm, LJ-14, atoms 193657 193660
multi-body bonded interactions: 30.871 nm, Angle, atoms 193656 193659
Minimum cell size due to bonded interactions: 33.959 nm
Maximum distance for 7 constraints, at 120 deg. angles, all-trans: 
1.139 nm

Estimated maximum distance required for P-LINCS: 1.139 nm
Guess for relative PME load: 0.44
Will use 2304 particle-particle and 1792 PME only nodes
This is a guess, check the performance at the end of the log file
Using 1792 separate PME nodes
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 2304 cells with a minimum initial size 
of 42.448 nm

The maximum allowed number of cells is: X 1 Y 1 Z 0


Now, I'm wondering why do I have such big bond interation length.. 31nm!
I guess that the problems in the DD arises from this.

Can you give me some suggestions?



Were the molecules whole in the coordinate file you replicated?  If not, the 
bonds will now be assigned across the entire box.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] genconf and bonded interactions


On 07/26/2011 04:19 PM, Justin A. Lemkul wrote:



Were the molecules whole in the coordinate file you replicated? If not,
the bonds will now be assigned across the entire box.

-Justin


Yes and not, depending on what you mean by "whole".
It is an ion channel, so it's made of four chains.
This clarifies? (i guess not..)

F

--
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SuperComputing Applications and Innovation Department
CINECA - via Magnanelli, 6/3, 40033 Casalecchio di Reno (Bologna) - ITALY
Tel: +39 051 6171794  Fax: +39 051 6132198
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Re: [gmx-users] genconf and bonded interactions




Fabio Affinito wrote:

On 07/26/2011 04:19 PM, Justin A. Lemkul wrote:



Were the molecules whole in the coordinate file you replicated? If not,
the bonds will now be assigned across the entire box.

-Justin


Yes and not, depending on what you mean by "whole".
It is an ion channel, so it's made of four chains.
This clarifies? (i guess not..)


By whole, I mean that the molecules are not split across periodic boundaries in 
the initial configuration that you replicated.  If you replicate a periodic 
break, then you split the molecules by a distance equal to the new periodic 
distance.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] genconf and bonded interactions


On 07/26/2011 04:30 PM, Justin A. Lemkul wrote:



Fabio Affinito wrote:

On 07/26/2011 04:19 PM, Justin A. Lemkul wrote:



Were the molecules whole in the coordinate file you replicated? If not,
the bonds will now be assigned across the entire box.

-Justin


Yes and not, depending on what you mean by "whole".
It is an ion channel, so it's made of four chains.
This clarifies? (i guess not..)


By whole, I mean that the molecules are not split across periodic
boundaries in the initial configuration that you replicated. If you
replicate a periodic break, then you split the molecules by a distance
equal to the new periodic distance.

-Justin


Ok, so: no, it's not broken.


--
Fabio Affinito, PhD
SuperComputing Applications and Innovation Department
CINECA - via Magnanelli, 6/3, 40033 Casalecchio di Reno (Bologna) - ITALY
Tel: +39 051 6171794  Fax: +39 051 6132198
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Re: [gmx-users] genconf and bonded interactions




Fabio Affinito wrote:

On 07/26/2011 04:30 PM, Justin A. Lemkul wrote:



Fabio Affinito wrote:

On 07/26/2011 04:19 PM, Justin A. Lemkul wrote:



Were the molecules whole in the coordinate file you replicated? If not,
the bonds will now be assigned across the entire box.

-Justin


Yes and not, depending on what you mean by "whole".
It is an ion channel, so it's made of four chains.
This clarifies? (i guess not..)


By whole, I mean that the molecules are not split across periodic
boundaries in the initial configuration that you replicated. If you
replicate a periodic break, then you split the molecules by a distance
equal to the new periodic distance.

-Justin


Ok, so: no, it's not broken.



What you need to do is use the information mdrun provided you to diagnose what's 
going on.  Apparently atoms 193657 193660 are separated by 31 nm.  What are your 
box vectors?  Where are these atoms in the system?  Then you'll have your 
answer.  The only reason I can think of for such extreme distances is a 
periodicity issue.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] genconf and bonded interactions

Maybe this is a different issue... but it's ok that after the 99,999th 
atom the counter restarts from zero?



 21374SOL OW9  12.986   9.021   7.036 -0.0037 -0.4345  0.3977
 21374SOLHW10  13.069   8.987   7.081  0.5916  0.5409  0.0638


Could this be the origin of my problem?

Thanks again,

Fabio

On 07/26/2011 04:38 PM, Justin A. Lemkul wrote:



Fabio Affinito wrote:

On 07/26/2011 04:30 PM, Justin A. Lemkul wrote:



Fabio Affinito wrote:

On 07/26/2011 04:19 PM, Justin A. Lemkul wrote:



Were the molecules whole in the coordinate file you replicated? If
not,
the bonds will now be assigned across the entire box.

-Justin


Yes and not, depending on what you mean by "whole".
It is an ion channel, so it's made of four chains.
This clarifies? (i guess not..)


By whole, I mean that the molecules are not split across periodic
boundaries in the initial configuration that you replicated. If you
replicate a periodic break, then you split the molecules by a distance
equal to the new periodic distance.

-Justin


Ok, so: no, it's not broken.



What you need to do is use the information mdrun provided you to
diagnose what's going on. Apparently atoms 193657 193660 are separated
by 31 nm. What are your box vectors? Where are these atoms in the
system? Then you'll have your answer. The only reason I can think of for
such extreme distances is a periodicity issue.

-Justin




--
Fabio Affinito, PhD
SuperComputing Applications and Innovation Department
CINECA - via Magnanelli, 6/3, 40033 Casalecchio di Reno (Bologna) - ITALY
Tel: +39 051 6171794  Fax: +39 051 6132198
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Re: [gmx-users] genconf and bonded interactions




Fabio Affinito wrote:
Maybe this is a different issue... but it's ok that after the 99,999th 
atom the counter restarts from zero?



 21374SOL OW9  12.986   9.021   7.036 -0.0037 -0.4345  0.3977
 21374SOLHW10  13.069   8.987   7.081  0.5916  0.5409  0.0638


Could this be the origin of my problem?



Atom numbering is not the problem.  This happens all the time for systems of 
hundreds of thousands of atoms, which Gromacs handles just fine.  Please 
investigate the points I suggested before.


-Justin


Thanks again,

Fabio

On 07/26/2011 04:38 PM, Justin A. Lemkul wrote:



Fabio Affinito wrote:

On 07/26/2011 04:30 PM, Justin A. Lemkul wrote:



Fabio Affinito wrote:

On 07/26/2011 04:19 PM, Justin A. Lemkul wrote:



Were the molecules whole in the coordinate file you replicated? If
not,
the bonds will now be assigned across the entire box.

-Justin


Yes and not, depending on what you mean by "whole".
It is an ion channel, so it's made of four chains.
This clarifies? (i guess not..)


By whole, I mean that the molecules are not split across periodic
boundaries in the initial configuration that you replicated. If you
replicate a periodic break, then you split the molecules by a distance
equal to the new periodic distance.

-Justin


Ok, so: no, it's not broken.



What you need to do is use the information mdrun provided you to
diagnose what's going on. Apparently atoms 193657 193660 are separated
by 31 nm. What are your box vectors? Where are these atoms in the
system? Then you'll have your answer. The only reason I can think of for
such extreme distances is a periodicity issue.

-Justin






--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] genconf and bonded interactions


On 07/26/2011 05:06 PM, Justin A. Lemkul wrote:



Fabio Affinito wrote:

Maybe this is a different issue... but it's ok that after the 99,999th
atom the counter restarts from zero?


21374SOL OW9 12.986 9.021 7.036 -0.0037 -0.4345 0.3977
21374SOL HW1 0 13.069 8.987 7.081 0.5916 0.5409 0.0638


Could this be the origin of my problem?



Atom numbering is not the problem. This happens all the time for systems
of hundreds of thousands of atoms, which Gromacs handles just fine.
Please investigate the points I suggested before.


Yes, but this doesn't make things easier! :-)
According to the log the atoms to consider are 159986 and 159990

Browsing the conf.gro, if I didn't make mistakes this atoms are:


 30040POPGOE59986   0.080  13.158   2.964  0.0885  0.4154 -0.0859



 30040POPG   C1C59990   0.219  26.034   3.221  0.6449  0.0750  0.1313


But their distance is 12.8nm, while md.log reports 38.911 nm...

So what?

F.






-Justin


Thanks again,

Fabio

On 07/26/2011 04:38 PM, Justin A. Lemkul wrote:



Fabio Affinito wrote:

On 07/26/2011 04:30 PM, Justin A. Lemkul wrote:



Fabio Affinito wrote:

On 07/26/2011 04:19 PM, Justin A. Lemkul wrote:



Were the molecules whole in the coordinate file you replicated? If
not,
the bonds will now be assigned across the entire box.

-Justin


Yes and not, depending on what you mean by "whole".
It is an ion channel, so it's made of four chains.
This clarifies? (i guess not..)


By whole, I mean that the molecules are not split across periodic
boundaries in the initial configuration that you replicated. If you
replicate a periodic break, then you split the molecules by a distance
equal to the new periodic distance.

-Justin


Ok, so: no, it's not broken.



What you need to do is use the information mdrun provided you to
diagnose what's going on. Apparently atoms 193657 193660 are separated
by 31 nm. What are your box vectors? Where are these atoms in the
system? Then you'll have your answer. The only reason I can think of for
such extreme distances is a periodicity issue.

-Justin









--
Fabio Affinito, PhD
SuperComputing Applications and Innovation Department
CINECA - via Magnanelli, 6/3, 40033 Casalecchio di Reno (Bologna) - ITALY
Tel: +39 051 6171794  Fax: +39 051 6132198
--
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[gmx-users] On computing entropies using g_anaeig

2011-07-26 Thread Hari Shankar M

Gmx-users,

There has been a earlier post on differences in entropies computed using the 
covariance analysis and normal mode analysis 
(http://lists.gromacs.org/pipermail/gmx-users/2009-April/041535.html). I 
discovered the reason for the differences and thought that this information 
might be useful to others.

