[gmx-users] how to find conformational free energy?

2009-04-03 Thread ajani haresh 
can anyone tell me how to find the conformational free energy?
i have the one peptide which have 12 amino residue.
i was run the simulation. and found the g_energy from trajectory file.
i have potential energy.
now i want to find the conformational free energy and entropy and enthalpy.

any one know plz help me.
thanks...

-- 
Ajani Haresh
NIPER-IICB
KOLKATA
9836182127
___
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 find conformational free energy?

2009-04-03 Thread David van der Spoel 

ajani haresh wrote:

can anyone tell me how to find the conformational free energy?
i have the one peptide which have 12 amino residue.
i was run the simulation. and found the g_energy from trajectory file.
i have potential energy.
now i want to find the conformational free energy and entropy and enthalpy.

any one know plz help me.
thanks...

You can estimate the conformational entropy using g_covar and g_anaeig 
(Quasi-harmonic and Schlitter). You probably need to do some literature 
search as well, these are difficult topics.


--
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] grompp error in running simultion of membrane protein with lipid bilayer

2009-04-03 Thread Justin A. Lemkul 



nitu sharma wrote:

Dear all,

   I am trying to do simulation of membrane protein with 
lipid bilayer  for this I have made topology file like this-

; topology for tap in 128 dmpc lipids plus water.
; rr1_A.itp and rr1_B.itp can be made in a straightforward manner with 
pdb2gmx, starting

; with a pdb file of tap transporter.
; make sure lipid.itp,dmpc.itp and rr1.itp are in a location where
; grompp can find them (GMXLIB, current directory, or directory given in
; the .mdp file with the include option.
#include "ffoplsaa.itp"
#include "lipid.itp"
#include "dmpc.itp"


This will not work.  I said the exact same thing to someone else not two or 
three days ago.  You cannot combine OPLS-AA with the standard Berger lipid 
parameters; the Berger atom types are for use with a Gromos force field.


You have three options:

1. Use a Gromos force field variant.  You still can't simply #include 
"lipid.itp," however, you will have to append the relevant directives to the 
ff*nb.itp and ff*bon.itp and use these modified files.


2. Modify lipid.itp to be in accordance with OPLS-AA conventions.  Chris Neale 
has posted a detailed procedure to do this; search the list archive.


3. Use the self-consistent Gromos96 53a6 force field parameters that have been 
uploaded to the Users' Contributions section of the website.


The choice is up to you, based on which setup you think is best for your system.

when I am trying to run grompp after solvating the system I am getting 
error like this-

Program grompp, VERSION 4.0.3
Source code file: toppush.c, line: 843

Fatal error:
Atomtype C not found
--


Right, do you see atomtype "C" anywhere in ffoplsaa.atp?  This atomtype belongs 
to a Gromos force field.


-Justin


my command  line like this-
grompp -f em.mdp -p rr1-dmpc.top -c solvated-tapp-mod.pdb -o tapp-mod-em.tpr
 if anyone know about this please suggest me right thing to do.
thanks.

Nitu Sharma
School of life sciences
Jawaherlal Nehru University
New Delhi India





___
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
Graduate Research Assistant
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] Re: PDB structure quality

2009-04-03 Thread Alan 
We've recently announced iCing, which includes whatif as well. Please, take
a look at http://nmr.cmbi.ru.nl/cing/Home.html.
If it happens that your complex is from NMR and deposit in PDB so you can
find it here (http://nmr.cmbi.ru.nl/NRG-CING/index/index.html) already
evaluated.

Cheers,
Alan

On Fri, Apr 3, 2009 at 11:00,  wrote:

>
> Chih-Ying Lin wrote:
> >
> >
> >
> > HI
> > The program WHATIF can perform a proper validation of the structure.
> > But, it is not free software.
> >
> > Can anyone tell me how to test the protein structure manually or by
> Gromacs?
> >
> > What is the criteria to determine the quality of the structure?
>
> That depends on your objective - but you have to define that. Ultimately
> some protein structure generated by a piece of software has to match in
> a relevant way the structure found in biological systems. What that
> means varies with what experimental information you have available.
> Various computational tools might assist in estimating that match.
>
> Mark
>
>

-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
___
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] New topology generation tool available

2009-04-03 Thread Justin A. Lemkul 


Hi All,

I have added a new program to the Users' Contributions section of the website. 
TopolGen is yet another topology-building tool that will produce a rough 
OPLS-AA-compatible topology from an all-atom PDB file.  Please refer to the 
README included with the program (written in Perl) for specific implementation 
details.  The main advantage to the script is that it makes use of the CONECT 
records in the PDB file to determine all bonded parameters.


The caveat is that TopolGen thus far makes no effort to assign atom types and 
charges.  This is an area of further development, but is not much more work for 
the user than the modifications that one often makes to e.g. PRODRG-generated 
topologies.


Please feel free to contact me on this list or privately if you have questions, 
comments, suggestions, or you find a bug.


Enjoy!

-Justin

--


Justin A. Lemkul
Graduate Research Assistant
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] query regarding coming out of ligand from protein during simulation

2009-04-03 Thread sangeeta kundu 
Dear all,
 
 
 
    I am trying to perform simulation of a protein with several ligands, in 
case of certain ligands I found that the ligand  is coming out of the protein 
after 5-6 ns. I have checked the energy of the system, but it does not show any 
abrupt change, still the ligand is coming out of protein after a certain 
time.Is it due to steric hindrance during the course of the simulation or 
something else?   I can not debug, please help. Thanks in advance. 
 
 
regards
Sangeeta


  Add more friends to your messenger and enjoy! Go to 
http://messenger.yahoo.com/invite/___
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] query regarding coming out of ligand from protein during simulation

2009-04-03 Thread Justin A. Lemkul 



sangeeta kundu wrote:

Dear all,

 

 

 

I am trying to perform simulation of a protein with several ligands, 
in case of certain ligands I found that the ligand  is coming out of the 
protein after 5-6 ns. I have checked the energy of the system, but it 
does not show any abrupt change, still the ligand is coming out of 
protein after a certain time.Is it due to steric hindrance during the 
course of the simulation or something else?   I can not debug, please 
help. Thanks in advance.


