Re: [gmx-users] Simulation of membrane protein

[James Starlight]

Justin


Sure, you could do all of it within a shell script that loops the commands
> and checks the printed output.


As I understood in that iterations only step with scalling by factor 0.95
and futher energy minimization must be included until desired S per lipid
will be reached. Could you provide me with a small example of such script
for better understanding of the syntax. I've never done unix's shell scripts
before :)


Could you tell me where I could found experimental valuee for Area per lipid
for differen cases (e.g I'll be work with large membrane proteins such as
membrane receptors so i wounder to know what values of S per lipid as well
as S per protein I might expect in that case)

Also I have a question about solvation of my membrane protein via GENBOX. I
found 2 possible ways to exclude water from the insertion into membrane
- Changing vdv radii for the C atoms- So i've copied  vdwradii.dat to my
work dirrectory and changed vdv R. How I should to define that genbox uses
exactly that modified file located in my working directory instead of
default vdwradii.dat? Finally how I can check that there are not waters
within the membrane ? (I've tried to visualize via VMD but the overal
picture is very unclear :) )


- Also I've found that I can Running short md to exclude those waters via
hyfrophobic effect.  What parametries would be opti,al for that simulation
in case of KALP as well as other more larger proteins ?


Thank you for your help,

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

[gmx-users] Implicit solvation

[Soumya Lipsa Rath]

I am a new gromacs user. I wanted to simulate a membrane protein without the
lipid bilayer using the IMM1 force field of CHARMM27. I really would
appreciate if someone can help me solve this or direct me towards implicit
solvation tutorial in gromacs


Regards,

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

Re: [gmx-users] Implicit solvation

[bipin singh]

Check the below link:
http://www.gromacs.org/Documentation/Terminology/Implicit_Solvent

On Mon, Oct 17, 2011 at 13:47, Soumya Lipsa Rath
 wrote:
> I am a new gromacs user. I wanted to simulate a membrane protein without the
> lipid bilayer using the IMM1 force field of CHARMM27. I really would
> appreciate if someone can help me solve this or direct me towards implicit
> solvation tutorial in gromacs
>
>
> Regards,
>
> Soumya
>
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
---
Regards,
Bipin Singh
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] CHARMM GUI to Gromacs

[Roy Lee]

Dear all,



I would like to simulate my protein in a lipid bilayer using gromacs 4.5.4,
and a forcefield of gromos96. However i don't have the topologies files for
lipid bilayer for POPE and DMPE. Anybody knows where can i get the
topologies file for POPE and DMPE ? Before that, i had actually used the
CHARMM GUI to put my protein into the lipid bilayer. From there, i am not
sure how i am able to use the output from CHARMM GUI to do md simulation in
gromacs



Any help is much appreciated.



Thanks a lot!
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] CHARMM GUI to Gromacs

[bipin singh]

There is already tutorial for creating lipid bilayer and insertion of
protein into that for GROMACS
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html
Why you have used Charmmgui I am not able to understand.
You can get some useful topologies from below link,but I don't know how useful
it might be for your case.
http://people.ucalgary.ca/~tieleman/download.html

On Mon, Oct 17, 2011 at 14:31, Roy Lee  wrote:
> Dear all,
>
>
>
> I would like to simulate my protein in a lipid bilayer using gromacs 4.5.4,
> and a forcefield of gromos96. However i don't have the topologies files for
> lipid bilayer for POPE and DMPE. Anybody knows where can i get the
> topologies file for POPE and DMPE ? Before that, i had actually used the
> CHARMM GUI to put my protein into the lipid bilayer. From there, i am not
> sure how i am able to use the output from CHARMM GUI to do md simulation in
> gromacs
>
>
>
> Any help is much appreciated.
>
>
>
> Thanks a lot!
>
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
---
Regards,
Bipin Singh
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] High temperature Simulation

[Kavyashree M]

Dear users,

For simulating a protein at high temperature (more than 300K,
less than 400K) using OPLSAA forcefield, what are the parameters
other than Temperature that need to be taken care of?
Does the energy minimization step also needs to be done at high
temperature? (here my aim is not to simulate an unfolding event)
I have a reference -
Biophysical Journal Volume 94 June 2008 –4453

Any other references or suggestions will be helpful.

Thanking you
With Regards
M. Kavyashree
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] High temperature Simulation

[bipin singh]

As far as I know we do energy minimization at room temperature only.
Only during equilibration
(NVT and NPT) we use high temperature for maintaining proper density
before starting the final production run.