1. g_anaeig tool used to compute the entropy, computes entropies from the 
eigenvalues of the covariance matrix only. So, feeding the eigenvalues obtained 
from the mass-weighted Hessian to g_anaeig gives meaningless entropy values. 
Probably, this information should be clearly stated in the manual to prevent 
any potential abuse of g_anaeig. I compared the results on a diatomic molecule 
(oxygen) and benzene, and found very different results. The values differ by an 
order of magnitude. Also, looking at the source code of gmx_anaeig.c, it is 
clear that the entropies are computed from the covariance eigenvalues and not 
the eigenvalues of the Hessian. 

2. There is a user-developed code distributed on the gromacs website called 
'calc_entropies.pl'. This script can be used to compute entropies from 
eigenvalues obtained by covariance analysis or normal mode analysis. However, 
there seems to be a bug in this code. While the conversion of the eigenvalues 
to eigenfrequencies is done correctly in this code, there is a huge difference 
in the formula used to compute the entropy in the case of normal modes (for 
entropy formula refer to Karplus and Kushik 1981 paper). After correcting the 
entropy formula, I was able to get similar results with either method. If you 
are interested in the corrected script, you could email me at hari...@yahoo.com.

I hope this information is helpful for those who are working on entropies.

Best,
Hari
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[gmx-users] (no subject)

Hi all

I used the genion to add a concentration and to neutalize the system in the
same time by using the

   *genion -s file.tpr -conc 0.2 -neutral -o file.gro -random

   so it did add the NA and Cl but it did not neutralize the system,
the net charge of the system still the same negative.

   so i tried to use the genion seperate to neutralize the charge
using the file.tpr and out file as the file.gro,
   however it reset the file.gro and i lose the NA And CL ions added
for the concentration.

   any suggestions
   *
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[gmx-users] g_covar -xmpa

2011-07-26 Thread E. Nihal Korkmaz

Dear all,

Is there a "trick" to get the numbers for g_covar -xmpa?
If not how can i calculate -xmpa results from -xpm -ascii results?

Thanks
Nihal

-- 
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Research Assistant
University of Wisconsin - Biophysics
Member of Qiang Cui & Thomas Record Labs
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Re: [gmx-users] genconf and bonded interactions




Fabio Affinito wrote:

On 07/26/2011 05:06 PM, Justin A. Lemkul wrote:



Fabio Affinito wrote:

Maybe this is a different issue... but it's ok that after the 99,999th
atom the counter restarts from zero?


21374SOL OW9 12.986 9.021 7.036 -0.0037 -0.4345 0.3977
21374SOL HW1 0 13.069 8.987 7.081 0.5916 0.5409 0.0638


Could this be the origin of my problem?



Atom numbering is not the problem. This happens all the time for systems
of hundreds of thousands of atoms, which Gromacs handles just fine.
Please investigate the points I suggested before.


Yes, but this doesn't make things easier! :-)
According to the log the atoms to consider are 159986 and 159990



That's not what you posted before.  The .log output indicated atoms 193657 and 
193660 were problematic.



Browsing the conf.gro, if I didn't make mistakes this atoms are:


 30040POPGOE59986   0.080  13.158   2.964  0.0885  0.4154 -0.0859



 30040POPG   C1C59990   0.219  26.034   3.221  0.6449  0.0750  0.1313


But their distance is 12.8nm, while md.log reports 38.911 nm...



In any case, why are atoms four bonds (based on the original .log output of 1-4 
interactions being a problem) away separated by 12.8 nm?  Seems very odd to me. 
 I ask yet again - what are your box vectors, before and after manipulation 
with genconf?


-Justin


So what?

F.






-Justin


Thanks again,

Fabio

On 07/26/2011 04:38 PM, Justin A. Lemkul wrote:



Fabio Affinito wrote:

On 07/26/2011 04:30 PM, Justin A. Lemkul wrote:



Fabio Affinito wrote:

On 07/26/2011 04:19 PM, Justin A. Lemkul wrote:



Were the molecules whole in the coordinate file you replicated? If
not,
the bonds will now be assigned across the entire box.

-Justin


Yes and not, depending on what you mean by "whole".
It is an ion channel, so it's made of four chains.
This clarifies? (i guess not..)


By whole, I mean that the molecules are not split across periodic
boundaries in the initial configuration that you replicated. If you
replicate a periodic break, then you split the molecules by a 
distance

equal to the new periodic distance.

-Justin


Ok, so: no, it's not broken.



What you need to do is use the information mdrun provided you to
diagnose what's going on. Apparently atoms 193657 193660 are separated
by 31 nm. What are your box vectors? Where are these atoms in the
system? Then you'll have your answer. The only reason I can think of 
for

such extreme distances is a periodicity issue.

-Justin











--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] (no subject)

Sara baretller wrote:

Hi all

I used the genion to add a concentration and to neutalize the system in
the same time by using the

*genion -s file.tpr -conc 0.2 -neutral -o file.gro -random

so it did add the NA and Cl but it did not neutralize the system, the net
charge of the system still the same negative.

I find this hard to believe. The application of genion -conc -neutral has
worked in every instance I've tried it along every Gromacs version. Check your
output again.

so i tried to use the genion seperate to neutralize the charge using the file.tpr and out file as the file.gro,
however it reset the file.gro and i lose the NA And CL ions added for the concentration.

Without the actual sequence of commands, this is not a useful description.
genion adds ions based on whatever it finds in the .tpr file (which is
presumably not neutralized). If you do not re-create a .tpr file in between
different additions of ions, you're going to be undoing work you thought you did.

-Justin

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] PhD-position at the Institute for Physical and Theoretical Chemistry (IPTC) at Regensburg University, Germany

2011-07-26 Thread Emanuel Peter

Please excuse the spam if you are not interested in a PhD-position. Otherwise,
please read on ...

PhD-position at the Institute for Physical and Theoretical Chemistry (IPTC) at
Regensburg
University, Germany

We are seeking a highly motivated candidate for a PhD-position in the field of
Computational
Biophysical Chemistry. The project will involve the development and application
of multiscale
simulation techniques for studying of the interplay and signaling of
multi-protein complexes.
The successful candidate will be part of an interdisciplinary research
consortium „Chemical
Photocatalysis - GRK 1626“ funded by Deutsche Forschungsgemeinschaft (DFG) (see
for more
information http://www.chemie.uni-regensburg.de/fakultaet/forschung/grk1626/)

Candidates should have a Master degree in Chemistry, Computational Biophysics
or related fields,
as well as significant expertise in Molecular Dynamics simulations, Molecular
Modeling and/or
Monte Carlo techniques. Good programming skills in FORTRAN and/or C++ as well
as working
knowledge of unix operating systems would be beneficial.

The research project will be carried out within the Theory & Computation of
Advanced Materials
and Sensors group under guidance and supervision of PD Dr. Stephan A. Baeurle,
in collaboration
with experimentalists from the IPTC. Main working location will be the
Department of Physical
Chemistry at the Faculty of Chemistry and Pharmacy of Regensburg University.

To apply, please send a short motivation letter, CV, list of publications, and
contact details of
three references by 31 August 2011 to:

Stephan A. Baeurle
Priv.-Doz. Dr. rer. nat. habil.
Institut für Physikalische und Theoretische Chemie
Universität Regensburg
Universitätsstr. 31
D-93053 Regensburg
Telefon: +49 941 943 4470
E-mail: stephan.baeu...@chemie.uni-regensburg.de
Internet: 
www-dick.chemie.uni-regensburg.de/group/stephan_baeurle/9,0,group,index,0.html




PhD-Multiscale-Doktorandenstelle2.pdf
Description: Adobe PDF document
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Re: [gmx-users] Micelle Modeling

2011-07-26 Thread Janowicz, Adrianna C.

Im sorry for the confusion.
I used an .itp file from the UCalgary site for dpc, I input a line

[ molecules ]
; molecule name nr.
DPC 65
SOL 6305

in the dpc.top file.

However, I generated the .gro file directly from the m65.pdb file from the
UCalgary site using the editconf command.

>> WARNING 1 [file dpc.top, line 28]:
>>   18915 non-matching atom names
>>   atom names from dpc.top will be used <=(taken from 1 dpc.itp x 65)
>>   atom names from dpc.gro will be ignore <=(made from 65 dpc molecule pdb)


On Mon, July 25, 2011 8:21 am, Justin A. Lemkul wrote:
>
>
> Janowicz, Adrianna C. wrote:
>> I used your tutorial but am getting the error message
>>
>> WARNING 1 [file dpc.top, line 28]:
>>   18915 non-matching atom names
>>   atom names from dpc.top will be used
>>   atom names from dpc.gro will be ignore
>>
>> probably because my .top file was generated using a file generated thru
>> PRODRG (only inputing 23 DPC molecules and then specifying 65 of those
>> units) while the .gro file was created using the whole .pdb file of the
>> micelle containing all 65 units. How can I fix this error? -maxwarn 1
>> doesn't seem to be doing the trick.
>>
>
> I don't completely understand what you've done.  PRODRG uses a single
> molecule
> to produce a topology that can then be #included in the system topology.
> I
> don't know how you inputted 23 molecules and then specified 65.  What does
> this
> mean?
>
> Also note that PRODRG topologies are usually insufficiently accurate for
> actual
> use in simulations:
>
> http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips
>
> The source of the error could be one of several problems, please see:
>
> http://www.gromacs.org/Documentation/Errors#XXX_non-matching_atom_names
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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
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Re: [gmx-users] (no subject)

Hi All

I used the genion command using like this "genion -s file.tpr -conc 0.2
-neutral -o file.gro -random "  again and i checked the md.log file and it
says that the net charge is negative like it was before using the genion
command.

so can anybody tell me what is wrong with the line  genion -s file.tpr -conc
0.2 -neutral -o file.gro -random .