 



Several possibilities:

1. You have lousy parameters for your ligand.
2. Periodicity effects (search the archive).
3. The ligand doesn't bind strongly, so this is normal.

#1 and #2 are the most likely, given the time scale you've used.

-Justin

 


regards

Sangeeta



Add more friends to your messenger and enjoy! Invite them 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


--


Justin A. Lemkul
Graduate Research Assistant
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] Hydrogen bonds from interface - gOH(z)

2009-04-03 Thread Eudes Fileti 
Hi everyone,
I am working with water in interface with air
and I would examine how the hydrogen bonds vary
with the distance from the interface. Something like that
(
http://pubs.acs.org/appl/literatum/publisher/achs/journals/production/langd5/2009/langd5.2009.25.issue-3/la803324x/images/large/la-2008-03324x_0005.jpeg)

However, I am not getting any GMX-tool to perform this analysis.
Coul anybody help me to calculated this?
bests
eef
___
Eudes Eterno Fileti
Centro de Ciências Naturais e Humanas
Universidade Federal do ABC
Rua Santa Adélia, 166 - Bloco B, Sala 1048
09210-170  Santo André - SP Brasil
+55.11.4437-8408
skype: eefileti
http://cromo.ufabc.edu.br/~fileti/
___
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 find Enthalpy And Entropy ?

2009-04-03 Thread ajani haresh 
Hello,
 I have trajectory file. i was run simulation at 20ns. they genrate the
trajectory file.

i was also found the g_energy and g_rmsd.
i want to find the Enthalpy and Entropy of this peptide simulation. so i can
know abt these peptide conformation.

any one know how to find the enthalpy and entropy from this file.
any one know plz help me...

-- 
Ajani Haresh
NIPER-IICB
KOLKATA
9836182127
___
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] Couette flow

2009-04-03 Thread Manik Mayur 
Hi,

With reference to

http://www.mail-archive.com/gmx-users@gromacs.org/msg13374.html

I would like to know if anybody has successfully simulated couette flow
using GROMACS. If yes, then please suggest what specific steps has to be
taken. If no, then are the developers planning to implement giving constant
velocity to a group of atoms, as we can do in LAMMPS, in future versions.

It will really be a life saver if GROMACS can be used for such problems.
Also can we build GROMACS as a library to be called from customized codes?

Thanks,
-- 
Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
INDIA
___
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 find Enthalpy And Entropy ?

2009-04-03 Thread Justin A. Lemkul 



ajani haresh wrote:

Hello,
 I have trajectory file. i was run simulation at 20ns. they genrate the 
trajectory file.
 
i was also found the g_energy and g_rmsd.
i want to find the Enthalpy and Entropy of this peptide simulation. so i 
can know abt these peptide conformation.
 
any one know how to find the enthalpy and entropy from this file.
any one know plz help me... 



You got an answer to this question already:

http://www.gromacs.org/pipermail/gmx-users/2009-April/040983.html

Demonstrate that you have attempted to follow the advice given, done the 
appropriate background reading, and then pose a new question.


-Justin


--
Ajani Haresh
NIPER-IICB
KOLKATA
9836182127




___
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
Graduate Research Assistant
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] Couette flow

2009-04-03 Thread David van der Spoel 

Manik Mayur wrote:

Hi,

With reference to

http://www.mail-archive.com/gmx-users@gromacs.org/msg13374.html

I would like to know if anybody has successfully simulated couette flow 
using GROMACS. If yes, then please suggest what specific steps has to be 
taken. If no, then are the developers planning to implement giving 
constant velocity to a group of atoms, as we can do in LAMMPS, in future 
versions.


It will really be a life saver if GROMACS can be used for such problems. 


As the mail you pointed to suggest, it is quite simple to do yourself. 
As a first guess look for routine

static void do_update_md(int start,int homenr,double dt,

in src/mdlib/update.c

and find this line:

  /* do not scale the mean velocities u */
  vn = gstat[ga].u[d] + accel[ga][d]*dt + vnrel;

and replace it by

  /* do not scale the mean velocities u */
  vn = gstat[ga].u[d] + accel[ga][d] + vnrel;

and recompile.

As you see, I just removed the multiplication by the time step. Now in 
the input file (mdp) you enter the velocity instead of the acceleration 
in the appropriate entries, and you are good to go. You may need to 
remove the mean velocity of the group as well...



Also can we build GROMACS as a library to be called from customized codes?

