[gmx-users] Regarding the broken compiler gcc 4.1.x

[rashmi_chem]

Dear gmxusers,

The warning on the GROMACS download page says :

WARNING: do not use the gcc 4.1.x set of compilers. They are broken. These
compilers come with recent Linux distrubutions like Fedora 5/6 etc.


So I installed CentOS 4.3 with gcc 3.4.5 and Fedora 10 with gcc 4.3.2 on
two different machines with same configuration( quad core dual xeon
machine clock 2 GHz). In both the machines Gromacs-4.0.4 was installed and
tetsed using corresponding gmxtest set. Many tests failed as following:

All 16 simple tests PASSED
FAILED. Check files in field
FAILED. Check files in tip4p
FAILED. Check files in tip4pflex
FAILED. Check files in water
4 out of 14 complex tests FAILED
FAILED. Check files in kernel020
FAILED. Check files in kernel120
FAILED. Check files in kernel121
FAILED. Check files in kernel122
FAILED. Check files in kernel123
FAILED. Check files in kernel124
FAILED. Check files in kernel220
FAILED. Check files in kernel221
FAILED. Check files in kernel222
FAILED. Check files in kernel223
FAILED. Check files in kernel224
FAILED. Check files in kernel320
FAILED. Check files in kernel321
FAILED. Check files in kernel322
FAILED. Check files in kernel323
FAILED. Check files in kernel324
16 out of 63 kernel tests FAILED
 pdb2gmx tests PASSED


But when the same tests were performed on CentOS 5.0 with "gcc 4.1.2" (so
called "broken compiler"), all tests passed except one.

All 16 simple tests PASSED
FAILED. Check files in dec+water
1 out of 14 complex tests FAILED
All 63 kernel tests PASSED
All 45 pdb2gmx tests PASSED


These results are quite confusing and puts a question about the validity
of the gmxtest set. The reference files in gmxtest-4.0.4 set (new) are
similar to gmxtest-3.3.2 set (old) and have not been updated.
If so how can one perform these tests on gromacs-4.0.4 and compare the
newly  generated files with the reference files?


If gcc 4.1.x is supposed to be "broken" and should not be used for
installing Gromacs, then why are gmxtests performing better in this case?


Are gcc 4.1.x series of compilers still broken? because the message on
gromacs download page is quite old.

Thanxs in advance.

regards
Rashmi

___
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

Re: [gmx-users] Where are the good tutorials?

[Tsjerk Wassenaar]

Casey,

Could you expand your criticism? You must have found the tutorials section
on the wiki. Then please note the specific points you dislike about the
tutorials there (especially the beginners) and provide some ideas you would
think improve them.

To my opinion, a beginners tutorial provides a set of standard parameters,
which will do for most of the simulations most of the users will encounter.
There is not much benefit in writing such a file from scratch, although one
should introduce the file and explain, also pointing to the file format. But
then, if you have a .pdb file and parameters, md simulations are little more
than 'punch in some commands', on top of the thinking about the process that
is effected by that.

I forgive students who feel that they don't need to go beyond punching the
commands to get the credits. But for someone like you, searching for a
tutorial to get into MD, I would think that the commands and the surrounding
text would be sufficient to keep you from only punching them in and obtain
the output. It will by all means be sufficient for someone interested to
extract the insights needed for getting started with MD. If you really want
to go beyond that (but that's not tutorial work), you'll find the Gromacs
documentation, explaining topologies and parameters in detail.

Cheers,

Tsjerk


On Thu, May 14, 2009 at 12:24 AM, Joseph Johnson wrote:

>  Are there any good tutorials that start from the very beginning, like
> assuming you only have a .pdb file?  It seems that most of the tutorials
> I've found have already generated the files you need and then all you have
> to do is punch in some commands.  Where can I learn to actually write the
> molecular dynamics input file and all that good stuff?
>
> Thanks for your time and help,
> Casey
>
> --
> Windows Live™: Keep your life in sync. Check it 
> out.
>
> ___
> 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
>



-- 
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
___
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

Re: [gmx-users] Regarding the broken compiler gcc 4.1.x

[Jussi Lehtola]

On Thu, 2009-05-14 at 12:13 +0530, rashmi_c...@iitb.ac.in wrote:
> Dear gmxusers,
> 
> The warning on the GROMACS download page says :
> 
> WARNING: do not use the gcc 4.1.x set of compilers. They are broken. These
> compilers come with recent Linux distrubutions like Fedora 5/6 etc.
> 
> 
> So I installed CentOS 4.3 with gcc 3.4.5 and Fedora 10 with gcc 4.3.2 on
> two different machines with same configuration( quad core dual xeon
> machine clock 2 GHz). In both the machines Gromacs-4.0.4 was installed and
> tetsed using corresponding gmxtest set. Many tests failed as following:
> 
> 16 out of 63 kernel tests FAILED
>  pdb2gmx tests PASSED
> 
> 
> But when the same tests were performed on CentOS 5.0 with "gcc 4.1.2" (so
> called "broken compiler"), all tests passed except one.