Sara



On Tue, Jul 26, 2011 at 1:05 PM, Justin A. Lemkul  wrote:

>
>
> Sara baretller wrote:
>
>> Hi all
>>
>> I used the genion to add a concentration and to neutalize the system in
>> the same time by using the
>>
>>  *genion -s file.tpr -conc 0.2 -neutral -o file.gro -random
>>  so it did add the NA and Cl but it did not neutralize the system, the
>> net charge of the system still the same negative.
>>
>>
> I find this hard to believe.  The application of genion -conc -neutral has
> worked in every instance I've tried it along every Gromacs version.  Check
> your output again.
>
>
>   so i tried to use the genion seperate to neutralize the charge using
>> the file.tpr and out file as the file.gro,   however it reset the
>> file.gro and i lose the NA And CL ions added for the concentration.
>>
>>
> Without the actual sequence of commands, this is not a useful description.
> genion adds ions based on whatever it finds in the .tpr file (which is
> presumably not neutralized).  If you do not re-create a .tpr file in between
> different additions of ions, you're going to be undoing work you thought you
> did.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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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> Support/Mailing_Lists/Searchbefore
>  posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
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> Can't post? Read 
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Re: [gmx-users] Micelle Modeling




Janowicz, Adrianna C. wrote:

Im sorry for the confusion.
I used an .itp file from the UCalgary site for dpc, I input a line

[ molecules ]
; molecule name nr.
DPC 65
SOL 6305

in the dpc.top file.

However, I generated the .gro file directly from the m65.pdb file from the
UCalgary site using the editconf command.


WARNING 1 [file dpc.top, line 28]:
  18915 non-matching atom names
  atom names from dpc.top will be used <=(taken from 1 dpc.itp x 65)
  atom names from dpc.gro will be ignore <=(made from 65 dpc molecule pdb)




I replicated the error.  The original coordinate file names its water hydrogens 
as HW2 and HW3 rather than HW1 and HW2, as expected by most common water models. 
 It is safe to ignore this error.


-Justin



On Mon, July 25, 2011 8:21 am, Justin A. Lemkul wrote:


Janowicz, Adrianna C. wrote:

I used your tutorial but am getting the error message

WARNING 1 [file dpc.top, line 28]:
  18915 non-matching atom names
  atom names from dpc.top will be used
  atom names from dpc.gro will be ignore

probably because my .top file was generated using a file generated thru
PRODRG (only inputing 23 DPC molecules and then specifying 65 of those
units) while the .gro file was created using the whole .pdb file of the
micelle containing all 65 units. How can I fix this error? -maxwarn 1
doesn't seem to be doing the trick.


I don't completely understand what you've done.  PRODRG uses a single
molecule
to produce a topology that can then be #included in the system topology.
I
don't know how you inputted 23 molecules and then specified 65.  What does
this
mean?

Also note that PRODRG topologies are usually insufficiently accurate for
actual
use in simulations:

http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips

The source of the error could be one of several problems, please see:

http://www.gromacs.org/Documentation/Errors#XXX_non-matching_atom_names

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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
MILES-IGERT Trainee
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] (no subject)




Sara baretller wrote:

Hi All

I used the genion command using like this "genion -s file.tpr -conc 0.2 
-neutral -o file.gro -random "  again and i checked the md.log file and 
it says that the net charge is negative like it was before using the 
genion command.


so can anybody tell me what is wrong with the line  genion -s file.tpr 
-conc 0.2 -neutral -o file.gro -random . 



Please copy and paste the exact (pertinent) output from the log file.

-Justin


Sara



On Tue, Jul 26, 2011 at 1:05 PM, Justin A. Lemkul > wrote:




Sara baretller wrote:

Hi all

I used the genion to add a concentration and to neutalize the
system in the same time by using the

 *genion -s file.tpr -conc 0.2 -neutral -o file.gro -random
 so it did add the NA and Cl but it did not neutralize the
system, the net charge of the system still the same negative.


I find this hard to believe.  The application of genion -conc
-neutral has worked in every instance I've tried it along every
Gromacs version.  Check your output again.


 so i tried to use the genion seperate to neutralize the
charge using the file.tpr and out file as the file.gro,  
however it reset the file.gro and i lose the NA And CL ions

added for the concentration.


Without the actual sequence of commands, this is not a useful
description. genion adds ions based on whatever it finds in the .tpr
file (which is presumably not neutralized).  If you do not re-create
a .tpr file in between different additions of ions, you're going to
be undoing work you thought you did.

-Justin

-- 
==__==


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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
MILES-IGERT Trainee
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] (no subject)

Hi

this a part of the md.log  where the system has -50 charge

  two-body bonded interactions: 0.407 nm, Bond, atoms 514 515
  multi-body bonded interactions: 0.731 nm, G96Angle, atoms 1272 1275
Minimum cell size due to bonded interactions: 0.804 nm
Maximum distance for 9 constraints, at 120 deg. angles, all-trans: 0.810 nm
Estimated maximum distance required for P-LINCS: 0.810 nm
This distance will limit the DD cell size, you can override this with -rcon
Optimizing the DD grid for 4 cells with a minimum initial size of 0.810 nm
The maximum allowed number of cells is: X 11 Y 11 Z 11
Domain decomposition grid 4 x 1 x 1, separate PME nodes 0
Domain decomposition nodeid 0, coordinates 0 0 0

Table routines are used for coulomb: TRUE
Table routines are used for vdw: TRUE
Using shifted Lennard-Jones, switch between 0.9 and 1.2 nm
Cut-off's:   NS: 1.2   Coulomb: 1.2   LJ: 1.2
System total charge: -50.000
Generated table with 1100 data points for Shift.
Tabscale = 500 points/nm
Generated table with 1100 data points for LJ6Shift.
Tabscale = 500 points/nm
Generated table with 1100 data points for LJ12Shift.
Tabscale = 500 points/nm
Configuring nonbonded kernels...
Configuring standard C nonbonded kernels...
Testing ia32 SSE2 support... present

On Tue, Jul 26, 2011 at 2:18 PM, Justin A. Lemkul  wrote:

>
>
> Sara baretller wrote:
>
>> Hi All
>>
>> I used the genion command using like this "genion -s file.tpr -conc 0.2
>> -neutral -o file.gro -random "  again and i checked the md.log file and it
>> says that the net charge is negative like it was before using the genion
>> command.
>>
>> so can anybody tell me what is wrong with the line  genion -s file.tpr
>> -conc 0.2 -neutral -o file.gro -random .
>>
>
> Please copy and paste the exact (pertinent) output from the log file.
>
> -Justin
>
>  Sara
>>
>>
>>
>>
>> On Tue, Jul 26, 2011 at 1:05 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Sara baretller wrote:
>>
>>Hi all
>>
>>I used the genion to add a concentration and to neutalize the
>>system in the same time by using the
>>
>> *genion -s file.tpr -conc 0.2 -neutral -o file.gro -random
>> so it did add the NA and Cl but it did not neutralize the
>>system, the net charge of the system still the same negative.
>>
>>
>>I find this hard to believe.  The application of genion -conc
>>-neutral has worked in every instance I've tried it along every
>>Gromacs version.  Check your output again.
>>
>>
>> so i tried to use the genion seperate to neutralize the
>>charge using the file.tpr and out file as the file.gro,
>>  however it reset the file.gro and i lose the NA And CL ions
>>added for the concentration.
>>
>>
>>Without the actual sequence of commands, this is not a useful
>>description. genion adds ions based on whatever it finds in the .tpr
>>file (which is presumably not neutralized).  If you do not re-create
>>a .tpr file in between different additions of ions, you're going to
>>be undoing work you thought you did.
>>
>>-Justin
>>
>>-- ==**__==
>>
>>Justin A. Lemkul
>>Ph.D. Candidate
>>ICTAS Doctoral Scholar
>>MILES-IGERT Trainee
>>Department of Biochemistry
>>Virginia Tech
>>Blacksburg, VA
>>jalemkul[at]vt.edu  | (540) 231-9080
>>
>>
>>
>> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin
>>
>> 
>> >
>>
>>==**__==
>>-- gmx-users mailing listgmx-users@gromacs.org
>>
>>
>>
>> http://lists.gromacs.org/__**mailman/listinfo/gmx-users
>>
>> 
>> >
>>Please search the archive at
>>
>> http://www.gromacs.org/__**Support/Mailing_Lists/Search
>>
>> >
>> before posting!
>>Please don't post (un)subscribe requests to the list. Use the www
>>interface or send it to gmx-users-requ...@gromacs.org
>>> >.
>>
>>Can't post? Read 
>> http://www.gromacs.org/__**Support/Mailing_Lists
>>
>> 
>> >
>>
>>
>>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.e

Re: [gmx-users] (no subject)

Sara baretller wrote:

Hi

this a part of the md.log  where the system has -50 charge

  two-body bonded interactions: 0.407 nm, Bond, atoms 514 515
  multi-body bonded interactions: 0.731 nm, G96Angle, atoms 1272 1275
Minimum cell size due to bonded interactions: 0.804 nm
Maximum distance for 9 constraints, at 120 deg. angles, all-trans: 0.810 nm
Estimated maximum distance required for P-LINCS: 0.810 nm
This distance will limit the DD cell size, you can override this with -rcon
Optimizing the DD grid for 4 cells with a minimum initial size of 0.810 nm
The maximum allowed number of cells is: X 11 Y 11 Z 11
Domain decomposition grid 4 x 1 x 1, separate PME nodes 0
Domain decomposition nodeid 0, coordinates 0 0 0

Table routines are used for coulomb: TRUE
Table routines are used for vdw: TRUE
Using shifted Lennard-Jones, switch between 0.9 and 1.2 nm
Cut-off's:   NS: 1.2   Coulomb: 1.2   LJ: 1.2
System total charge: -50.000
Generated table with 1100 data points for Shift.
Tabscale = 500 points/nm
Generated table with 1100 data points for LJ6Shift.
Tabscale = 500 points/nm
Generated table with 1100 data points for LJ12Shift.
Tabscale = 500 points/nm
Configuring nonbonded kernels...
Configuring standard C nonbonded kernels...
Testing ia32 SSE2 support... present

There's nothing abnormal here.  genion reports that it finds a -50 charge on the 
system.  That's what it's supposed to do.  Based on what it finds in the 
topology, it adds neutralizing ions and any additional ions to reach the 
specified concentration.  You only have a problem if grompp later complains that 
there's still some residual charge (excluding tiny rounding discrepancies).