Thanks,
--
Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
INDIA




___
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.

David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
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] Couette flow

2009-04-03 Thread Manik Mayur 
On Fri, Apr 3, 2009 at 8:25 PM, David van der Spoel wrote:

> Manik Mayur wrote:
>
>> Hi,
>>
>> With reference to
>>
>> http://www.mail-archive.com/gmx-users@gromacs.org/msg13374.html
>>
>> I would like to know if anybody has successfully simulated couette flow
>> using GROMACS. If yes, then please suggest what specific steps has to be
>> taken. If no, then are the developers planning to implement giving constant
>> velocity to a group of atoms, as we can do in LAMMPS, in future versions.
>>
>> It will really be a life saver if GROMACS can be used for such problems.
>>
>
> As the mail you pointed to suggest, it is quite simple to do yourself. As a
> first guess look for routine
> static void do_update_md(int start,int homenr,double dt,
>
> in src/mdlib/update.c
>
> and find this line:
>
>  /* do not scale the mean velocities u */
>  vn = gstat[ga].u[d] + accel[ga][d]*dt + vnrel;
>
> and replace it by
>
>  /* do not scale the mean velocities u */
>  vn = gstat[ga].u[d] + accel[ga][d] + vnrel;
>
> and recompile.
>
> As you see, I just removed the multiplication by the time step. Now in the
> input file (mdp) you enter the velocity instead of the acceleration in the
> appropriate entries, and you are good to go. You may need to remove the mean
> velocity of the group as well...


Thanks a lot for the suggestion. But will this work if I have 2 groups, one
with constant velocity and another with constant acceleration? Like a
superposition of couette and poiseuille flow.


>
>
>  Also can we build GROMACS as a library to be called from customized codes?
>>
>> Thanks,
>> --
>> Manik Mayur
>> Graduate student
>> Microfluidics Lab
>> Dept. of Mechanical Engg.
>> IIT Kharagpur
>> INDIA
>>
>>
>> 
>>
>> ___
>> 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.
> 
> David van der Spoel, PhD, Professor of Biology
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,  75124 Uppsala, Sweden
> phone:  46 18 471 4205  fax: 46 18 511 755
> 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
>



-- 
Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
INDIA
___
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] Couette flow

2009-04-03 Thread David van der Spoel 

Manik Mayur wrote:



On Fri, Apr 3, 2009 at 8:25 PM, David van der Spoel 
mailto:sp...@xray.bmc.uu.se>> wrote:


Manik Mayur wrote:

Hi,

With reference to

http://www.mail-archive.com/gmx-users@gromacs.org/msg13374.html

I would like to know if anybody has successfully simulated
couette flow using GROMACS. If yes, then please suggest what
specific steps has to be taken. If no, then are the developers
planning to implement giving constant velocity to a group of
atoms, as we can do in LAMMPS, in future versions.

It will really be a life saver if GROMACS can be used for such
problems.


As the mail you pointed to suggest, it is quite simple to do
yourself. As a first guess look for routine
static void do_update_md(int start,int homenr,double dt,

in src/mdlib/update.c

and find this line:

 /* do not scale the mean velocities u */
 vn = gstat[ga].u[d] + accel[ga][d]*dt + vnrel;

and replace it by

 /* do not scale the mean velocities u */
 vn = gstat[ga].u[d] + accel[ga][d] + vnrel;

and recompile.

As you see, I just removed the multiplication by the time step. Now
in the input file (mdp) you enter the velocity instead of the
acceleration in the appropriate entries, and you are good to go. You
may need to remove the mean velocity of the group as well...


Thanks a lot for the suggestion. But will this work if I have 2 groups, 
one with constant velocity and another with constant acceleration? Like 
a superposition of couette and poiseuille flow.

You didn't mention that :(.
No, you will have to do some more hacking, but you could e.g. make group 
0 to have acceleration and group 1 a velocity.



 




Also can we build GROMACS as a library to be called from
customized codes?

Thanks,
-- 
Manik Mayur

Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
INDIA




___
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.


David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
sp...@xray.bmc.uu.se   
 sp...@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




--
Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
INDIA




___
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.

David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
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.gromac

Re: [gmx-users] Couette flow

2009-04-03 Thread Manik Mayur 
On Fri, Apr 3, 2009 at 9:48 PM, David van der Spoel wrote:

> Manik Mayur wrote:
>
>>
>>
>> On Fri, Apr 3, 2009 at 8:25 PM, David van der Spoel 
>> > sp...@xray.bmc.uu.se>> wrote:
>>
>>Manik Mayur wrote:
>>
>>Hi,
>>
>>With reference to
>>
>>http://www.mail-archive.com/gmx-users@gromacs.org/msg13374.html
>>
>>I would like to know if anybody has successfully simulated
>>couette flow using GROMACS. If yes, then please suggest what
>>specific steps has to be taken. If no, then are the developers
>>planning to implement giving constant velocity to a group of
>>atoms, as we can do in LAMMPS, in future versions.
>>
>>It will really be a life saver if GROMACS can be used for such
>>problems.
>>
>>
>>As the mail you pointed to suggest, it is quite simple to do
>>yourself. As a first guess look for routine
>>static void do_update_md(int start,int homenr,double dt,
>>
>>in src/mdlib/update.c
>>
>>and find this line:
>>
>> /* do not scale the mean velocities u */
>> vn = gstat[ga].u[d] + accel[ga][d]*dt + vnrel;
>>
>>and replace it by
>>
>> /* do not scale the mean velocities u */
>> vn = gstat[ga].u[d] + accel[ga][d] + vnrel;
>>
>>and recompile.
>>
>>As you see, I just removed the multiplication by the time step. Now
>>in the input file (mdp) you enter the velocity instead of the
>>acceleration in the appropriate entries, and you are good to go. You
>>may need to remove the mean velocity of the group as well...
>>
>>
>> Thanks a lot for the suggestion. But will this work if I have 2 groups,
>> one with constant velocity and another with constant acceleration? Like a
>> superposition of couette and poiseuille flow.
>>
> You didn't mention that :(.
> No, you will have to do some more hacking, but you could e.g. make group 0
> to have acceleration and group 1 a velocity.
>

Can you provide more insight on how to achieve it, as from your suggestion
it turns out, I can have either constant velocity build of GROMACS or the
constant acceleration one.