You're talking of CentOS 4.3 and 5.0, both are obsolete: you should
update to 4.7 and 5.3, respectively.


> Are gcc 4.1.x series of compilers still broken? because the message on
> gromacs download page is quite old.

RedHat has backported a lot of fixes into their gcc, and thus the CentOS
version works.
-- 
--
Jussi Lehtola, FM, Tohtorikoulutettava
Fysiikan laitos, Helsingin Yliopisto
jussi.leht...@helsinki.fi, p. 191 50632
--
Mr. Jussi Lehtola, M. Sc., Doctoral Student
Department of Physics, University of Helsinki, Finland
jussi.leht...@helsinki.fi
--


___
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

[gmx-users] problem in simulation of dna-protein complex

[nitu sharma]

Dear all ,
I am doing simulation of DNA-protein complex.
  Is anybody have idea about  .hdb of DNA  becoz in mannual
nothing is wrritten about DNA hydrogen database .I have edited The database
like this-
ADE 9
2   6  H5*  C5* C4* O5*
1   5  H4*  C4* O4* C5* C3*
1   5  H3*  C3* C2* C4* O3*
1   5  H2*  C2* C3* C1* O2`
1   2  H2`  O2` C2* C3*
1   5  H1*  C1* N9  O4* C2*
1   1  H2   C2  N1  N3
2   3  H6   N6  C6  C5
1   1  H8   C8  N9  N7

But when I run pdb2gmx command on DNA-protein pdb file the error comes like
this-
Program pdb2gmx, VERSION 4.0.3
Source code file: h_db.c, line: 96

Fatal error:
Error in hdb file ffoplsaano.hdb:
Wrong number of control atoms (3 iso 4) on line:
1   5  H4* C4* O4* C5*

If anybody have Idea what short of changes it needed please help me.
Thanks a lot in advance.

Nitu sharma
___
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

Re: [gmx-users] problem in simulation of dna-protein complex

[Mark Abraham]

nitu sharma wrote:

Dear all ,
I am doing simulation of DNA-protein complex.
  Is anybody have idea about  .hdb of DNA  becoz in mannual 
nothing is wrritten about DNA hydrogen database .I have edited The 
database like this-

ADE 9
2   6  H5*  C5* C4* O5*
1   5  H4*  C4* O4* C5* C3*
1   5  H3*  C3* C2* C4* O3*
1   5  H2*  C2* C3* C1* O2`
1   2  H2`  O2` C2* C3*
1   5  H1*  C1* N9  O4* C2*
1   1  H2   C2  N1  N3
2   3  H6   N6  C6  C5
1   1  H8   C8  N9  N7

But when I run pdb2gmx command on DNA-protein pdb file the error comes 
like this-

Program pdb2gmx, VERSION 4.0.3
Source code file: h_db.c, line: 96

Fatal error:
Error in hdb file ffoplsaano.hdb:
Wrong number of control atoms (3 iso 4) on line:
1   5  H4* C4* O4* C5*   
 
If anybody have Idea what short of changes it needed please help me.


The hydrogen database format is described in chapter 5. The description 
is not a work of art, but you should start looking there.


Mark
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] How to remove water from lipid bilayer core

[Anirban Ghosh]

Hi ALL,

I have a built a system of protein embeded in lipid bilayer and solvated it 
according to the GROMACS membrane simulation tutorial. I want to delete a few 
water molecules that are there in the hydrophobic core of the bilayer. I 
deleted them manually from the .gro file and corrected the atom numbers, but 
still getting an error:
-
Invalid line in prt_genbox_MOD.gro for atom 73510:
  10.81119  10.81119  10.01306
-

How can I modify the last line and get a correct .gro file by removing the 
unwanted waters? In the tutorial it is stated that there are some scripts to 
remove the unwanted waters. Can anyone provide me such a script.
Any suggestion is welcome.