On Mon, Oct 17, 2011 at 15:15, Kavyashree M  wrote:
> Dear users,
>
> For simulating a protein at high temperature (more than 300K,
> less than 400K) using OPLSAA forcefield, what are the parameters
> other than Temperature that need to be taken care of?
> Does the energy minimization step also needs to be done at high
> temperature? (here my aim is not to simulate an unfolding event)
> I have a reference -
> Biophysical Journal Volume 94 June 2008 –4453
>
> Any other references or suggestions will be helpful.
>
> Thanking you
> With Regards
> M. Kavyashree
>
>
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
---
Regards,
Bipin Singh
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] topologies for POPE and DMPE

[Thomas Piggot]

Hi Roy,

PE lipids are less frequently used than PC ones and there are fewer 
topologies available. Also it has been shown that using the Berger PC 
lipid topologies (the most frequently used united-atom PC lipids) and 
simply changing the CH3 atoms in the head group to H is not a good 
approach for PE (de Vries et al. DOI: 10.1021/jp0366926 is I think the 
first mention of this).


Other PE topologies I am aware of are either the all-atom CHARMM (27 or 
36) lipids or there are two united-atom GROMOS PE topologies:


The first is the GROMOS43A1-S3 force field which has a POPE topology 
(you can download this from the contributions section on the GROMACS 
website). I have simulated a POPE membrane using these parameters before 
with no problems.


The second (and here is a shameless plug for some of my work, sorry!) is 
a GROMOS53A6 based PE described in a paper we have just got accepted 
into J. Phys. Chem B (http://dx.doi.org/10.1021/jp207013v). The 
supplementary information for this paper (which is not yet available) 
has an analysis/validation of POPE and DPPE membrane using these 
parameters which are based upon the PC topologies of Kukol (DOI: 
10.1021/ct8003468) and Chandrasekhar (DOI: 10.1007/s00249-002-0269-4). 
If you (or anyone else) wish to use these PE topologies send me an email 
off-list and I can let you have them. I have not tested DMPE yet but I 
would imagine it should be similar to DPPE and you can also make a DMPE 
bilayer from a DPPE one by simply removing two CH2 groups from each 
lipid tail and equilibrating the new membrane.


Cheers

Tom

Roy Lee wrote:

Dear all,

 

I would like to simulate my protein in a lipid bilayer using gromacs 
4.5.4, and a forcefield of gromos96. However i don't have the topologies 
files for lipid bilayer for POPE and DMPE. Anybody knows where can i get 
the topologies file for POPE and DMPE ?


 


Any help is much appreciated.

 


Thanks a lot!

 


Roy



--
Dr Thomas Piggot
University of Southampton, UK.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] High temperature Simulation

[Kavyashree M]

Thank you,

What about the pressure that need to be used at that temperature
(for a system of a protein in tip4p water)

Thank you
With Regards
Kavya

On Mon, Oct 17, 2011 at 3:29 PM, bipin singh  wrote:

> As far as I know we do energy minimization at room temperature only.
> Only during equilibration
> (NVT and NPT) we use high temperature for maintaining proper density
> before starting the final production run.
>
> On Mon, Oct 17, 2011 at 15:15, Kavyashree M  wrote:
> > Dear users,
> >
> > For simulating a protein at high temperature (more than 300K,
> > less than 400K) using OPLSAA forcefield, what are the parameters
> > other than Temperature that need to be taken care of?
> > Does the energy minimization step also needs to be done at high
> > temperature? (here my aim is not to simulate an unfolding event)
> > I have a reference -
> > Biophysical Journal Volume 94 June 2008 –4453
> >
> > Any other references or suggestions will be helpful.
> >
> > Thanking you
> > With Regards
> > M. Kavyashree
> >
> >
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
>
>
>
> --
> ---
> Regards,
> Bipin Singh
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] trjconv:solute at the center

[Justin A. Lemkul]

Nilesh Dhumal wrote:

Hello,

I have system with solute is surrounded by 256 solvent molecules. I run
the simulation for 20 ns. I save the snap shot at 500 ps using following
command.

trjconv -f 3.trr -s 3.tpr -n 500-1.ndx -b 500.0 -e 501.0 -dt 1.0 -pbc
nojump -center   -o 500-11.pdb

I tried to keep the solute at the center box. In visualization, the solute
is not at center , its close to box edges.

How can I keep the solute at the center.