>
>>
>>
>>Also can we build GROMACS as a library to be called from
>>customized codes?
>>
>>Thanks,
>>--Manik Mayur
>>Graduate student
>>Microfluidics Lab
>>Dept. of Mechanical Engg.
>>IIT Kharagpur
>>INDIA
>>
>>
>>
>>  
>>
>>___
>>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.
>>
>>  
>>David van der Spoel, PhD, Professor of Biology
>>Dept. of Cell and Molecular Biology, Uppsala University.
>>Husargatan 3, Box 596,  75124 Uppsala, Sweden
>>phone:  46 18 471 4205  fax: 46 18 511 755
>>sp...@xray.bmc.uu.se 
>> sp...@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
>>
>>
>>
>>
>> --
>> Manik Mayur
>> Graduate student
>> Microfluidics Lab
>> Dept. of Mechanical Engg.
>> IIT Kharagpur
>> INDIA
>>
>>
>> 
>>
>> ___
>> 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.
> 
> David van der Spoel, PhD, Professor of Biology

Re: [gmx-users] Couette flow

2009-04-03 Thread David van der Spoel 

Manik Mayur wrote:



On Fri, Apr 3, 2009 at 9:48 PM, David van der Spoel 
mailto:sp...@xray.bmc.uu.se>> wrote:


Manik Mayur wrote:



On Fri, Apr 3, 2009 at 8:25 PM, David van der Spoel
mailto:sp...@xray.bmc.uu.se>
>> wrote:

   Manik Mayur wrote:

   Hi,

   With reference to

 
 http://www.mail-archive.com/gmx-users@gromacs.org/msg13374.html


   I would like to know if anybody has successfully simulated
   couette flow using GROMACS. If yes, then please suggest what
   specific steps has to be taken. If no, then are the
developers
   planning to implement giving constant velocity to a group of
   atoms, as we can do in LAMMPS, in future versions.

   It will really be a life saver if GROMACS can be used for
such
   problems.


   As the mail you pointed to suggest, it is quite simple to do
   yourself. As a first guess look for routine
   static void do_update_md(int start,int homenr,double dt,

   in src/mdlib/update.c

   and find this line:

/* do not scale the mean velocities u */
vn = gstat[ga].u[d] + accel[ga][d]*dt +
vnrel;

   and replace it by

/* do not scale the mean velocities u */
vn = gstat[ga].u[d] + accel[ga][d] + vnrel;

   and recompile.

   As you see, I just removed the multiplication by the time
step. Now
   in the input file (mdp) you enter the velocity instead of the
   acceleration in the appropriate entries, and you are good to
go. You
   may need to remove the mean velocity of the group as well...


Thanks a lot for the suggestion. But will this work if I have 2
groups, one with constant velocity and another with constant
acceleration? Like a superposition of couette and poiseuille flow.

You didn't mention that :(.
No, you will have to do some more hacking, but you could e.g. make
group 0 to have acceleration and group 1 a velocity.


Can you provide more insight on how to achieve it, as from your 
suggestion it turns out, I can have either constant velocity build of 
GROMACS or the constant acceleration one.

if  (g == 0)
APPLy acceleration
else if (g == 1)
apply velocity
else
do normal update



 



   Also can we build GROMACS as a library to be called from
   customized codes?

   Thanks,
   --Manik Mayur
   Graduate student
   Microfluidics Lab
   Dept. of Mechanical Engg.
   IIT Kharagpur
   INDIA


 
 


   ___
   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.
 
 

   David van der Spoel, PhD, Professor of Biology
   Dept. of Cell and Molecular Biology, Uppsala University.
   Husargatan 3, Box 596,  75124 Uppsala, Sweden
   phone:  46 18 471 4205  fax: 46 18 511 755
   sp...@xray.bmc.uu.se 
>
  sp...@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.

Re: [gmx-users] Couette flow

2009-04-03 Thread Manik Mayur 
On Fri, Apr 3, 2009 at 10:47 PM, David van der Spoel
wrote:

> Manik Mayur wrote:
>
>>
>>
>> On Fri, Apr 3, 2009 at 9:48 PM, David van der Spoel 
>> > sp...@xray.bmc.uu.se>> wrote:
>>
>>Manik Mayur wrote:
>>
>>
>>
>>On Fri, Apr 3, 2009 at 8:25 PM, David van der Spoel
>>mailto:sp...@xray.bmc.uu.se>
>>>>
>> wrote:
>>
>>   Manik Mayur wrote:
>>
>>   Hi,
>>
>>   With reference to
>>
>>
>> http://www.mail-archive.com/gmx-users@gromacs.org/msg13374.html
>>
>>   I would like to know if anybody has successfully simulated
>>   couette flow using GROMACS. If yes, then please suggest what
>>   specific steps has to be taken. If no, then are the
>>developers
>>   planning to implement giving constant velocity to a group of
>>   atoms, as we can do in LAMMPS, in future versions.
>>
>>   It will really be a life saver if GROMACS can be used for
>>such
>>   problems.
>>
>>
>>   As the mail you pointed to suggest, it is quite simple to do
>>   yourself. As a first guess look for routine
>>   static void do_update_md(int start,int homenr,double dt,
>>
>>   in src/mdlib/update.c
>>
>>   and find this line:
>>
>>/* do not scale the mean velocities u */
>>vn = gstat[ga].u[d] + accel[ga][d]*dt +
>>vnrel;
>>
>>   and replace it by
>>
>>/* do not scale the mean velocities u */
>>vn = gstat[ga].u[d] + accel[ga][d] + vnrel;
>>
>>   and recompile.
>>
>>   As you see, I just removed the multiplication by the time
>>step. Now
>>   in the input file (mdp) you enter the velocity instead of the
>>   acceleration in the appropriate entries, and you are good to
>>go. You
>>   may need to remove the mean velocity of the group as well...
>>
>>
>>Thanks a lot for the suggestion. But will this work if I have 2
>>groups, one with constant velocity and another with constant
>>acceleration? Like a superposition of couette and poiseuille flow.
>>
>>You didn't mention that :(.
>>No, you will have to do some more hacking, but you could e.g. make
>>group 0 to have acceleration and group 1 a velocity.
>>
>>
>> Can you provide more insight on how to achieve it, as from your suggestion
>> it turns out, I can have either constant velocity build of GROMACS or the
>> constant acceleration one.
>>
> if  (g == 0)
> APPLy acceleration
> else if (g == 1)
> apply velocity
> else
> do normal update
>
>>
I really appreciate your help. One last doubt, what is this 'g' or the group
you are talking about? As we define acc_grps by their names and not numbers
in the mdp file. Do we have to introduce some new parameter 'g' which will
be defined as 0 or 1 accordingly?