Regards,


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



  From Chandigarh to Chennai - find friends all over India. Go to 
http://in.promos.yahoo.com/groups/citygroups/___
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

Re: [gmx-users] How to remove water from lipid bilayer core

[Pawan Kumar]

Hello Anirban,

Greetings from Pawan.
You can find the scripts in this webiste :
http://wiki.gromacs.org/index.php/Membrane_Simulations

Regards,
Pawan

On Thu, May 14, 2009 at 3:01 PM, Anirban Ghosh wrote:

> Hi ALL,
>
> I have a built a system of protein embeded in lipid bilayer and solvated it
> according to the GROMACS membrane simulation tutorial. I want to delete a
> few water molecules that are there in the hydrophobic core of the bilayer. I
> deleted them manually from the .gro file and corrected the atom numbers, but
> still getting an error:
> -
> Invalid line in prt_genbox_MOD.gro for atom 73510:
>   10.81119  10.81119  10.01306
> -
>
> How can I modify the last line and get a correct .gro file by removing the
> unwanted waters? In the tutorial it is stated that there are some scripts to
> remove the unwanted waters. Can anyone provide me such a script.
> Any suggestion is welcome.
>
>
>
> 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!
> ___
> 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
>
___
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

[gmx-users] How to set up dihedrals

[Thomas Schlesier]

Dear all,
i'm making a .rtp for a sugar for the OPLS-AA force-field. To start i
made a topology with the PRODRG server, so i have a list with all bonds,
angles and dihedrals, but the problem is, that i'm missing the unpolar
hydrogens. How to set up the bonds and angles entrys is no problem, but
with the dihedrals i have problems.

If i have for example the the following molecule (should look like a
double Y):

L1\   /R1
   L-R
L2/   \R2

(L1 and L2 bounded to L, then L to R, and R is bounded to R1 and R2)
In this case i have the dihedral between L and R, but i have 4
possibilities to set it up:
L1-L-R-R1
L1-L-R-R2
L2-L-R-R1
L2-L-R-R2
So my problem is how to choose which possibility should i use. If L1, L2
and R1, R2 are equal there is no problem, because then the 4
possibilities are all equal.

Hope somebody can help me.

Greetings
Thomas
___
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

[gmx-users] problem regarding dna-protein simulation

[nitu sharma]

Hello mark

thanks for your suggestion . but i already did these these
things which u suggest . There is nothing about nucleic acid database as i
mentioned in my previous mail .
I have solved the problem regarding aminoacid hydrogen database problem but
it not valid in case of nucleic acid thats why I have left the mail on users
list .
so If anybody solved this type of problem previously can help me.

Thanks a lot.
Nitu sharma
___
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

Re: [gmx-users] problem regarding dna-protein simulation

[Justin A. Lemkul]

nitu sharma wrote:

Hello mark

thanks for your suggestion . but i already did these these 
things which u suggest . There is nothing about nucleic acid database as 
i mentioned in my previous mail .
I have solved the problem regarding aminoacid hydrogen database problem 
but it not valid in case of nucleic acid thats why I have left the mail 
on users list .

so If anybody solved this type of problem previously can help me.



Your problem is not specific to nucleic acids.  Read about the hydrogen 
database; you have an inappropriate amount of control atoms for the type of 
addition you are specifying.


-Justin


Thanks a lot.
Nitu sharma




___
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/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

[gmx-users] Protein is not at the centre of octahedron box

[sukesh chandra gain]

Dear All,
I am doing a simulation for ligand-enzyme complex in a octahedron box. I 
have mentioned -c with editconf, but after energy minimization the 
protein is placed at the top of the box. Could you please suggest me how 
could I keep the protein at the centre of the octahedron box?

Here are the details:
After
editconf>
Volume =283.195nm^3
System size : 6.852 5.060 7.638
genbex>
box_margin = 0.315
Removed 29370 atoms that were outside the box
grompp>
Using a fourier grid of 88x88x88, spacing 0.115 0.115 0.115

Thank You,
Regards,
Sukesh
___
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

Re: [gmx-users] Protein is not at the centre of octahedron box

[Justin A. Lemkul]

sukesh chandra gain wrote:

Dear All,
I am doing a simulation for ligand-enzyme complex in a octahedron box. I 
have mentioned -c with editconf, but after energy minimization the 
protein is placed at the top of the box. Could you please suggest me how 
could I keep the protein at the centre of the octahedron box?


This is simply a visualization artifact.  Use trjconv -pbc mol -ur compact to 
"correct" your structure.  But do be aware that this is simply a convenience for 
visualization, in an infinite system (with PBC), there is no "center" of a box.


-Justin


Here are the details:
After
editconf>
Volume =283.195nm^3
System size : 6.852 5.060 7.638
genbex>
box_margin = 0.315
Removed 29370 atoms that were outside the box
grompp>
Using a fourier grid of 88x88x88, spacing 0.115 0.115 0.115

Thank You,
Regards,
Sukesh
___
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/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

Re: [gmx-users] How to set up dihedrals

[Mark Abraham]

Thomas Schlesier wrote:

Dear all,
i'm making a .rtp for a sugar for the OPLS-AA force-field. To start i
made a topology with the PRODRG server, so i have a list with all bonds,
angles and dihedrals, but the problem is, that i'm missing the unpolar
hydrogens. How to set up the bonds and angles entrys is no problem, but
with the dihedrals i have problems.