You're doing too many things at once.  Split the trjconv operation:

1. Run trjconv -pbc mol on the whole trajectory
2. Run trjconv -center on the output of (1)
3. Run trjconv -dump 500 on the output of (2)

-Justin


I am using Gromacs 4.0.7 version.

Thanks

Nilesh












--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Simulation of membrane protein

[Justin A. Lemkul]

James Starlight wrote:

Justin


Sure, you could do all of it within a shell script that loops the
commands and checks the printed output.


As I understood in that iterations only step with scalling by factor 
0.95 and futher energy minimization must be included until desired S per 
lipid will be reached. Could you provide me with a small example of such 
script for better understanding of the syntax. I've never done unix's 
shell scripts before :)





I don't have one on hand, sorry.  An hour or so spent with shell scripting 
tutorials will probably lead you to it, though.


Could you tell me where I could found experimental valuee for Area per 
lipid for differen cases (e.g I'll be work with large membrane proteins 
such as membrane receptors so i wounder to know what values of S per 
lipid as well as S per protein I might expect in that case)




Some are given in the tutorial, along with references.  If you're a lipid that's 
not listed, you'll have to find such information in the literature.


Also I have a question about solvation of my membrane protein via 
GENBOX. I found 2 possible ways to exclude water from the insertion into 
membrane
- Changing vdv radii for the C atoms- So i've copied  vdwradii.dat to my 
work dirrectory and changed vdv R. How I should to define that genbox 
uses exactly that modified file located in my working directory instead 
of default vdwradii.dat? Finally how I can check that there are not 
waters within the membrane ? (I've tried to visualize via VMD but the 
overal picture is very unclear :) )





The working directory is always searched first.  This is true for all Gromacs 
programs.  Visualization is the only way to tell.  Perhaps you need to render a 
more clear image.  Simply loading the .gro file and not making any refinements 
to the representation is a good way to go cross-eyed :)


- Also I've found that I can Running short md to exclude those waters 
via hyfrophobic effect.  What parametries would be opti,al for that 
simulation in case of KALP as well as other more larger proteins ?





The same parameters that you would use to run normal MD on such a system; 
there's nothing special about this procedure.  Restraints would be advisable.


-Justin


Thank you for your help,

James




--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] High temperature Simulation

[Justin A. Lemkul]

bipin singh wrote:

As far as I know we do energy minimization at room temperature only.


Energy minimization is (theoretically) at 0 K, as there are no velocities and it 
is not a true dynamical process.



Only during equilibration
(NVT and NPT) we use high temperature for maintaining proper density
before starting the final production run.



Maintaining density is but one possible goal for NPT; defining the desired 
ensemble and therefore the sampling distribution is the main reason.


-Justin


On Mon, Oct 17, 2011 at 15:15, Kavyashree M  wrote:

Dear users,

For simulating a protein at high temperature (more than 300K,
less than 400K) using OPLSAA forcefield, what are the parameters
other than Temperature that need to be taken care of?
Does the energy minimization step also needs to be done at high
temperature? (here my aim is not to simulate an unfolding event)
I have a reference -
Biophysical Journal Volume 94 June 2008 –4453

Any other references or suggestions will be helpful.

Thanking you
With Regards
M. Kavyashree


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







--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] High temperature Simulation

[Justin A. Lemkul]

Kavyashree M wrote:

Thank you,

What about the pressure that need to be used at that temperature
(for a system of a protein in tip4p water)



The set pressure should reflect whatever system you are trying to model.

-Justin


Thank you
With Regards
Kavya

On Mon, Oct 17, 2011 at 3:29 PM, bipin singh > wrote:


As far as I know we do energy minimization at room temperature only.
Only during equilibration
(NVT and NPT) we use high temperature for maintaining proper density
before starting the final production run.

On Mon, Oct 17, 2011 at 15:15, Kavyashree M mailto:hmkv...@gmail.com>> wrote:
 > Dear users,
 >
 > For simulating a protein at high temperature (more than 300K,
 > less than 400K) using OPLSAA forcefield, what are the parameters
 > other than Temperature that need to be taken care of?
 > Does the energy minimization step also needs to be done at high
 > temperature? (here my aim is not to simulate an unfolding event)
 > I have a reference -
 > Biophysical Journal Volume 94 June 2008 –4453
 >
 > Any other references or suggestions will be helpful.
 >
 > Thanking you
 > With Regards
 > M. Kavyashree
 >
 >
 > --
 > gmx-users mailing listgmx-users@gromacs.org