Also, can't we have this feature in the main stream GROMACS rather than
having our own custom build, something like vel_grps? Just a suggestion.

Thanks,


>>
>>
>>   Also can we build GROMACS as a library to be called from
>>   customized codes?
>>
>>   Thanks,
>>   --Manik Mayur
>>   Graduate student
>>   Microfluidics Lab
>>   Dept. of Mechanical Engg.
>>   IIT Kharagpur
>>   INDIA
>>
>>
>>
>> 
>>
>>   ___
>>   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.
>>
>> 
>>   David van der Spoel, PhD, Professor of Biology
>>   Dept. of Cell and Molecular Biology, Uppsala University.
>>   Husargatan 3, Box 596,  75124 Uppsala, Sweden
>>   phone:  46 18 471 4205  fax: 46 18 511 755
>>   sp...@xray.bmc.uu.se 
>>>
>>sp...@gromacs.org

Re: [gmx-users] Couette flow

2009-04-03 Thread David van der Spoel 

Manik Mayur wrote:



On Fri, Apr 3, 2009 at 10:47 PM, David van der Spoel 
mailto:sp...@xray.bmc.uu.se>> wrote:


Manik Mayur wrote:



On Fri, Apr 3, 2009 at 9:48 PM, David van der Spoel
mailto:sp...@xray.bmc.uu.se>
>> wrote:

   Manik Mayur wrote:



   On Fri, Apr 3, 2009 at 8:25 PM, David van der Spoel
   mailto:sp...@xray.bmc.uu.se>
>
    
   >
   >>


  http://www.gromacs.org/mailman/listinfo/gmx-users
  Please search the archive at
http://www.gromacs.org/search

[gmx-users] dssp install problems

2009-04-03 Thread KS Rotondi 

All,

I've looked at the site and cannot figure this out, so apologies if  
this is a painful often seen question.


I'm trying to install dssp for use with do_dssp on an OSX.5 PPC system  
with the following steps, in the dssp folder:


./DsspCompileCC

cd..

sudo mv dssp /usr/local

cd /usr/local/bin

sudo ln -s /usr/local/dssp/dsspcmbi

Having done that I can type dsspcmbi in a terminal and run the dssp  
program. However, running do_dssp returns


---
Program do_dssp, VERSION 4.0.4
Source code file: do_dssp.c, line: 422

Fatal error:
DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP)
---

My problem is compiling the dssp source does not return a 'dssp' file,  
rather the 'dsspcmbi' executable, as advertised. I feel I'm missing a  
minor last step and would appreciate any help.


Thanks,

Ken

Dr. K.S. Rotondi
Departments of Chemistry, BIochemistry and Molecular Biology
914G LGRT
The University of Massachusetts - Amherst
Amherst, MA 01003

"If there's a solution, why worry?, If there's no solution, why worry?"
His Holiness, the Dalai Llama



___
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] Couette flow

2009-04-03 Thread Manik Mayur 
On Fri, Apr 3, 2009 at 11:11 PM, David van der Spoel
wrote:

> Manik Mayur wrote:
>
>>
>>
>> On Fri, Apr 3, 2009 at 10:47 PM, David van der Spoel <
>> sp...@xray.bmc.uu.se > wrote:
>>
>>Manik Mayur wrote:
>>
>>
>>
>>On Fri, Apr 3, 2009 at 9:48 PM, David van der Spoel
>>mailto:sp...@xray.bmc.uu.se>
>>>>
>> wrote:
>>
>>   Manik Mayur wrote:
>>
>>
>>
>>   On Fri, Apr 3, 2009 at 8:25 PM, David van der Spoel
>>   mailto:sp...@xray.bmc.uu.se>
>>>
>>   > >>
>>  Manik Mayur wrote:
>>
>>  Hi,
>>
>>  With reference to
>>
>>
>> http://www.mail-archive.com/gmx-users@gromacs.org/msg13374.html
>>
>>  I would like to know if anybody has successfully
>>simulated
>>  couette flow using GROMACS. If yes, then please
>>suggest what
>>  specific steps has to be taken. If no, then are the
>>   developers
>>  planning to implement giving constant velocity to
>>a group of
>>  atoms, as we can do in LAMMPS, in future versions.
>>
>>  It will really be a life saver if GROMACS can be
>>used for
>>   such
>>  problems.
>>
>>
>>  As the mail you pointed to suggest, it is quite simple
>>to do
>>  yourself. As a first guess look for routine
>>  static void do_update_md(int start,int homenr,double dt,
>>
>>  in src/mdlib/update.c
>>
>>  and find this line:
>>
>>   /* do not scale the mean velocities u */
>>   vn = gstat[ga].u[d] +
>>accel[ga][d]*dt +
>>   vnrel;
>>
>>  and replace it by
>>
>>   /* do not scale the mean velocities u */
>>   vn = gstat[ga].u[d] +
>>accel[ga][d] + vnrel;
>>
>>  and recompile.
>>
>>  As you see, I just removed the multiplication by the time
>>   step. Now
>>  in the input file (mdp) you enter the velocity instead
>>of the
>>  acceleration in the appropriate entries, and you are
>>good to
>>   go. You
>>  may need to remove the mean velocity of the group as
>>well...
>>
>>
>>   Thanks a lot for the suggestion. But will this work if I
>>have 2
>>   groups, one with constant velocity and another with constant
>>   acceleration? Like a superposition of couette and
>>poiseuille flow.
>>
>>   You didn't mention that :(.
>>   No, you will have to do some more hacking, but you could e.g.
>>make
>>   group 0 to have acceleration and group 1 a velocity.
>>
>>
>>Can you provide more insight on how to achieve it, as from your
>>suggestion it turns out, I can have either constant velocity
>>build of GROMACS or the constant acceleration one.
>>
>>if  (g == 0)
>>APPLy acceleration
>>else if (g == 1)
>>apply velocity
>>else
>>do normal update
>>
>>  I really appreciate your help. One last doubt, what is this 'g' or the
>> group you are talking about? As we define acc_grps by their names and not
>> numbers in the mdp file. Do we have to introduce some new parameter 'g'
>> which will be defined as 0 or 1 accordingly?
>>
> EasY:
>
> acc_groups = Cucumber TOmata
> means Cucumber = 0, Tomato = 1
>

Got it. :) Thanks a lot.


>> Also, can't we have this feature in the main stream GROMACS rather than
>> having our own custom build, something like vel_grps? Just a suggestion.
>>
> Sure, but that doesn't help you now.
>

Yes, but I would like to see my favorite MD package as one of the most
versatile package available :)


>> Thanks,
>>
>>
>>
>>  Also can we build GROMACS as a library to be
>>called from
>>  customized codes?
>>
>>  Thanks,
>>  --Manik Mayur
>>  Graduate student
>>  Microfluidics Lab
>>  Dept. of Mechanical Engg.
>>  IIT Kharagpur
>>  INDIA
>>
>>
>>
>>  
>>
>>  ___
>>  gmx-users mailing listgmx-users@gromacs.org
>>
>

Re: [gmx-users] dssp install problems

2009-04-03 Thread Justin A. Lemkul 



KS Rotondi wrote:
All, 

I've looked at the site and cannot figure this out, so apologies if this 
is a painful often seen question. 

I'm trying to install dssp for use with do_dssp on an OSX.5 PPC system 
with the following steps, in the dssp folder:


./DsspCompileCC

cd..

sudo mv dssp /usr/local

cd /usr/local/bin

sudo ln -s /usr/local/dssp/dsspcmbi

Having done that I can type dsspcmbi in a terminal and run the dssp 
program. However, running do_dssp returns


---
Program do_dssp, VERSION 4.0.4
Source code file: do_dssp.c, line: 422

Fatal error:
DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP)
---

My problem is compiling the dssp source does not return a 'dssp' file, 
rather the 'dsspcmbi' executable, as advertised. I feel I'm missing a 
minor last step and would appreciate any help.


Right, so rename the dsspcmbi executable dssp and move it /usr/local/bin, 
nothing fancy.  The other option is to export DSSP=/path/to/your/dssp


-Justin



Thanks, 


Ken

Dr. K.S. Rotondi
Departments of Chemistry, BIochemistry and Molecular Biology
914G LGRT
The University of Massachusetts - Amherst
Amherst, MA 01003

"If there's a solution, why worry?, If there's no solution, why worry?"
His Holiness, the Dalai Llama






___
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
Graduate Research Assistant
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] dssp install problems

2009-04-03 Thread J. Rui Rodrigues 
Hi,

Try this:

cd /usr/local/bin
sudo ln -s dsspcmbi dssp

Hope this help,
Rui Rodrigues


On Fri, 3 Apr 2009 13:44:56 -0400, KS Rotondi wrote
> All,
> 
> I've looked at the site and cannot figure this out, so apologies if  
> this is a painful often seen question.
> 
> I'm trying to install dssp for use with do_dssp on an OSX.5 PPC system  
> with the following steps, in the dssp folder:
> 
> ./DsspCompileCC
> 
> cd..
> 
> sudo mv dssp /usr/local
> 
> cd /usr/local/bin
> 
> sudo ln -s /usr/local/dssp/dsspcmbi
> 
> Having done that I can type dsspcmbi in a terminal and run the dssp  
> program. However, running do_dssp returns
> 
> ---
> Program do_dssp, VERSION 4.0.4
> Source code file: do_dssp.c, line: 422
> 
> Fatal error:
> DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP)
> ---
> 
> My problem is compiling the dssp source does not return a 'dssp' file,  
> rather the 'dsspcmbi' executable, as advertised. I feel I'm missing a  
> minor last step and would appreciate any help.
> 
> Thanks,
> 
> Ken
> 
> Dr. K.S. Rotondi
> Departments of Chemistry, BIochemistry and Molecular Biology
> 914G LGRT
> The University of Massachusetts - Amherst
> Amherst, MA 01003
> 
> "If there's a solution, why worry?, If there's no solution, why worry?"
>   His Holiness, the Dalai Llama


--
Webmail ESTG de Leiria (http://webmail.estg.ipleiria.pt)


___
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] dssp install problems

2009-04-03 Thread KS Rotondi 
Many thanks to Mr. Lemkul and Mr. Rodrigues, their solution was, as  
they say, the ticket.