If i have for example the the following molecule (should look like a
double Y):

L1\   /R1
   L-R
L2/   \R2

(L1 and L2 bounded to L, then L to R, and R is bounded to R1 and R2)
In this case i have the dihedral between L and R, but i have 4
possibilities to set it up:
L1-L-R-R1
L1-L-R-R2
L2-L-R-R1
L2-L-R-R2
So my problem is how to choose which possibility should i use. If L1, L2
and R1, R2 are equal there is no problem, because then the 4
possibilities are all equal.


The only way to be sure is to read the primary literature for OPLS/AA. 
You might also look at some other .rtp file entries that have the 
topology you're considering.


Mark
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] gromacs benchmark SGI ALTIX ICE with Intel Quad-Core E5472

[intra\sa175950]

Hi all 

 

For a research project, I need to know how gromacs work/scale (especially
gmx 4.0.4) in SGI ALTIX ICE 8200 EX  machine cluster with Intel Quad-Core
E5472. I want to simulate a molecular system (with 14 amino acid peptide +/-
5000 water molecules) in explicit conditions with PME and 32 - 64 CPU. I
need only to have a (rough) estimation (in ns/day). Does somebody have an
example?  

 

Thanks in advance for your help

 

Stef

 

___
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

Re: [gmx-users] gromacs benchmark SGI ALTIX ICE with Intel Quad-Core E5472

[Justin A. Lemkul]

intra\sa175950 wrote:

Hi all

 

For a research project, I need to know how gromacs work/scale 
(especially gmx 4.0.4) in SGI ALTIX ICE 8200 EX  machine cluster with 
Intel Quad-Core E5472. I want to simulate a molecular system (with 14 
amino acid peptide +/- 5000 water molecules) in explicit conditions with 
PME and 32 – 64 CPU. I need only to have a (rough) estimation (in 
ns/day). Does somebody have an example?  

 


There are benchmarks in the Gromacs 4 paper, as well as on the website.  The 
actual performance will depend upon the connections between your nodes (i.e., 
Infiniband is much faster than Gigabit Ethernet) and the parameters you set in 
the .mdp file (dt, cutoff's, fourierspacing, etc.)


-Justin



Thanks in advance for your help

 


Stef

 





___
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/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

[gmx-users] Constraints specified in .mdp as well as in .top files

[Vishwanath Dalvi]

Hi!

I have a question about a possible redundancy/conflict in specifying 
bond-constraints.

I have in my simulation (among other things) a number of bonds - some of which 
are harmonic while some are rigid (or constrained).

I specify the bonds in the .itp (or ultimately in the .top) files as follows:

[ bonds ]
;  index1  index2func deq(nm)   k(kJ/mol/nm2)
   1   2   10.152900   224262.40
   1  32   10.181000   185769.60
   2   3   10.152900   224262.40
   3   4   10.152900   224262.40
[ constraints ]
;  index1  index2   funct  length(nm)
   1  30   10.109000
   1  31   10.109000
   2  28   10.109000
   2  29   10.109000

However, it turns out that the .mdp file also requires one to specify 
constraints in the form of:
constraints  =  all-bonds/h-bonds etc

Do we have to specify constraints in the .mdp file if we already have specified 
them in the .itp file?

Thanks!

Ashwin



  Explore and discover exciting holidays and getaways with Yahoo! India 
Travel http://in.travel.yahoo.com/___
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

[gmx-users] Coulomb energies for a charge seperated species

[Ali Hassanali]

Dear Gromacs Users,

I am simulating a system that consists of a tryptophan linked to a thymine 
dimer (two thymine bases stacked together) and am interested in how the 
configurational properties of neutral tryptophan linked to neutral thymine 
compares with tryptophan cation linked to thymine anion.


Using ab initio calculations, I constructed a simple model where I adjust 
the charges on the Trp and on the Thymine dimer so that the overall charge 
of the system is still zero but where the Trp charge is +1 and the thymine 
charge is -1.


I am trying to validate as best as I possibly can, this rather crude model 
so that I can trust the results I am getting and am hoping someone can 
comment or help with this. I have calculated the total Coulomb interaction 
(Coulomb SR+LR) between the Tryptophan cation and Thymine anion over the 
course of a long simulation. Several things that I observe:


* There appear to be 2 distinct states: a charge seperated (by solvent) 
and a charge-charge state where the the cation and anion stack together. 
I would imagine that if you could tether Na+ and Cl- in water with some 
linker, one would see something similar.


* The total coulomb potential energy between the cation and anion 
fluctuates between -50 to -150 KJ/mol. So there is roughly about a 1eV 
coulomb energy difference between the two states. If I take the 
free energy of this coulomb potential energy, the 2 states differ by 
roughly 0.6 kcal/mol (very small). (Please see attached figure). Do these 
fluctuations (range) and energetics seem reasonable?