-Justin

On Tue, Jul 26, 2011 at 2:18 PM, Justin A. Lemkul > wrote:

Sara baretller wrote:

Hi All

I used the genion command using like this "genion -s file.tpr
-conc 0.2 -neutral -o file.gro -random "  again and i checked
the md.log file and it says that the net charge is negative like
it was before using the genion command.

so can anybody tell me what is wrong with the line  genion -s
file.tpr -conc 0.2 -neutral -o file.gro -random .

Please copy and paste the exact (pertinent) output from the log file.

-Justin

Sara

On Tue, Jul 26, 2011 at 1:05 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:

   Sara baretller wrote:

   Hi all

   I used the genion to add a concentration and to neutalize the
   system in the same time by using the

*genion -s file.tpr -conc 0.2 -neutral -o file.gro
-random
so it did add the NA and Cl but it did not
neutralize the
   system, the net charge of the system still the same negative.

   I find this hard to believe.  The application of genion -conc
   -neutral has worked in every instance I've tried it along every
   Gromacs version.  Check your output again.

so i tried to use the genion seperate to neutralize the
   charge using the file.tpr and out file as the file.gro,  
   however it reset the file.gro and i lose the NA And

CL ions
   added for the concentration.

   Without the actual sequence of commands, this is not a useful
   description. genion adds ions based on whatever it finds in
the .tpr
   file (which is presumably not neutralized).  If you do not
re-create
   a .tpr file in between different additions of ions, you're
going to
   be undoing work you thought you did.

   -Justin

   -- ====

   Justin A. Lemkul
   Ph.D. Candidate
   ICTAS Doctoral Scholar
   MILES-IGERT Trainee
   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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   >

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Re: [gmx-users] Micelle Modeling

2011-07-26 Thread Janowicz, Adrianna C.


thanks! one last problem:
Im using the dpc.itp file & I keep getting an error having a problem with
the 0 mass for the atoms 11-23 (I've searched forums & haven't found
anyone having a problem with the 0 masses), along with   No default Proper
Dih. types,  No default Bond types  No default Ryckaert-Bell. types &  No
default LJ-14 types!!



DPC.itp from UCalgary site:
1 CH3   1DPC  C1   1 0.4; qtot: 0.248
 2 CH3   1DPC  C2   1 0.4   ; qtot: 0.496
 3 CH3   1DPC  C3   1 0.4   ; qtot: 0.744
 4  NL   1DPC  N4   1-0.5   ; qtot: 0.752
 5 CH2   1DPC  C5   1 0.3   ; qtot: 1
 6 CH2   1DPC  C6   1 0.4   ; qtot: 1
 7  LOS   1DPC  O7   1-0.8  ; qtot: 0.64
 8   P   1DPC  P8   1 1.7   ; qtot: 1.64
 9  OM   1DPC  O9   1-0.8   ; qtot: 1
10  OM   1DPC O10   1-0.8   ; qtot: 0.36
11  LOS   1DPC O11   1-0.7  ; qtot: 0
12 CH2   1DPC C12   5 0 ; qtot: 0
13 CH2   1DPC C13   6 0 ; qtot: 0
14 CH2   1DPC C14   7 0 ; qtot: 0
15 CH2   1DPC C15   8 0 ; qtot: 0
16 CH2   1DPC C16   9 0 ; qtot: 0
17 CH2   1DPC C17  10 0 ; qtot: 0
18 CH2   1DPC C18  11 0 ; qtot: 0
19 CH2   1DPC C19  12 0 ; qtot: 0
20 CH2   1DPC C20  13 0 ; qtot: 0
21 CH2   1DPC C21  14 0 ; qtot: 0
22 CH2   1DPC C22  15 0 ; qtot: 0
23 CH3   1DPC C23  16 0 ; qtot: 0




On Tue, July 26, 2011 1:16 pm, Justin A. Lemkul wrote:
>
>
> Janowicz, Adrianna C. wrote:
>> Im sorry for the confusion.
>> I used an .itp file from the UCalgary site for dpc, I input a line
>>
>> [ molecules ]
>> ; molecule name nr.
>> DPC 65
>> SOL 6305
>>
>> in the dpc.top file.
>>
>> However, I generated the .gro file directly from the m65.pdb file from
>> the
>> UCalgary site using the editconf command.
>>
 WARNING 1 [file dpc.top, line 28]:
   18915 non-matching atom names
   atom names from dpc.top will be used <=(taken from 1 dpc.itp x 65)
   atom names from dpc.gro will be ignore <=(made from 65 dpc molecule
 pdb)
>>
>
> I replicated the error.  The original coordinate file names its water
> hydrogens
> as HW2 and HW3 rather than HW1 and HW2, as expected by most common water
> models.
>   It is safe to ignore this error.
>
> -Justin
>
>>
>> On Mon, July 25, 2011 8:21 am, Justin A. Lemkul wrote:
>>>
>>> Janowicz, Adrianna C. wrote:
 I used your tutorial but am getting the error message

 WARNING 1 [file dpc.top, line 28]:
   18915 non-matching atom names
   atom names from dpc.top will be used
   atom names from dpc.gro will be ignore

 probably because my .top file was generated using a file generated
 thru
 PRODRG (only inputing 23 DPC molecules and then specifying 65 of those
 units) while the .gro file was created using the whole .pdb file of
 the
 micelle containing all 65 units. How can I fix this error? -maxwarn 1
 doesn't seem to be doing the trick.

>>> I don't completely understand what you've done.  PRODRG uses a single
>>> molecule
>>> to produce a topology that can then be #included in the system
>>> topology.
>>> I
>>> don't know how you inputted 23 molecules and then specified 65.  What
>>> does
>>> this
>>> mean?
>>>
>>> Also note that PRODRG topologies are usually insufficiently accurate
>>> for
>>> actual
>>> use in simulations:
>>>
>>> http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips
>>>
>>> The source of the error could be one of several problems, please see:
>>>
>>> http://www.gromacs.org/Documentation/Errors#XXX_non-matching_atom_names
>>>
>>> -Justin
>>>
>>> --
>>> 
>>>
>>> Justin A. Lemkul
>>> Ph.D. Candidate
>>> ICTAS Doctoral Scholar
>>> MILES-IGERT Trainee
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>> 
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it

Re: [gmx-users] Micelle Modeling




Janowicz, Adrianna C. wrote:

thanks! one last problem:
Im using the dpc.itp file & I keep getting an error having a problem with
the 0 mass for the atoms 11-23 (I've searched forums & haven't found
anyone having a problem with the 0 masses), along with   No default Proper
Dih. types,  No default Bond types  No default Ryckaert-Bell. types &  No
default LJ-14 types!!



These errors come up all the time, I'm surprised you haven't found the answers 
in the archive.


With respect to the zero masses, it's because the [atoms] section does not list 
masses, so they're set to zero.  The proper format would have mass listed in the 
column to the right of charge.  The reason it's missing is because the topology 
posted online is for (1) an ancient version of Gromacs (probably in the 3.x 
series) and (2) for use with the deprecated ffgmx force field, which had some 
different internal mechanics.  Note that this is not a reason to use ffgmx 
(please refer to the manual for the full explanation as to why you shouldn't use 
it).


The missing parameters are also probably due to similar issues.  I believe you 
said you were using my tutorial as a basis for your simulations, so you'll have 
to make all the parameters conform to the 53a6 nomenclature.  For instance, atom 
type OS was replaced by either OE or OA, depending on the functional group. 
You'll have to update the topology accordingly.  There are probably other such 
issues, as well.


-Justin




DPC.itp from UCalgary site:
1 CH3   1DPC  C1   1 0.4; qtot: 0.248
 2 CH3   1DPC  C2   1 0.4   ; qtot: 0.496
 3 CH3   1DPC  C3   1 0.4   ; qtot: 0.744
 4  NL   1DPC  N4   1-0.5   ; qtot: 0.752
 5 CH2   1DPC  C5   1 0.3   ; qtot: 1
 6 CH2   1DPC  C6   1 0.4   ; qtot: 1
 7  LOS   1DPC  O7   1-0.8  ; qtot: 0.64
 8   P   1DPC  P8   1 1.7   ; qtot: 1.64
 9  OM   1DPC  O9   1-0.8   ; qtot: 1
10  OM   1DPC O10   1-0.8   ; qtot: 0.36
11  LOS   1DPC O11   1-0.7  ; qtot: 0
12 CH2   1DPC C12   5 0 ; qtot: 0
13 CH2   1DPC C13   6 0 ; qtot: 0
14 CH2   1DPC C14   7 0 ; qtot: 0
15 CH2   1DPC C15   8 0 ; qtot: 0
16 CH2   1DPC C16   9 0 ; qtot: 0
17 CH2   1DPC C17  10 0 ; qtot: 0
18 CH2   1DPC C18  11 0 ; qtot: 0
19 CH2   1DPC C19  12 0 ; qtot: 0
20 CH2   1DPC C20  13 0 ; qtot: 0
21 CH2   1DPC C21  14 0 ; qtot: 0
22 CH2   1DPC C22  15 0 ; qtot: 0
23 CH3   1DPC C23  16 0 ; qtot: 0




On Tue, July 26, 2011 1:16 pm, Justin A. Lemkul wrote:


Janowicz, Adrianna C. wrote:

Im sorry for the confusion.
I used an .itp file from the UCalgary site for dpc, I input a line

[ molecules ]
; molecule name nr.
DPC 65
SOL 6305

in the dpc.top file.