 > http://lists.gromacs.org/mailman/listinfo/gmx-users
 > Please search the archive at
 > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
 > Please don't post (un)subscribe requests to the list. Use the
 > www interface or send it to gmx-users-requ...@gromacs.org
.
 > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 >



--
---
Regards,
Bipin Singh
--
gmx-users mailing listgmx-users@gromacs.org

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




--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] High temperature Simulation

[bipin singh]

Well,as I found in literatures people have used same( 1 atm) pressure
at high temperature simulations(NPT simulations).
with different water models.As most of the force field parameters are
determined generally at 300K and 1 atm.
What would be the the possible drawbacks of using the same pressure(or
even high pressure) at different temperatures(300K-400K ranges) for a
given force field.

On Mon, Oct 17, 2011 at 17:04, Justin A. Lemkul  wrote:
>
>
> Kavyashree M wrote:
>>
>> Thank you,
>>
>> What about the pressure that need to be used at that temperature
>> (for a system of a protein in tip4p water)
>>
>
> The set pressure should reflect whatever system you are trying to model.
>
> -Justin
>
>> Thank you
>> With Regards
>> Kavya
>>
>> On Mon, Oct 17, 2011 at 3:29 PM, bipin singh > > wrote:
>>
>>    As far as I know we do energy minimization at room temperature only.
>>    Only during equilibration
>>    (NVT and NPT) we use high temperature for maintaining proper density
>>    before starting the final production run.
>>
>>    On Mon, Oct 17, 2011 at 15:15, Kavyashree M >    > wrote:
>>     > Dear users,
>>     >
>>     > For simulating a protein at high temperature (more than 300K,
>>     > less than 400K) using OPLSAA forcefield, what are the parameters
>>     > other than Temperature that need to be taken care of?
>>     > Does the energy minimization step also needs to be done at high
>>     > temperature? (here my aim is not to simulate an unfolding event)
>>     > I have a reference -
>>     > Biophysical Journal Volume 94 June 2008 –4453
>>     >
>>     > Any other references or suggestions will be helpful.
>>     >
>>     > Thanking you
>>     > With Regards
>>     > M. Kavyashree
>>     >
>>     >
>>     > --
>>     > gmx-users mailing list    gmx-users@gromacs.org
>>    
>>     > http://lists.gromacs.org/mailman/listinfo/gmx-users
>>     > Please search the archive at
>>     > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>     > Please don't post (un)subscribe requests to the list. Use the
>>     > www interface or send it to gmx-users-requ...@gromacs.org
>>    .
>>     > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>     >
>>
>>
>>
>>    --
>>    ---
>>    Regards,
>>    Bipin Singh
>>    --
>>    gmx-users mailing list    gmx-users@gromacs.org
>>    
>>    http://lists.gromacs.org/mailman/listinfo/gmx-users
>>    Please search the archive at
>>    http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>    Please don't post (un)subscribe requests to the list. Use the
>>    www interface or send it to gmx-users-requ...@gromacs.org
>>    .
>>    Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
---
Regards,
Bipin Singh
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Simulation of membrane protein

[James Starlight]

James,

As the consequence the correct orientation of the peptide in the membrane as
well as futher solvation are caused many questions :)


Firsly, following by tutorial guide I've done orientation of KALP peptide in
the membrane by

1- perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5
area_shrink1.dat
2- minimization
3- perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat


4- minimization

after six iterations of the  3rd and 4th steps I've obtained 6,5 nm^2
value for the area per lipid

Next I've done solvation of my protein ( including big vdv radii for carbons )


Finally my sytem is consisted of 7 atoms. I think that it's too
big ammount of water molecules for such small protein like KALP

so its seems that i've done some mistakes-
1- During shrinking of my peptide- I think that obtained structure
(http://www.sendspace.com/file/wenkf4) consist of too big distances
beetween peptides so it should be futher shrinked.


But how many iterations must be? I've found in the tutorial that 65
A^2 is good value for that system. But maybe I've used wrong
parametries in the pl program?

2- Or maybe too many waters are moved within the membrane in spite of
increased VDV radius for carbon atoms. So what I should do for the
excluding all unnecessary water from my structure?


E.g I want to simulate hydrophobic effect. What length of that
simulation must be ?
How I can evaluate the ammount of water before and after simulations?
Finally, What other options of Genbox could I use for preventing
insertion of water into my membrane ?