Ken

On Apr 3, 2009, at 1:57 PM, Justin A. Lemkul wrote:




KS Rotondi wrote:
All, I've looked at the site and cannot figure this out, so  
apologies if this is a painful often seen question. I'm trying to  
install dssp for use with do_dssp on an OSX.5 PPC system with the  
following steps, in the dssp folder:

./DsspCompileCC
cd..
sudo mv dssp /usr/local
cd /usr/local/bin
sudo ln -s /usr/local/dssp/dsspcmbi
Having done that I can type dsspcmbi in a terminal and run the dssp  
program. However, running do_dssp returns

---
Program do_dssp, VERSION 4.0.4
Source code file: do_dssp.c, line: 422
Fatal error:
DSSP executable (/usr/local/bin/dssp) does not exist (use setenv  
DSSP)

---
My problem is compiling the dssp source does not return a 'dssp'  
file, rather the 'dsspcmbi' executable, as advertised. I feel I'm  
missing a minor last step and would appreciate any help.


Right, so rename the dsspcmbi executable dssp and move it /usr/local/ 
bin, nothing fancy.  The other option is to export DSSP=/path/to/ 
your/dssp


-Justin


Thanks, Ken
Dr. K.S. Rotondi
Departments of Chemistry, BIochemistry and Molecular Biology
914G LGRT
The University of Massachusetts - Amherst
Amherst, MA 01003
"If there's a solution, why worry?, If there's no solution, why  
worry?"

His Holiness, the Dalai Llama

___
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
Graduate Research Assistant
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 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] The free energy calculation in Manual Chapter 4

2009-04-03 Thread Chih-Ying Lin 
Hi
I read the free energy calculation in Manual Chapter 4.
What condition could I use this free energy calculation of the Gromacs MD
package?


>From tutorial, the solvation free energy can be calculated by Gromacs.
how about the free energy of the micelle forming system?
Can i apply the free energy calculation on the micelle forming system?

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] HF/6-31G** ESP derived charges to replace PRODRGassigned ones

2009-04-03 Thread Lucio Montero 

I was thinking that's not such a problem switching tha OPLS-AA, since most
of the atoms in my system are from water, that will remain being spc.

--
From: "Lucio Ricardo Montero Valenzuela" 
Sent: Wednesday, April 01, 2009 12:59 AM
To: "Discussion list for GROMACS users" 
Subject: Re: [gmx-users] HF/6-31G** ESP derived charges to replace
PRODRGassigned ones


I wanted the OPLS-UA because my system is large (3 proteins with 2 organic
molecules, in water), and, if the G43a1 forcefield gives me a MD speed of
70
ps/day, an all atom model will result much slower. So what else can I do
to
speed up my MD, to get results in 1-3 months?.
Mensaje citado por David van der Spoel :


Lucio Ricardo Montero Valenzuela wrote:
> So it 's better to switch to the OPLS forcefield if I want to compute
> the
> charges?.
> How can I implement the OPLS-UA if my gromacs (version 3.3) only
> includes
the
> OPLS-AA?

We don't support United atom OPLS because Jorgensen himself does not use
it anymore. That if something should indicate for you that the united
atom force field has been superseded by the all-atom. Jorgensen himself
uses OPLS-AA with TIP4P, so this is probably the best recommendation.
Most important, if you chose to use another combination, you basically
have to prove that this "works" as well (whatever that means...)

> Mensaje citado por "Justin A. Lemkul" :
>
>>
>> Lucio Montero wrote:
>>> How about MOPAC to calculate the charges for 3-methyladenine (this
>>> molecule has a charge +1) for using the G43a1 force field?.
>>>
>>>
>> That may not be a bad place to start, but any parameters applied to a
Gromos
>> molecule have to reproduce condensed phase thermodynamic observables.
>> Empirical
>> fitting of the initial parameters may be required.  Refer to the
>> primary
>> literature.  The reference for the 53a5 and 53a6 parameter sets are
published
>> in
>> JCC, which may provide you with some useful information.
>>
>> -Justin
>>
>>> --
>>> From: "Ran Friedman, Biochemisches Inst." 
>>> Sent: Friday, March 27, 2009 2:35 PM
>>> To: ; "Discussion list for GROMACS users"
>>> 
>>> Subject: Re: [gmx-users] HF/6-31G** ESP derived charges to replace
>>> PRODRGassignedones
>>>
 Dear Josmar,

 You haven't written which force field you plan to use. For OPLS and
 AMBER QM-based optimisation should be fine. In Gromos, the FF was
 developed with the aim of reproducing experimental results and I'm
 not
 sure if you can find a better solution than examining other residues
 with the same chemical moieties or use the same approach as reported
 in the relevant manuscripts. Some software packages can also be
 used -
 these are mostly proprietary and not so easy to use.

 Once you derive the parameters, it's a good idea to make some test
 runs of the ligands and see if they behave as expected before you
 actually run a simulation with the protein. For example, if a
 conjugate ring system isn't planar something may be wrong in the
setting.

 There's no easy solution - this is why it's considered an advanced
 topic. It is, however, very important. I've encountered a ligand
 that
 leaves its binding site during a simulation due to wrong parameters
 (in this case, the protonation of a protein side chain - FEBS  581,
 Pages 4120-4124, 2007).