However, I generated the .gro file directly from the m65.pdb file from
the
UCalgary site using the editconf command.


WARNING 1 [file dpc.top, line 28]:
  18915 non-matching atom names
  atom names from dpc.top will be used <=(taken from 1 dpc.itp x 65)
  atom names from dpc.gro will be ignore <=(made from 65 dpc molecule
pdb)

I replicated the error.  The original coordinate file names its water
hydrogens
as HW2 and HW3 rather than HW1 and HW2, as expected by most common water
models.
  It is safe to ignore this error.

-Justin


On Mon, July 25, 2011 8:21 am, Justin A. Lemkul wrote:

Janowicz, Adrianna C. wrote:

I used your tutorial but am getting the error message

WARNING 1 [file dpc.top, line 28]:
  18915 non-matching atom names
  atom names from dpc.top will be used
  atom names from dpc.gro will be ignore

probably because my .top file was generated using a file generated
thru
PRODRG (only inputing 23 DPC molecules and then specifying 65 of those
units) while the .gro file was created using the whole .pdb file of
the
micelle containing all 65 units. How can I fix this error? -maxwarn 1
doesn't seem to be doing the trick.


I don't completely understand what you've done.  PRODRG uses a single
molecule
to produce a topology that can then be #included in the system
topology.
I
don't know how you inputted 23 molecules and then specified 65.  What
does
this
mean?

Also note that PRODRG topologies are usually insufficiently accurate
for
actual
use in simulations:

http://www.gromacs.org

[gmx-users] QMMM Semi-empirical Error

2011-07-26 Thread Yao Yao

Hi Guys,

I met a problem when I ran qmmm using semi-empirical method in gmx,



"Subscript out of range on file line 659, procedure moldat.
Attempt to access the 0-th element of variable eheat.
Aborted"

I googled it, but there seems no archived info online. Has anyone met this 
before?

Thanks,

Yao Yao-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Re: [gmx-users] (no subject)

thanks but i want to neutralize the system , why genion -s file.tpr -conc
0.2 -neutral -o file.gro -random  does not neutralize the system to 0 .


On Tue, Jul 26, 2011 at 3:48 PM, Justin A. Lemkul  wrote:

>
>
> Sara baretller wrote:
>
>> Hi
>>
>> this a part of the md.log  where the system has -50 charge
>>
>>  two-body bonded interactions: 0.407 nm, Bond, atoms 514 515
>>  multi-body bonded interactions: 0.731 nm, G96Angle, atoms 1272 1275
>> Minimum cell size due to bonded interactions: 0.804 nm
>> Maximum distance for 9 constraints, at 120 deg. angles, all-trans: 0.810
>> nm
>> Estimated maximum distance required for P-LINCS: 0.810 nm
>> This distance will limit the DD cell size, you can override this with
>> -rcon
>> Optimizing the DD grid for 4 cells with a minimum initial size of 0.810 nm
>> The maximum allowed number of cells is: X 11 Y 11 Z 11
>> Domain decomposition grid 4 x 1 x 1, separate PME nodes 0
>> Domain decomposition nodeid 0, coordinates 0 0 0
>>
>> Table routines are used for coulomb: TRUE
>> Table routines are used for vdw: TRUE
>> Using shifted Lennard-Jones, switch between 0.9 and 1.2 nm
>> Cut-off's:   NS: 1.2   Coulomb: 1.2   LJ: 1.2
>> System total charge: -50.000
>> Generated table with 1100 data points for Shift.
>> Tabscale = 500 points/nm
>> Generated table with 1100 data points for LJ6Shift.
>> Tabscale = 500 points/nm
>> Generated table with 1100 data points for LJ12Shift.
>> Tabscale = 500 points/nm
>> Configuring nonbonded kernels...
>> Configuring standard C nonbonded kernels...
>> Testing ia32 SSE2 support... present
>>
>>
> There's nothing abnormal here.  genion reports that it finds a -50 charge
> on the system.  That's what it's supposed to do.  Based on what it finds in
> the topology, it adds neutralizing ions and any additional ions to reach the
> specified concentration.  You only have a problem if grompp later complains
> that there's still some residual charge (excluding tiny rounding
> discrepancies).
>
> -Justin
>
>  On Tue, Jul 26, 2011 at 2:18 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Sara baretller wrote:
>>
>>Hi All
>>
>>I used the genion command using like this "genion -s file.tpr
>>-conc 0.2 -neutral -o file.gro -random "  again and i checked
>>the md.log file and it says that the net charge is negative like
>>it was before using the genion command.
>>
>>so can anybody tell me what is wrong with the line  genion -s
>>file.tpr -conc 0.2 -neutral -o file.gro -random .
>>
>>
>>Please copy and paste the exact (pertinent) output from the log file.
>>
>>-Justin
>>
>>Sara
>>
>>
>>
>>
>>On Tue, Jul 26, 2011 at 1:05 PM, Justin A. Lemkul
>>mailto:jalem...@vt.edu>
>>>> wrote:
>>
>>
>>
>>   Sara baretller wrote:
>>
>>   Hi all
>>
>>   I used the genion to add a concentration and to neutalize
>> the
>>   system in the same time by using the
>>
>>*genion -s file.tpr -conc 0.2 -neutral -o file.gro
>>-random
>>so it did add the NA and Cl but it did not
>>neutralize the
>>   system, the net charge of the system still the same
>> negative.
>>
>>
>>   I find this hard to believe.  The application of genion -conc
>>   -neutral has worked in every instance I've tried it along every
>>   Gromacs version.  Check your output again.
>>
>>
>>so i tried to use the genion seperate to neutralize the
>>   charge using the file.tpr and out file as the file.gro,
>> however it reset the file.gro and i lose the NA And
>>CL ions
>>   added for the concentration.
>>
>>
>>   Without the actual sequence of commands, this is not a useful
>>   description. genion adds ions based on whatever it finds in
>>the .tpr
>>   file (which is presumably not neutralized).  If you do not
>>re-create
>>   a .tpr file in between different additions of ions, you're
>>going to
>>   be undoing work you thought you did.
>>
>>   -Justin
>>
>>   -- ==**==
>>
>>   Justin A. Lemkul
>>   Ph.D. Candidate
>>   ICTAS Doctoral Scholar
>>   MILES-IGERT Trainee
>>   Department of Biochemistry
>>   Virginia Tech
>>   Blacksburg, VA
>>   jalemkul[at]vt.edu   | (540)
>>
>>231-9080 
>>   
>>
>>   http://www.bevanlab.biochem.__**__vt.edu/Pages/Personal/justin
>>
>> 
>> >
>>
>>   >
>>

Re: [gmx-users] (no subject)

2011-07-26 Thread Warren Gallin

You are not specifying the ions to be added using the -pname and -nname options 
with the genion command.

Perhaps that is a problem?

Warren Gallin

On 2011-07-26, at 2:49 PM, Sara baretller wrote:

> thanks but i want to neutralize the system , why genion -s file.tpr -conc 0.2 
> -neutral -o file.gro -random  does not neutralize the system to 0 .
> 
> 
> On Tue, Jul 26, 2011 at 3:48 PM, Justin A. Lemkul  wrote:
> 
> 
> Sara baretller wrote:
> Hi
> 
> this a part of the md.log  where the system has -50 charge
> 
>  two-body bonded interactions: 0.407 nm, Bond, atoms 514 515
>  multi-body bonded interactions: 0.731 nm, G96Angle, atoms 1272 1275
> Minimum cell size due to bonded interactions: 0.804 nm
> Maximum distance for 9 constraints, at 120 deg. angles, all-trans: 0.810 nm
> Estimated maximum distance required for P-LINCS: 0.810 nm
> This distance will limit the DD cell size, you can override this with -rcon
> Optimizing the DD grid for 4 cells with a minimum initial size of 0.810 nm
> The maximum allowed number of cells is: X 11 Y 11 Z 11
> Domain decomposition grid 4 x 1 x 1, separate PME nodes 0
> Domain decomposition nodeid 0, coordinates 0 0 0
> 
> Table routines are used for coulomb: TRUE
> Table routines are used for vdw: TRUE
> Using shifted Lennard-Jones, switch between 0.9 and 1.2 nm
> Cut-off's:   NS: 1.2   Coulomb: 1.2   LJ: 1.2
> System total charge: -50.000
> Generated table with 1100 data points for Shift.
> Tabscale = 500 points/nm
> Generated table with 1100 data points for LJ6Shift.
> Tabscale = 500 points/nm
> Generated table with 1100 data points for LJ12Shift.
> Tabscale = 500 points/nm
> Configuring nonbonded kernels...
> Configuring standard C nonbonded kernels...
> Testing ia32 SSE2 support... present
> 
> 
> There's nothing abnormal here.  genion reports that it finds a -50 charge on 
> the system.  That's what it's supposed to do.  Based on what it finds in the 
> topology, it adds neutralizing ions and any additional ions to reach the 
> specified concentration.  You only have a problem if grompp later complains 
> that there's still some residual charge (excluding tiny rounding 
> discrepancies).
> 
> -Justin
> 
> On Tue, Jul 26, 2011 at 2:18 PM, Justin A. Lemkul  > wrote:
> 
> 
> 
>Sara baretller wrote:
> 
>Hi All
> 
>I used the genion command using like this "genion -s file.tpr
>-conc 0.2 -neutral -o file.gro -random "  again and i checked
>the md.log file and it says that the net charge is negative like
>it was before using the genion command.
> 
>so can anybody tell me what is wrong with the line  genion -s
>file.tpr -conc 0.2 -neutral -o file.gro -random .
> 
> 
>Please copy and paste the exact (pertinent) output from the log file.
> 
>-Justin
> 
>Sara
> 
> 
> 
> 
>On Tue, Jul 26, 2011 at 1:05 PM, Justin A. Lemkul
>mailto:jalem...@vt.edu>
>>> wrote:
> 
> 
> 
>   Sara baretller wrote:
> 
>   Hi all
> 
>   I used the genion to add a concentration and to neutalize the
>   system in the same time by using the
> 
>*genion -s file.tpr -conc 0.2 -neutral -o file.gro
>-random
>so it did add the NA and Cl but it did not
>neutralize the
>   system, the net charge of the system still the same negative.
> 
> 
>   I find this hard to believe.  The application of genion -conc
>   -neutral has worked in every instance I've tried it along every
>   Gromacs version.  Check your output again.
> 
> 
>so i tried to use the genion seperate to neutralize the
>   charge using the file.tpr and out file as the file.gro, 
> however it reset the file.gro and i lose the NA And
>CL ions
>   added for the concentration.
> 
> 
>   Without the actual sequence of commands, this is not a useful
>   description. genion adds ions based on whatever it finds in
>the .tpr
>   file (which is presumably not neutralized).  If you do not
>re-create
>   a .tpr file in between different additions of ions, you're
>going to
>   be undoing work you thought you did.
> 
>   -Justin
> 
>   -- ====
> 
>   Justin A. Lemkul
>   Ph.D. Candidate
>   ICTAS Doctoral Scholar
>   MILES-IGERT Trainee
>   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] GROMACS+CPMD QM/MM