* As you can see in the attached figure, the Coulomb energy has the 1/r 
trend where r is the distance between the Trp+ and Thymine dimer anion.


Ali<>___
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

[gmx-users] Test Particle Insertion Problem-Gromacs 4.0.3

[Harry Saavedra]

Dear All,

I run a test molecule insertion simulation using Gromacs 4.0.3. All the 
molecules of the system work with two energy groups (two tabulated potentials), 
and every atom belongs to a different charge group; but Gromacs shows an error 
message: 

> grompp...
> mdrun ...

Program mdrun, VERSION 4.0.3
Source code file: force.c, line: 1068
Send
Fatal error:
The molecule to insert can not consist of multiple charge groups.
Make it a single charge group.


However,when I set all the atoms of the inserted molecule (A,B,C..) to the same 
charge group (cgnr in the top file), Gromacs displays :


>grompp... 

Program grompp, VERSION 4.0.3
Source code file: grompp.c, line: 150
Fatal error:
atoms A and B in charge group Z of molecule type 'Protein' are in different 
energy groups


There is any way to overcome this problem? How Gromacs can ignore the charge 
groups? 



Thanks in advance,


Harry Gustavo

_
Windows Live™: Keep your life in sync.
http://windowslive.com/explore?ocid=TXT_TAGLM_BR_life_in_synch_052009___
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

Re: [gmx-users] gromacs benchmark SGI ALTIX ICE with Intel Quad-Core E5472

[David van der Spoel]

intra\sa175950 wrote:

Hi all

 

For a research project, I need to know how gromacs work/scale 
(especially gmx 4.0.4) in SGI ALTIX ICE 8200 EX  machine cluster with 
Intel Quad-Core E5472. I want to simulate a molecular system (with 14 
amino acid peptide +/- 5000 water molecules) in explicit conditions with 
PME and 32 – 64 CPU. I need only to have a (rough) estimation (in 
ns/day). Does somebody have an example?  

Based on the DHFR benchmark in the 4.0 paper I estimate 200-300 ns/day 
on 64 cores, provided you have fast network. It could well be more. Best 
way is to test it obviously. Probably 32 cores is more CPU/$ efficient.


 


Thanks in advance for your help

 


Stef

 





___
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



--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se
___
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

Re: [gmx-users] Test Particle Insertion Problem-Gromacs 4.0.3

[Mark Abraham]

Harry Saavedra wrote:

Dear All,

I run a test molecule insertion simulation using Gromacs 4.0.3. All the 
molecules of the system work with two energy groups (two tabulated 
potentials), and every atom belongs to a different charge group; but 
Gromacs shows an error message:


 > grompp...
 > mdrun ...

Program mdrun, VERSION 4.0.3
Source code file: force.c, line: 1068 Send 
Fatal error:
The molecule to insert can not consist of multiple charge groups.
Make it a single charge group.


However,when I set all the atoms of the inserted molecule (A,B,C..) to 
the same charge group (cgnr in the top file), Gromacs displays :



 >grompp...

Program grompp, VERSION 4.0.3
Source code file: grompp.c, line: 150
Fatal error:
atoms A and B in charge group Z of molecule type 'Protein' are in 
different energy groups



There is any way to overcome this problem? How Gromacs can ignore the 
charge groups?


Energy groups are set in the .mdp file using the groups defined 
(implicitly) in the .ndx file. You need a charge group that is a subset 
of a single energy group.


Mark
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] Constraints specified in .mdp as well as in .top files

[Mark Abraham]

Vishwanath Dalvi wrote:

Hi!

I have a question about a possible redundancy/conflict in specifying 
bond-constraints.


I have in my simulation (among other things) a number of bonds - some of 
which are harmonic while some are rigid (or constrained).


I specify the bonds in the .itp (or ultimately in the .top) files as 
follows:


[ bonds ]
;  index1  index2func deq(nm)   k(kJ/mol/nm2)
   1   2   10.152900   224262.40
   1  32   10.181000   185769.60
   2   3   10.152900   224262.40
   3   4   10.152900   224262.40
[ constraints ]
;  index1  index2   funct  length(nm)
   1  30   10.109000
   1  31   10.109000
   2  28   10.109000
   2  29   10.109000

However, it turns out that the .mdp file also requires one to specify 
constraints in the form of:

constraints  =  all-bonds/h-bonds etc

Do we have to specify constraints in the .mdp file if we already have 
specified them in the .itp file?


I believe so. This is also true of restraints (which are a different 
concept in GROMACS).