Thank you for your help,


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

Re: [gmx-users] High temperature Simulation

[bipin singh]

I have not understood what you mean by
"Energy minimization is (theoretically) at 0 K, as there are no velocities
and it is not a true dynamical process."
It is clear to me that at 0K there would be no velocities but then why
during minimization we expect
some conformational rearrangement of side chains etc.


On Mon, Oct 17, 2011 at 17:03, Justin A. Lemkul  wrote:
>
>
> bipin singh wrote:
>>
>> As far as I know we do energy minimization at room temperature only.
>
> Energy minimization is (theoretically) at 0 K, as there are no velocities
> and it is not a true dynamical process.
>
>> Only during equilibration
>> (NVT and NPT) we use high temperature for maintaining proper density
>> before starting the final production run.
>>
>
> Maintaining density is but one possible goal for NPT; defining the desired
> ensemble and therefore the sampling distribution is the main reason.
>
> -Justin
>
>> On Mon, Oct 17, 2011 at 15:15, Kavyashree M  wrote:
>>>
>>> Dear users,
>>>
>>> For simulating a protein at high temperature (more than 300K,
>>> less than 400K) using OPLSAA forcefield, what are the parameters
>>> other than Temperature that need to be taken care of?
>>> Does the energy minimization step also needs to be done at high
>>> temperature? (here my aim is not to simulate an unfolding event)
>>> I have a reference -
>>> Biophysical Journal Volume 94 June 2008 –4453
>>>
>>> Any other references or suggestions will be helpful.
>>>
>>> Thanking you
>>> With Regards
>>> M. Kavyashree
>>>
>>>
>>> --
>>> gmx-users mailing list    gmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-requ...@gromacs.org.
>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>
>>
>>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
---
Regards,
Bipin Singh
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Simulation of membrane protein

[Justin A. Lemkul]

James Starlight wrote:


James,

As the consequence the correct orientation of the peptide in the 
membrane as well as futher solvation are caused many questions :)



Firsly, following by tutorial guide I've done orientation of KALP 
peptide in the membrane by


1- perl inflategro.pl  confout.gro 0.95 DPPC 0 
system_shrink1.gro 5 area_shrink1.dat
2- minimization
3- perl inflategro.pl  system.gro 4 DPPC 14 
system_inflated.gro 5 area.dat



4- minimization

after six iterations of the  3rd and 4th steps I've obtained 6,5 nm^2 value for 
the area per lipid



The tutorial suggests at least 26 or so iterations.  Your APL value is 100 times 
larger than it should be.



Next I've done solvation of my protein ( including big vdv radii for carbons )



Finally my sytem is consisted of 7 atoms. I think that it's too big ammount 
of water molecules for such small protein like KALP



Yes, because your membrane is not correctly packed.


so its seems that i've done some mistakes-
1- During shrinking of my peptide- I think that obtained structure 
(http://www.sendspace.com/file/wenkf4) consist of too big distances beetween 
peptides so it should be futher shrinked.



Correct.




But how many iterations must be? I've found in the tutorial that 65 A^2 is good 
value for that system. But maybe I've used wrong parametries in the pl program?



No, you just haven't done enough iterations.  See above.  Your value is 6.5 nm^2 
, which is 6500 A^2.



2- Or maybe too many waters are moved within the membrane in spite of increased 
VDV radius for carbon atoms. So what I should do for the excluding all 
unnecessary water from my structure?




Ignore this for now.  Your system simply isn't built correctly.



E.g I want to simulate hydrophobic effect. What length of that simulation must 
be ?


Perhaps tens of ns.


How I can evaluate the ammount of water before and after simulations?


Visualization.


Finally, What other options of Genbox could I use for preventing insertion of 
water into my membrane ?




None.  A better starting model is required.

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] High temperature Simulation

[Daniel Adriano Silva M]

In the energy minimisation step, any "conformational rearrangement" taking
place is not a function of time, it is just an algorithm for reaching a
basin of minimum energy:

(http://www.gromacs.org/Documentation/Terminology/Energy_Minimisation),

hence there are not velocities in the atoms of the system, and macroscopic
properties related to dynamics (like temperature) are not present.