2011-07-26 Thread Jacob Jantzi

Hello everyone,

I'm trying to run Gromacs, and use CPMD for QM. I have cpmd compiled and
running, but when I try to start mdrun_d with gromacs, I get the following
error:

QM/MM calculation requested.
Layer 0
nr of QM atoms 2
QMlevel: DIRECT/STO-3G

number of CPUs for gaussian = 1
memory for gaussian = 5000
accuracy in l510 = 8
NOT using cp-mcscf in l1003
Level of SA at start = 0
Segmentation fault

Does this mean that gromacs is attempting to use guassian for QM instead
of cpmd? I compiled gromacs with the options: --disable-float
--with-fftw=fftw3 --with-qmmm-cpmd.

I am using the cpmd-specific gromacs version 3.3.1 (available at
http://www.tougaloo.edu/research/qmmm/) with cpmd version 3.15.1.

Thanks for any help you can provide!

-Jacob Jantzi

-- 
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Please search the archive at 
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Re: [gmx-users] (no subject)




Warren Gallin wrote:

You are not specifying the ions to be added using the -pname and -nname options 
with the genion command.

Perhaps that is a problem?



They are not necessary; the default names are used and should be correct for all 
force fields now that naming has been standardized.


Thus far I have seen no evidence that genion is not doing what it is supposed 
to.  It reports finding a net -50 charge on the system.  What happens then? 
Does the output coordinate file contain ions?  The topology will not be modified 
because genion is not being told to (i.e. through the use of -p).


-Justin


Warren Gallin

On 2011-07-26, at 2:49 PM, Sara baretller wrote:


thanks but i want to neutralize the system , why genion -s file.tpr -conc 0.2 
-neutral -o file.gro -random  does not neutralize the system to 0 .


On Tue, Jul 26, 2011 at 3:48 PM, Justin A. Lemkul  wrote:


Sara baretller wrote:
Hi

this a part of the md.log  where the system has -50 charge

 two-body bonded interactions: 0.407 nm, Bond, atoms 514 515
 multi-body bonded interactions: 0.731 nm, G96Angle, atoms 1272 1275
Minimum cell size due to bonded interactions: 0.804 nm
Maximum distance for 9 constraints, at 120 deg. angles, all-trans: 0.810 nm
Estimated maximum distance required for P-LINCS: 0.810 nm
This distance will limit the DD cell size, you can override this with -rcon
Optimizing the DD grid for 4 cells with a minimum initial size of 0.810 nm
The maximum allowed number of cells is: X 11 Y 11 Z 11
Domain decomposition grid 4 x 1 x 1, separate PME nodes 0
Domain decomposition nodeid 0, coordinates 0 0 0

Table routines are used for coulomb: TRUE
Table routines are used for vdw: TRUE
Using shifted Lennard-Jones, switch between 0.9 and 1.2 nm
Cut-off's:   NS: 1.2   Coulomb: 1.2   LJ: 1.2
System total charge: -50.000
Generated table with 1100 data points for Shift.
Tabscale = 500 points/nm
Generated table with 1100 data points for LJ6Shift.
Tabscale = 500 points/nm
Generated table with 1100 data points for LJ12Shift.
Tabscale = 500 points/nm
Configuring nonbonded kernels...
Configuring standard C nonbonded kernels...
Testing ia32 SSE2 support... present


There's nothing abnormal here.  genion reports that it finds a -50 charge on 
the system.  That's what it's supposed to do.  Based on what it finds in the 
topology, it adds neutralizing ions and any additional ions to reach the 
specified concentration.  You only have a problem if grompp later complains 
that there's still some residual charge (excluding tiny rounding discrepancies).

-Justin

On Tue, Jul 26, 2011 at 2:18 PM, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote:



   Sara baretller wrote:

   Hi All

   I used the genion command using like this "genion -s file.tpr
   -conc 0.2 -neutral -o file.gro -random "  again and i checked
   the md.log file and it says that the net charge is negative like
   it was before using the genion command.

   so can anybody tell me what is wrong with the line  genion -s
   file.tpr -conc 0.2 -neutral -o file.gro -random .


   Please copy and paste the exact (pertinent) output from the log file.

   -Justin

   Sara




   On Tue, Jul 26, 2011 at 1:05 PM, Justin A. Lemkul
   mailto:jalem...@vt.edu>
   >> wrote:



  Sara baretller wrote:

  Hi all

  I used the genion to add a concentration and to neutalize the
  system in the same time by using the

   *genion -s file.tpr -conc 0.2 -neutral -o file.gro
   -random
   so it did add the NA and Cl but it did not
   neutralize the
  system, the net charge of the system still the same negative.


  I find this hard to believe.  The application of genion -conc
  -neutral has worked in every instance I've tried it along every
  Gromacs version.  Check your output again.


   so i tried to use the genion seperate to neutralize the
  charge using the file.tpr and out file as the file.gro,   
  however it reset the file.gro and i lose the NA And
   CL ions
  added for the concentration.


  Without the actual sequence of commands, this is not a useful
  description. genion adds ions based on whatever it finds in
   the .tpr
  file (which is presumably not neutralized).  If you do not
   re-create
  a .tpr file in between different additions of ions, you're
   going to
  be undoing work you thought you did.

  -Justin

  -- ====

  Justin A. Lemkul
  Ph.D. Candidate
  ICTAS Doctoral Scholar
  MILES-IGERT Trainee
  Department of Biochemistry
  Virginia Tech
  Blacksburg, VA
  jalemkul[at]vt.edu   | (540)

   231-9080

Re: [gmx-users] GROMACS+CPMD QM/MM

2011-07-26 Thread Kunze, Micha

Hey Jacob,

I think you also have to use the flag --without-qmmm-gaussian.

Cheers,
Micha

On 26 Jul 2011, at 21:26, Jacob Jantzi wrote:

> Hello everyone,
> 
> I'm trying to run Gromacs, and use CPMD for QM. I have cpmd compiled and
> running, but when I try to start mdrun_d with gromacs, I get the following
> error:
> 
> QM/MM calculation requested.
> Layer 0
> nr of QM atoms 2
> QMlevel: DIRECT/STO-3G
> 
> number of CPUs for gaussian = 1
> memory for gaussian = 5000
> accuracy in l510 = 8
> NOT using cp-mcscf in l1003
> Level of SA at start = 0
> Segmentation fault
> 
> Does this mean that gromacs is attempting to use guassian for QM instead
> of cpmd? I compiled gromacs with the options: --disable-float
> --with-fftw=fftw3 --with-qmmm-cpmd.
> 
> I am using the cpmd-specific gromacs version 3.3.1 (available at
> http://www.tougaloo.edu/research/qmmm/) with cpmd version 3.15.1.
> 
> Thanks for any help you can provide!
> 
> -Jacob Jantzi
> 
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-
Micha BA Kunze
PhD Student

Institute of Structural and Molecular Biology
Division of Biosciences
University College London
Gower Steet
London, WC1E 6BT
UK

Mail: micha.kunze...@ucl.ac.uk
Tel:   +44 7403 074054

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[gmx-users] vdW cutoff

2011-07-26 Thread Fabian Casteblanco

Hello,

I am quite confused on whether it is better to use a standard cut-off
scheme for vdW interactions or if its better to use a switch or shift
function for this.  I am doing a free energy calculation on the
solvation of a drug molecule in a solvent (on CHARMM ff) so I want to
be as accurate as possible.  The CHARMM paper does state that they use
some type of switch function between 10 A and 12 A but I'm confused on
the difference between 'Switch' and 'Shift'.  I ran the solvents alone
using these different types and it seems to give similar results.  Is
this a major decision to getting accurate free energy calculations?
Will using standard 14 A cutoffs with DispersionCorrection=EnerPres be
enough?

Thanks for anyone with knowledge in this area.