Mark
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] Pressure coupling and cut-off

[Yanmei Song]

Dear All:

I have question about the pressure coupling. I have done a 10ns simulation
with 19800 atoms for 120 large molecules using the following pressure
coupling.

Tcoupl  =  berendsen
tc_grps =  PDM
tau_t   =  0.1
ref_t   =  300

Pcoupl  =  berendsen
pcoupltype  =  isotropic
;pc-grps=  PDM
tau_p   =  1.0
ref_p   =  1.0
compressibility =  4.5e-5

Then I did g_energy for the last 3ns and got the results:

Energy  Average   RMSD Fluct.  Drift
Tot-Drift
---
Potential-98061  0  00.61668
1850.04
Temperature 303.561109.602109.602 0.000181791
0.545372
Pressure (bar)   4.48840.811109.8  -0.169835
-509.506

For such a long run the pressure drift is still too much and seem hasn't
approached 1bar. Does it mean the system hasn't reach equilibrium yet. I did
a similar system by using the same method. it just take 2 or 3ns to reach
the equilibrium. and the pressure is around 1.01after the run. The only
difference is the cutoff changing from 1.2 to 1.4.  Does the cufoff of 1.4
is too large to make the system running slower. Or the pressure coupling
method is not working well.  Anyone can give me any suggestions?


-- 
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University
___
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

Re: [gmx-users] Pressure coupling and cut-off

[Justin A. Lemkul]

Yanmei Song wrote:

Dear All:

I have question about the pressure coupling. I have done a 10ns 
simulation with 19800 atoms for 120 large molecules using the following 
pressure coupling.


Tcoupl  =  berendsen
tc_grps =  PDM
tau_t   =  0.1
ref_t   =  300

Pcoupl  =  berendsen
pcoupltype  =  isotropic
;pc-grps=  PDM
tau_p   =  1.0
ref_p   =  1.0
compressibility =  4.5e-5

Then I did g_energy for the last 3ns and got the results:

Energy  Average   RMSD Fluct.  Drift  
Tot-Drift

---
Potential-98061  0  00.61668
1850.04
Temperature 303.561109.602109.602 0.000181791   
0.545372
Pressure (bar)   4.48840.811109.8  -0.169835   
-509.506


For such a long run the pressure drift is still too much and seem hasn't 
approached 1bar. Does it mean the system hasn't reach equilibrium yet. I 
did a similar system by using the same method. it just take 2 or 3ns to 
reach the equilibrium. and the pressure is around 1.01after the run. The 
only difference is the cutoff changing from 1.2 to 1.4.  Does the cufoff 
of 1.4 is too large to make the system running slower. Or the pressure 
coupling method is not working well.  Anyone can give me any suggestions?





I think it will depend on the interplay of other parameters as well.  Posting a 
complete .mdp file may be more helpful.


-Justin


--
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University




___
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/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

Re: [gmx-users] Pressure coupling and cut-off

[Yanmei Song]

Dear Justin:

Thanks for your response. Here is the complete my .mdp file:

title   =  pdm
cpp =  /lib/cpp
constraints =  all_bonds
integrator  =  md
dt  =  0.004   ; ps !
nsteps  =  250   ; total 10ns.
nstcomm =  1
nstxout =  5
nstvout =  5
nstfout =  0
nstlog  =  5000
nstenergy   =  5000
nstxtcout   =  25000
nstlist =  10
ns_type =  grid
pbc =  xyz
coulombtype =  PME
rlist   =  1.4
rcoulomb=  1.4
rvdw=  1.4
fourierspacing  =  0.20
pme_order   =  4
ewald_rtol  =  1e-5
; Berendsen temperature coupling is on in one groups
Tcoupl  =  berendsen
tc_grps =  PDM
tau_t   =  0.1
ref_t   =  300
; Energy monitoring
energygrps  =  PDM
; Isotropic pressure coupling is now on
Pcoupl  =  berendsen
pcoupltype  =  isotropic
;pc-grps=  PDM
tau_p   =  1.0
ref_p   =  1.0
compressibility =  4.5e-5

; Generate velocites is off at 300 K.
gen_vel =  yes
gen_temp=  300.0
gen_seed=  10



On Thu, May 14, 2009 at 4:06 PM, Justin A. Lemkul  wrote:

>
>
> Yanmei Song wrote:
>
>> Dear All:
>>
>> I have question about the pressure coupling. I have done a 10ns simulation
>> with 19800 atoms for 120 large molecules using the following pressure
>> coupling.
>>
>> Tcoupl  =  berendsen
>> tc_grps =  PDM
>> tau_t   =  0.1
>> ref_t   =  300
>>
>> Pcoupl  =  berendsen
>> pcoupltype  =  isotropic
>> ;pc-grps=  PDM
>> tau_p   =  1.0
>> ref_p   =  1.0
>> compressibility =  4.5e-5
>>
>> Then I did g_energy for the last 3ns and got the results:
>>
>> Energy  Average   RMSD Fluct.  Drift
>>  Tot-Drift
>>
>> ---
>> Potential-98061  0  00.61668
>>  1850.04
>> Temperature 303.561109.602109.602 0.000181791
>> 0.545372
>> Pressure (bar)   4.48840.811109.8  -0.169835
>> -509.506
>>
>> For such a long run the pressure drift is still too much and seem hasn't
>> approached 1bar. Does it mean the system hasn't reach equilibrium yet. I did
>> a similar system by using the same method. it just take 2 or 3ns to reach
>> the equilibrium. and the pressure is around 1.01after the run. The only
>> difference is the cutoff changing from 1.2 to 1.4.  Does the cufoff of 1.4
>> is too large to make the system running slower. Or the pressure coupling
>> method is not working well.  Anyone can give me any suggestions?
>>
>>
>>
> I think it will depend on the interplay of other parameters as well.
>  Posting a complete .mdp file may be more helpful.
>
> -Justin
>
>  --
>> Yanmei Song
>> Ph.D. Candidate
>> Department of Chemical Engineering
>> Arizona State University
>>
>>
>> 
>>
>> ___
>> 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/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
>



-- 
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University
___
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

[gmx-users] -np switch

[Payman Pirzadeh]

Hello,

When we use 'mdrun' or 'grompp' with the switch '-np' we specify the number
of nodes according to the manual. Does it mean if the nodes have 2
processors, then the simulation will be run on 4 CPUs or in -np we should
specify 4 instead of 2?

 

Payman

 

 

 

___
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

Re: [gmx-users] -np switch

[Mark Abraham]

Payman Pirzadeh wrote:

Hello,

When we use ‘mdrun’ or ‘grompp’ with the switch ‘-np’ we specify the 
number of nodes according to the manual. Does it mean if the nodes have 
2 processors, then the simulation will be run on 4 CPUs or in –np we 
should specify 4 instead of 2?


Tell GROMACS the number of MPI processes you want. If you have two 
dual-core, dual-processor nodes, that might be 8 processes, etc. Your 
MPI setup may need to be configured to tell it how to distribute the 
processes.


grompp -np is not needed or available in GROMACS 4.x

Mark
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] -np switch

[Justin A. Lemkul]

Payman Pirzadeh wrote:

Hello,

When we use ‘mdrun’ or ‘grompp’ with the switch ‘-np’ we specify the 
number of nodes according to the manual. Does it mean if the nodes have 
2 processors, then the simulation will be run on 4 CPUs or in –np we 
should specify 4 instead of 2?




As of version 4.0, grompp no longer requires -np, and as a matter of fact, 
neither does mdrun (the -np comes into play when you invoke mpirun).


Anyway, -np = number of processors, so if you have two dual-core processors, you 
want -np 4 (for mpirun).


-Justin

 


Payman

 

 

 





___
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/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

Re: [gmx-users] Pressure coupling and cut-off

[Justin A. Lemkul]

Yanmei Song wrote:

Dear Justin:

Thanks for your response. Here is the complete my .mdp file:

title   =  pdm
cpp =  /lib/cpp
constraints =  all_bonds
integrator  =  md
dt  =  0.004   ; ps !
nsteps  =  250   ; total 10ns.
nstcomm =  1
nstxout =  5
nstvout =  5
nstfout =  0
nstlog  =  5000
nstenergy   =  5000
nstxtcout   =  25000
nstlist =  10
ns_type =  grid
pbc =  xyz
coulombtype =  PME
rlist   =  1.4
rcoulomb=  1.4
rvdw=  1.4
fourierspacing  =  0.20
pme_order   =  4
ewald_rtol  =  1e-5
; Berendsen temperature coupling is on in one groups
Tcoupl  =  berendsen
tc_grps =  PDM
tau_t   =  0.1
ref_t   =  300
; Energy monitoring
energygrps  =  PDM
; Isotropic pressure coupling is now on
Pcoupl  =  berendsen
pcoupltype  =  isotropic
;pc-grps=  PDM
tau_p   =  1.0
ref_p   =  1.0
compressibility =  4.5e-5

; Generate velocites is off at 300 K.
gen_vel =  yes
gen_temp=  300.0
gen_seed=  10




The problem you're seeing could be an artifact of the shorter cutoff.  Have you 
tried using DispCorr = EnerPres?  Or what about using a Shift function for 
vdwtype?  You might see better energy conservation in that case compared to a 
plain cutoff.