 Hope that helped,
 Ran

 On Fri, 27 Mar 2009 12:22:01 -0700 (PDT)
  "Josmar R. da Rocha"  wrote:
> Dear users,
>
> I have been reading some posts about using externally computed
> charges to replace Prodrg charges at ligand topology files. Many
> users commented on the low trustability given to Prodrg charges
> (e.g
> http://www.mail-archive.com/gmx-users@gromacs.org/msg02360.html ;
> http://www.mail-archive.com/gmx-users@gromacs.org/msg17351.html ).
> Dr. Verli pointed out the use of semi-empirical methods such as RM1
> in cases not involving simulations with sulphate or phosphate
> groups
> (what is not my case) and the use of QM methods with the 6-31G**
> basis set, for example, to obtain robust charges
> (http://www.mail-archive.com/gmx-users@gromacs.org/msg03410.html).
> On
> the other hand Dr. Mobley defined as a "a bad idea to compute
> charges
> for an all-atom case using QM and then try to convert these to a
> united atom force field". Other users advice that the best charges
> are that compatible with the force field parametrization
> (http://www.mail-archive.com/gmx-users@gromacs.org/msg10760.html ;
> http://www.mail-archive.com/gmx-users@gromacs.org/msg08308.html),
> usually pointing to
> http://wiki.gromacs.org/index.php/Parameterization. Dr Friedman
> suggested that "to calculate the electrostatic potential over the
> whole molecule, and fit the atomic charges so that they reproduc

[gmx-users] Help on Exclusions and 1-4 Interactions

2009-04-03 Thread feng chen 
Dear all,

  Recently,We have tried to implement our own version of frce felds into 
Gromacs 3.3.3. On the purpose of testing, we dumped out all the infrmation from 
tpr by using gmxdump. Everything goes fine except this 1-4 interactions terms. 
The prblem we had is that even though we had set number of exclusion to 3 in 
our itp files, but still got all 1-4 pairs generated(in gmexdump 
output), together with LJ-14 and Coulomb-14 energies( in log fiels). This is 
confusing, since based on our understanding whenever number of exclusion is 3, 
any kinda 1-4 interaction should be excluded. Thereforce, none of those 1-4 
pairs will be generated. Well,apparently, that's not the case here for gromacs. 
And we have no idea what's happenning here.

  Any hints or suggestions will be highly appreciated!

  kevin  



  ___
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] Help on Exclusions and 1-4 Interactions

2009-04-03 Thread Mark Abraham 

feng chen wrote:

Dear all,
 
  Recently,We have tried to implement our own version of frce felds into 
Gromacs 3.3.3. On the purpose of testing, we dumped out all the 
infrmation from tpr by using gmxdump. Everything goes fine except this 
1-4 interactions terms. The prblem we had is that even though we had set 
number of exclusion to 3 in our itp files, but still got all 1-4 pairs 
generated(in gmexdump output), together with LJ-14 and Coulomb-14 
energies( in log fiels). This is confusing, since based on our 
understanding whenever number of exclusion is 3, any kinda 1-4 
interaction should be excluded. Thereforce, none of those 1-4 pairs will 
be generated. Well,apparently, that's not the case here for gromacs. And 
we have no idea what's happenning here.
 
  Any hints or suggestions will be highly appreciated!


Other than reading chapter 5, I can only suggest that you're probably 
adding 1-4 interactions in your [ pairs ] section.


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] problem in topology file for protein+lipid bilayer system

2009-04-03 Thread nitu sharma 
Hello justin

thanks for ur suggestion . I am trying to do membrane protein simulation
with lipid bilayer . I have pdb file of inserted protein in dmpc lipid
bilayer. But I am facing problem in making topology file for this system.As
u told in previous mail you can't combine OPLS_AA with a standerd berger
lipid parameter right but   even if I used the force field ffgmx  than also
I am getting error

my topology file like this which I have made-


topology for 1 protein molecule in 128 dmpc lipids, water and 1 counter ion.
; rr1_A.itp and rr1_B.itp can be made in a straightforward manner with
pdb2gmx,
starting
; with a pdb file of tap transporter.
; make sure lipid.itp,dmpc.itp and rr1.itp are in a location where
; grompp can find them (GMXLIB, current directory, or directory given in
; the .mdp file with the include option.
; Include forcefield parameters
#include "ffgmx.itp"
#include "lipid.itp"
#include "dmpc.itp"

; Include chain topologies
#include "rr1_A.itp"
#include "rr1_B.itp"

; Include position restrain protein
;#ifdef POSRES_PROTEIN
;#include "posre_A.itp"
;#include "posre_B.itp"
;#endif
; Include position restrain lipid
;#ifdef POSRES_LIPID
;#include "lip_posre.itp
;#endif

; Include water topology
#ifdef FLEX_SPC
#include "flexspc.itp"
#else
#include "spc.itp"
#endif

#ifdef POSRES_WATER
;Position restraint for each water oxygen
[ position_restraints ]
; i funct  fcx  fcy  fcz
  1  1 1000 1000 1000
#endif

; Include generic topology for ions
#include "ions.itp"
[ system ]
; Name
PROTEIN IN DMPC BILAYER + WATER

[ molecules ]
; compound  #mols
Protein_A1
Protein_B1
DMPC128
SOL3552
Na   1

*and the error I am getting like this-

processing topology...
Opening library file /usr/local/gromacs/share/gromacs/top/ffgmx.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffgmxnb.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffgmxbon.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
Generated 1369 of the 2211 non-bonded parameter combinations

---
Program grompp, VERSION 4.0.3
Source code file: toppush.c, line: 947

Fatal error:
Atomtype opls_287 not found
---
can u please suggest me is their any error in topology file and where should
I have to make chnge.
If I want to use ffgmx force field.
as like if I want to use oplsaa  force field I have to make change in
lipid.itp.


please suggest me what should I have to do if I am using ffgmx force field.


Thanks a lot in advance.
___
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