-- 
Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
E:  fabian.castebla...@gmail.com
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Re: [gmx-users] (no subject)

hi all

yes the gro file does have all  ions,  NA + number of ions equal to CL
number. so when i use grep command , i have same number of NA and CL and
that what tells me that something is wrong , because i should have another
50 ions of NA extra  to neutralize the system

Thank you



On Tue, Jul 26, 2011 at 5:03 PM, Justin A. Lemkul  wrote:

>
>
> Warren Gallin wrote:
>
>> You are not specifying the ions to be added using the -pname and -nname
>> options with the genion command.
>>
>> Perhaps that is a problem?
>>
>>
> They are not necessary; the default names are used and should be correct
> for all force fields now that naming has been standardized.
>
> Thus far I have seen no evidence that genion is not doing what it is
> supposed to.  It reports finding a net -50 charge on the system.  What
> happens then? Does the output coordinate file contain ions?  The topology
> will not be modified because genion is not being told to (i.e. through the
> use of -p).
>
> -Justin
>
>
>  Warren Gallin
>>
>> On 2011-07-26, at 2:49 PM, Sara baretller wrote:
>>
>>  thanks but i want to neutralize the system , why genion -s file.tpr -conc
>>> 0.2 -neutral -o file.gro -random  does not neutralize the system to 0 .
>>>
>>>
>>> On Tue, Jul 26, 2011 at 3:48 PM, Justin A. Lemkul 
>>> wrote:
>>>
>>>
>>> Sara baretller wrote:
>>> Hi
>>>
>>> this a part of the md.log  where the system has -50 charge
>>>
>>>  two-body bonded interactions: 0.407 nm, Bond, atoms 514 515
>>>  multi-body bonded interactions: 0.731 nm, G96Angle, atoms 1272 1275
>>> Minimum cell size due to bonded interactions: 0.804 nm
>>> Maximum distance for 9 constraints, at 120 deg. angles, all-trans: 0.810
>>> nm
>>> Estimated maximum distance required for P-LINCS: 0.810 nm
>>> This distance will limit the DD cell size, you can override this with
>>> -rcon
>>> Optimizing the DD grid for 4 cells with a minimum initial size of 0.810
>>> nm
>>> The maximum allowed number of cells is: X 11 Y 11 Z 11
>>> Domain decomposition grid 4 x 1 x 1, separate PME nodes 0
>>> Domain decomposition nodeid 0, coordinates 0 0 0
>>>
>>> Table routines are used for coulomb: TRUE
>>> Table routines are used for vdw: TRUE
>>> Using shifted Lennard-Jones, switch between 0.9 and 1.2 nm
>>> Cut-off's:   NS: 1.2   Coulomb: 1.2   LJ: 1.2
>>> System total charge: -50.000
>>> Generated table with 1100 data points for Shift.
>>> Tabscale = 500 points/nm
>>> Generated table with 1100 data points for LJ6Shift.
>>> Tabscale = 500 points/nm
>>> Generated table with 1100 data points for LJ12Shift.
>>> Tabscale = 500 points/nm
>>> Configuring nonbonded kernels...
>>> Configuring standard C nonbonded kernels...
>>> Testing ia32 SSE2 support... present
>>>
>>>
>>> There's nothing abnormal here.  genion reports that it finds a -50 charge
>>> on the system.  That's what it's supposed to do.  Based on what it finds in
>>> the topology, it adds neutralizing ions and any additional ions to reach the
>>> specified concentration.  You only have a problem if grompp later complains
>>> that there's still some residual charge (excluding tiny rounding
>>> discrepancies).
>>>
>>> -Justin
>>>
>>> On Tue, Jul 26, 2011 at 2:18 PM, Justin A. Lemkul >> jalem...@vt.edu>> wrote:
>>>
>>>
>>>
>>>   Sara baretller wrote:
>>>
>>>   Hi All
>>>
>>>   I used the genion command using like this "genion -s file.tpr
>>>   -conc 0.2 -neutral -o file.gro -random "  again and i checked
>>>   the md.log file and it says that the net charge is negative like
>>>   it was before using the genion command.
>>>
>>>   so can anybody tell me what is wrong with the line  genion -s
>>>   file.tpr -conc 0.2 -neutral -o file.gro -random .
>>>
>>>
>>>   Please copy and paste the exact (pertinent) output from the log file.
>>>
>>>   -Justin
>>>
>>>   Sara
>>>
>>>
>>>
>>>
>>>   On Tue, Jul 26, 2011 at 1:05 PM, Justin A. Lemkul
>>>   mailto:jalem...@vt.edu>
>>>   >> wrote:
>>>
>>>
>>>
>>>  Sara baretller wrote:
>>>
>>>  Hi all
>>>
>>>  I used the genion to add a concentration and to neutalize
>>> the
>>>  system in the same time by using the
>>>
>>>   *genion -s file.tpr -conc 0.2 -neutral -o file.gro
>>>   -random
>>>   so it did add the NA and Cl but it did not
>>>   neutralize the
>>>  system, the net charge of the system still the same
>>> negative.
>>>
>>>
>>>  I find this hard to believe.  The application of genion -conc
>>>  -neutral has worked in every instance I've tried it along every
>>>  Gromacs version.  Check your output again.
>>>
>>>
>>>   so i tried to use the genion seperate to neutralize the
>>>  charge using the file.tpr and out file as the file.gro,
>>> however it reset the file.gro and i lose the NA And
>>>   CL ions
>>>  added for the concentration.
>>>
>>

Re: [gmx-users] vdW cutoff




Fabian Casteblanco wrote:

Hello,

I am quite confused on whether it is better to use a standard cut-off
scheme for vdW interactions or if its better to use a switch or shift
function for this.  I am doing a free energy calculation on the
solvation of a drug molecule in a solvent (on CHARMM ff) so I want to
be as accurate as possible.  The CHARMM paper does state that they use
some type of switch function between 10 A and 12 A but I'm confused on
the difference between 'Switch' and 'Shift'.  I ran the solvents alone


They're fundamentally the same.  See the discussion in the manual, section 
4.1.5.


using these different types and it seems to give similar results.  Is
this a major decision to getting accurate free energy calculations?
Will using standard 14 A cutoffs with DispersionCorrection=EnerPres be
enough?



You should stick with the prescribed force field methodology unless you can 
demonstrate your modified method is (a) equivalent or (b) superior.  In any 
case, you need a well-defined test case (i.e. something trusted and probably 
published and therefore thoroughly vetted) that you can play with until you're 
satisfied that your method is sufficiently accurate.  Reviewers want 
justification for deviations from what is expected.  At least, they should :)


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] to find out number of solvent molecules within certain radius of the protein

2011-07-26 Thread shivangi nangia

Dear gmx-users,

I wish to calculate the number of solvent molecules within certain radius of
the protein all through the trajectory.

Is there any utility available with gromacs to do so?

Thanks,
SN
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Re: [gmx-users] (no subject)

Sara baretller wrote:

hi all

yes the gro file does have all  ions,  NA + number of ions equal to CL 
number. so when i use grep command , i have same number of NA and CL and 
that what tells me that something is wrong , because i should have 
another 50 ions of NA extra  to neutralize the system

I've never seen genion do anything like this.  If you send me your .tpr file 
(off-list) I will see if I can uncover what's going on.  I also need to know 
which Gromacs version you're using.

-Justin

Thank you

On Tue, Jul 26, 2011 at 5:03 PM, Justin A. Lemkul > wrote:

Warren Gallin wrote:

You are not specifying the ions to be added using the -pname and
-nname options with the genion command.

Perhaps that is a problem?

They are not necessary; the default names are used and should be
correct for all force fields now that naming has been standardized.

Thus far I have seen no evidence that genion is not doing what it is
supposed to.  It reports finding a net -50 charge on the system.
 What happens then? Does the output coordinate file contain ions?
 The topology will not be modified because genion is not being told
to (i.e. through the use of -p).

-Justin

Warren Gallin

On 2011-07-26, at 2:49 PM, Sara baretller wrote:

thanks but i want to neutralize the system , why genion -s
file.tpr -conc 0.2 -neutral -o file.gro -random  does not
neutralize the system to 0 .

On Tue, Jul 26, 2011 at 3:48 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>> wrote:

Sara baretller wrote:
Hi

this a part of the md.log  where the system has -50 charge

 two-body bonded interactions: 0.407 nm, Bond, atoms 514 515
 multi-body bonded interactions: 0.731 nm, G96Angle, atoms
1272 1275
Minimum cell size due to bonded interactions: 0.804 nm
Maximum distance for 9 constraints, at 120 deg. angles,
all-trans: 0.810 nm
Estimated maximum distance required for P-LINCS: 0.810 nm
This distance will limit the DD cell size, you can override
this with -rcon
Optimizing the DD grid for 4 cells with a minimum initial
size of 0.810 nm
The maximum allowed number of cells is: X 11 Y 11 Z 11
Domain decomposition grid 4 x 1 x 1, separate PME nodes 0
Domain decomposition nodeid 0, coordinates 0 0 0

Table routines are used for coulomb: TRUE
Table routines are used for vdw: TRUE
Using shifted Lennard-Jones, switch between 0.9 and 1.2 nm
Cut-off's:   NS: 1.2   Coulomb: 1.2   LJ: 1.2
System total charge: -50.000
Generated table with 1100 data points for Shift.
Tabscale = 500 points/nm
Generated table with 1100 data points for LJ6Shift.
Tabscale = 500 points/nm
Generated table with 1100 data points for LJ12Shift.
Tabscale = 500 points/nm
Configuring nonbonded kernels...
Configuring standard C nonbonded kernels...
Testing ia32 SSE2 support... present

There's nothing abnormal here.  genion reports that it finds
a -50 charge on the system.  That's what it's supposed to
do.  Based on what it finds in the topology, it adds
neutralizing ions and any additional ions to reach the
specified concentration.  You only have a problem if grompp
later complains that there's still some residual charge
(excluding tiny rounding discrepancies).