-Justin



On Thu, May 14, 2009 at 4:06 PM, Justin A. Lemkul > wrote:




Yanmei Song wrote:

Dear All:

I have question about the pressure coupling. I have done a 10ns
simulation with 19800 atoms for 120 large molecules using the
following pressure coupling.

Tcoupl  =  berendsen
tc_grps =  PDM
tau_t   =  0.1
ref_t   =  300

Pcoupl  =  berendsen
pcoupltype  =  isotropic
;pc-grps=  PDM
tau_p   =  1.0
ref_p   =  1.0
compressibility =  4.5e-5

Then I did g_energy for the last 3ns and got the results:

Energy  Average   RMSD Fluct.
 Drift  Tot-Drift


---
Potential-98061  0  0  
 0.616681850.04

Temperature 303.561109.602109.602
0.000181791   0.545372
Pressure (bar)   4.48840.811109.8
 -0.169835   -509.506

For such a long run the pressure drift is still too much and
seem hasn't approached 1bar. Does it mean the system hasn't
reach equilibrium yet. I did a similar system by using the same
method. it just take 2 or 3ns to reach the equilibrium. and the
pressure is around 1.01after the run. The only difference is the
cutoff changing from 1.2 to 1.4.  Does the cufoff of 1.4 is too
large to make the system running slower. Or the pressure
coupling method is not working well.  Anyone can give me any
suggestions?



I think it will depend on the interplay of other parameters as well.
 Posting a complete .mdp file may be more helpful.

-Justin

-- 
Yanmei Song

Ph.D. Candidate
Department of Chemical Engineering
Arizona State University




___
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/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the l

[gmx-users] Protein-Ligand Docking?

[Chih-Ying Lin]

HI
Would you please give me an example of "definition" of DOCKed?

Thank you
Lin












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.
___
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

Re: [gmx-users] Protein-Ligand Docking?

[Justin A. Lemkul]

Chih-Ying Lin wrote:

HI
Would you please give me an example of "definition" of DOCKed?



You have to have some criteria to start with.  When we do true docking, we often 
start with a protein-ligand complex for which we know the position and 
orientation of some inhibitor, usually from X-ray diffraction data.  We test our 
model to see if we can replicate that interaction and then use those parameters 
to attempt similar associations with other compounds.


The bottom line is - you have to know what you are looking for.  What residues 
should be involved in the interaction (some known catalytic or binding site), 
and should the interaction even occur under relevant conditions?  If you don't 
know what you might be looking for, you will have a hard time convincing anyone 
that your results are meaningful.


-Justin


Thank you
Lin












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.
___
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/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

Re: [gmx-users] Protein-Ligand Docking?

[Mark Abraham]

Chih-Ying Lin wrote:

HI
Would you please give me an example of "definition" of DOCKed?


That's your job ;-) Try searching the web or literature.

Mark
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] Protein-Ligand Docking?

[Chih-Ying Lin]

Hi
1. If any one know the related paper of protein-ligand docking using
MD, please refer to to those papers.

2. from Justin =>
"we often start with a protein-ligand complex for which we know the position and
orientation of some inhibitor, usually from X-ray diffraction data.  We test our
model to see if we can replicate that interaction and then use those parameters
to attempt similar associations with other compounds."

=>do you mean that we can mimic  X-ray diffraction experimental data
from MD simulation?

=> what are "those parameters"?


3. I have been given the protein and the surfactant and tried to "see"
if  the surfactant will dock on the protein. => what is the next step
that I can do?


Thank you very much
Lin






Chih-Ying Lin wrote:
> HI
> Would you please give me an example of "definition" of DOCKed?
>

You have to have some criteria to start with.  When we do true docking, we often
start with a protein-ligand complex for which we know the position and
orientation of some inhibitor, usually from X-ray diffraction data.  We test our
model to see if we can replicate that interaction and then use those parameters
to attempt similar associations with other compounds.

The bottom line is - you have to know what you are looking for.  What residues
should be involved in the interaction (some known catalytic or binding site),
and should the interaction even occur under relevant conditions?  If you don't
know what you might be looking for, you will have a hard time convincing anyone
that your results are meaningful.

-Justin

> Thank you
> Lin
>
___
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

RE: [gmx-users] Protein-Ligand Docking?

[Dallas B. Warren]

Just as Mark and Justin have said, this is up to you to define this
question.

The reason I said that, is you were asking "how do I know if my molecule
is docked to the protein?".  The first step to answering that question
is defining what you mean by being docked.  Once you have a definition,
then you can look at your molecule / protein and see if it fulfills
those requirements.  I don't do docking, but from what I have seen is
that what is of interest is how well something fits into a pocket,
proximity to some groups, and interactions between the molecule and the
protein (hydrogen bonding and hydrophobic).

You really need to search the literature, as others will be doing
something similar.  And docking has been going on for a long time.

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.
___
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