-Justin

On Tue, Jul 26, 2011 at 2:18 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:

  Sara baretller wrote:

  Hi All

  I used the genion command using like this "genion -s
file.tpr
  -conc 0.2 -neutral -o file.gro -random "  again and i
checked
  the md.log file and it says that the net charge is
negative like
  it was before using the genion command.

  so can anybody tell me what is wrong with the line
 genion -s
  file.tpr -conc 0.2 -neutral -o file.gro -random .

  Please copy and paste the exact (pertinent) output from
the log file.

  -Justin

  Sara

  On Tue, Jul 26, 2011 at 1:05 PM, Justin A. Lemkul
  mailto:jalem...@vt.edu>
>

Re: [gmx-users] to find out number of solvent molecules within certain radius of the protein




shivangi nangia wrote:

Dear gmx-users,

I wish to calculate the number of solvent molecules within certain 
radius of the protein all through the trajectory.


Is there any utility available with gromacs to do so?



Dynamic selections can be made with g_select.

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] On computing entropies using g_anaeig




Hari Shankar M wrote:

Gmx-users,

There has been a earlier post on differences in entropies computed using 
the covariance analysis and normal mode analysis 
(http://lists.gromacs.org/pipermail/gmx-users/2009-April/041535.html). I 
discovered the reason for the differences and thought that this 
information might be useful to others.


1. g_anaeig tool used to compute the entropy, computes entropies from 
the eigenvalues of the covariance matrix only. So, feeding the 
eigenvalues obtained from the mass-weighted Hessian to g_anaeig gives 
meaningless entropy values. Probably, this information should be clearly 
stated in the manual to prevent any potential abuse of g_anaeig. I 
compared the results on a diatomic molecule (oxygen) and benzene, and 
found very different results. The values differ by an order of 
magnitude. Also, looking at the source code of gmx_anaeig.c, it is clear 
that the entropies are computed from the covariance eigenvalues and not 
the eigenvalues of the Hessian.




I have created a new bug report on the redmine site for this issue.  If you have 
a code patch or any additional information to contribute, please do so:


http://redmine.gromacs.org/issues/785

2. There is a user-developed code distributed on the gromacs website 
called 'calc_entropies.pl'. This script can be used to compute entropies 
from eigenvalues obtained by covariance analysis or normal mode 
analysis. However, there seems to be a bug in this code. While the 
conversion of the eigenvalues to eigenfrequencies is done correctly in 
this code, there is a huge difference in the formula used to compute the 
entropy in the case of normal modes (for entropy formula refer to 
Karplus and Kushik 1981 paper). After correcting the entropy formula, I 
was able to get similar results with either method. If you are 
interested in the corrected script, you could email me at hari...@yahoo.com.




This would make a nice contribution to the Gromacs website.  Please consider 
uploading it to the User Contributions page with a suitable description.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] to find out number of solvent molecules within certain radius of the protein

2011-07-26 Thread shivangi nangia

Hi,

Where can I find the documentation for g_select?

Thanks,
SN



On Tue, Jul 26, 2011 at 6:07 PM, Justin A. Lemkul  wrote:

>
>
> shivangi nangia wrote:
>
>> Dear gmx-users,
>>
>> I wish to calculate the number of solvent molecules within certain radius
>> of the protein all through the trajectory.
>>
>> Is there any utility available with gromacs to do so?
>>
>>
> Dynamic selections can be made with g_select.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
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> Support/Mailing_Lists/Searchbefore
>  posting!
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[gmx-users] Re: g_msd bug

2011-07-26 Thread Simon Butler

Dear Gromacsers,

This seems more suited to gmx-developers but as the original thread was on
gmx-users, I'm posting it here.

Anyway, regarding the excessive memory usage of g_msd when using the -mol
flag, as reported recently, I believe I've identified the source of the
problem: the array of per-molecule MSD data in curr->lsq. In particular, it
appears that the call to gmx_stats_add_point on line 476 is the key
offender.

I haven't the time at the moment to dig any further than this,
unfortunately, but the attached patch (gmx_msd.mem.patch) may be of
temporary use to users of g_msd. It merely comments out the call to
gmx_stats_init and the printmol routine. If anybody wishes to retain the
calculation of D for each individual molecule, they will need to recode the
data accumulation in the style of that for the overall calculation I expect.

There is also the problem of the large difference in the calculated results
when using the -mol flag, as reported by Florian. I think the cause of this
is an error in the logic within the corr_loop routine. The original sequence
is:

1. If first iteration, copy current frame to previous
2. If -mol, make molecules whole
3. Remove PBC jumps
4. If -mol, calculate molecule COMs and copy to xa array

I believe the correct order for this sequence should be 2, 4, 1, 3. The
original order results in xa[prev] containing zero for every position on
step 1 and also in the PBC step operating on an array that hasn't been
repopulated yet, with the result that jumps are not removed correctly.

I've tested the new sequence for a single PF6 molecule and for the
corresponding P atom (which is almost exactly at the COM) and obtained very
nearly identical results for each (which wasn't the case previously). I've
attached a separate patch to reorder these function calls
(gmx_msd.mol.patch). Both patches are for the v4.5.4 copy of gmx_msd.c, by
the way.

cheers,

Simon

===
Dr. Simon Butler

Theorie Physikaliche Chemie
Eduard-Zintl-Institut
Technische Universität Darmstadt
Petersenstrasse 20
64287 Darmstadt
Deutschland

Tel: +49-6151-16 6537
Email: s.but...@theo.chemie.tu-darmstadt.de
===
474a475,476
> /* disabled due to memory issues  */
> /*
476a479
> */
629c632
<   curr->lsq[curr->nrestart-1][i]  = gmx_stats_init();
---
>   curr->lsq[curr->nrestart-1][i]  = NULL; /* gmx_stats_init(); */ /* disabled due to memory issues */
811c814
< printmol(msd,mol_file,pdb_file,index[0],top,x,ePBC,box,oenv);
---
> /* printmol(msd,mol_file,pdb_file,index[0],top,x,ePBC,box,oenv); */ /* disabled due to memory issues  */
664a682,689
> /* make the molecules whole */
> if (bMol)
>   gmx_rmpbc(gpbc,natoms,box,x[cur]);
> 
> /* calculate the molecules' centers of masses and put them into xa */
> if (bMol)
> calc_mol_com(gnx[0],index[0],&top->mols,&top->atoms, x[cur],xa[cur]);
> 
671,674d695
< /* make the molecules whole */
< if (bMol)
<   gmx_rmpbc(gpbc,natoms,box,x[cur]);
< 
689,692d709
< /* calculate the molecules' centers of masses and put them into xa */
< if (bMol)
< calc_mol_com(gnx[0],index[0],&top->mols,&top->atoms, x[cur],xa[cur]);
< 
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Re: [gmx-users] to find out number of solvent molecules within certain radius of the protein




shivangi nangia wrote:

Hi,

Where can I find the documentation for g_select?



Manual section 8.1.2 or g_select -h.  For specific usage examples search the 
list archive (there are a number of posts on related topics) or:


g_select -select "help all"

-Justin


Thanks,
SN



On Tue, Jul 26, 2011 at 6:07 PM, Justin A. Lemkul > wrote:




shivangi nangia wrote:

Dear gmx-users,

I wish to calculate the number of solvent molecules within
certain radius of the protein all through the trajectory.

Is there any utility available with gromacs to do so?


Dynamic selections can be made with g_select.

-Justin

-- 
==__==


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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
MILES-IGERT Trainee
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] Fwd: density error bars

2011-07-26 Thread XAvier Periole



You may have wanted to have sent the message to the gmx list!

XAvier.

Begin forwarded message:


From: nicoletta liguori 
Date: July 26, 2011 5:28:29 PM MDT (CA)
To: x.peri...@rug.nl
Subject: density error bars

Hi,
I'm using Gromacs and its tools to sample some kind of membranes and  
characterize their features.

Actually I don't know what to do about error bars.
For example when I calculate the density mass distribution along the  
axis parallel to the normal to the
membrane surface I average on all trajectories using g_density_d on  
my set contained

in the .xtc file.
Considering that, for what I understood, it makes the average on  
time of the density, but without
adding any kind of error (there are no possibilities with this tool)  
I tried to check if there are other tools

available to calculate the error bars but seem not to exist!!
For example g_analyze reads directly the already averaged set of  
data (in this case) cause the only

possible input is a .xvg file!
So I was thinking to (not yet know how, is my first computational  
trial) to calculate the error with a simple
standard deviation (I was thinking to use matlab ), but to do this,  
I suppose that

I have to consider all the points indipendent, and to do this
I'd have to look at the autocorrelation function of density itself!
but how to do this??
there are again no tools available
how do you do when u deal with errors?
Thanks for attention and for the help
Nicoletta


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[gmx-users] About force field for CNT and Lonsdaleite

2011-07-26 Thread jhon michael espinosa duran







Dear Friends

Does any of you know where can I obtain a FF for simulation of CNT and 
Lonsdaleite solvated in water, that also contain parameters for N, H, O, P, Cl 
and F.

Thanks

John Michael Espinosa-Duran
Electronics Engineer. M.Eng.
Universidad del Valle. 
Cali, Colombia, South America.


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[gmx-users] How to exert different lateral pressure profile of a membrane to study its influence on a protein inserted in the double layer membrane?

2011-07-26 Thread KONG Xian

Dear all:

 

 I am working on a research to study whether the Lateral pressure
profile influence the protein function.

 

 To get different lateral pressure profile, I used Parinello-Rahman
P coupling method and anisotropic pressure coupling with different p_ref
values(such as 0.9bar, 1bar, 1.1bar, .,2bar) in xy.

 

 I wonder whether this method feasible. 

 

If it is not feasible, could anyone please give me a hint on how to do it.

 

Thank you 

 

KONG Xian

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Re: [gmx-users] How to exert different lateral pressure profile of a membrane to study its influence on a protein inserted in the double layer membrane?