Daniel Silva


2011/10/17 bipin singh 

> I have not understood what you mean by
> "Energy minimization is (theoretically) at 0 K, as there are no velocities
> and it is not a true dynamical process."
> It is clear to me that at 0K there would be no velocities but then why
> during minimization we expect
> some conformational rearrangement of side chains etc.
>
>
> On Mon, Oct 17, 2011 at 17:03, Justin A. Lemkul  wrote:
> >
> >
> > bipin singh wrote:
> >>
> >> As far as I know we do energy minimization at room temperature only.
> >
> > Energy minimization is (theoretically) at 0 K, as there are no velocities
> > and it is not a true dynamical process.
> >
> >> Only during equilibration
> >> (NVT and NPT) we use high temperature for maintaining proper density
> >> before starting the final production run.
> >>
> >
> > Maintaining density is but one possible goal for NPT; defining the
> desired
> > ensemble and therefore the sampling distribution is the main reason.
> >
> > -Justin
> >
> >> On Mon, Oct 17, 2011 at 15:15, Kavyashree M  wrote:
> >>>
> >>> Dear users,
> >>>
> >>> For simulating a protein at high temperature (more than 300K,
> >>> less than 400K) using OPLSAA forcefield, what are the parameters
> >>> other than Temperature that need to be taken care of?
> >>> Does the energy minimization step also needs to be done at high
> >>> temperature? (here my aim is not to simulate an unfolding event)
> >>> I have a reference -
> >>> Biophysical Journal Volume 94 June 2008 –4453
> >>>
> >>> Any other references or suggestions will be helpful.
> >>>
> >>> Thanking you
> >>> With Regards
> >>> M. Kavyashree
> >>>
> >>>
> >>> --
> >>> gmx-users mailing listgmx-users@gromacs.org
> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >>> Please search the archive at
> >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >>> Please don't post (un)subscribe requests to the list. Use the
> >>> www interface or send it to gmx-users-requ...@gromacs.org.
> >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>>
> >>
> >>
> >>
> >
> > --
> > 
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > MILES-IGERT Trainee
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > 
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > Please don't post (un)subscribe requests to the list. Use the www
> interface
> > or send it to gmx-users-requ...@gromacs.org.
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
>
>
>
> --
> ---
> Regards,
> Bipin Singh
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] High temperature Simulation

[Mark Abraham]

On 17/10/2011 10:58 PM, bipin singh wrote:

I have not understood what you mean by
"Energy minimization is (theoretically) at 0 K, as there are no velocities
and it is not a true dynamical process."
It is clear to me that at 0K there would be no velocities but then why
during minimization we expect
some conformational rearrangement of side chains etc.


There's still an energy, and we can compute its gradient with respect to 
atomic coordinates, i.e. forces. EM algorithms move the atoms according 
to those forces to see a stationary point on the potential energy 
surface. MD algorithms use the forces to update velocities and 
positions, integrating Newton's second law with a finite time step.


Mark




On Mon, Oct 17, 2011 at 17:03, Justin A. Lemkul  wrote:


bipin singh wrote:

As far as I know we do energy minimization at room temperature only.

Energy minimization is (theoretically) at 0 K, as there are no velocities
and it is not a true dynamical process.


Only during equilibration
(NVT and NPT) we use high temperature for maintaining proper density
before starting the final production run.


Maintaining density is but one possible goal for NPT; defining the desired
ensemble and therefore the sampling distribution is the main reason.

-Justin


On Mon, Oct 17, 2011 at 15:15, Kavyashree M  wrote:

Dear users,

For simulating a protein at high temperature (more than 300K,
less than 400K) using OPLSAA forcefield, what are the parameters
other than Temperature that need to be taken care of?
Does the energy minimization step also needs to be done at high
temperature? (here my aim is not to simulate an unfolding event)
I have a reference -
Biophysical Journal Volume 94 June 2008 –4453

Any other references or suggestions will be helpful.

Thanking you
With Regards
M. Kavyashree


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





--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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






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

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] cyclosporine A

[Mark Abraham]

On 17/10/2011 5:01 PM, Алексей Раевский wrote:

Hi!
I need an advice concerninng topology building of such substance like 
cyclosporine A. I've tried to make it with antechamber tool, cause I 
wanted to use amber99sb forcefield. But the program gave me an error 
in the begining and no results in the end after 12 hours of 
calculations ))) Can you give any suggestions for my next steps? This 
compound is a peptide chain built from acyl-adenylated amino acids 
(L-valine, L-leucine, L-alanine, L-glycine, 2-aminobutyric acid, 
4-methylthreonine, and D-alanine).

Thank you very much!


If you're asking for antechamber help, you're on the wrong forum.

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

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] RE:Free energy methods Protein-Protein

[lloyd riggs]

Dear All,

I tried to post this once before.  In any case;

Basically I am doing free energies quickly, and then plan on doing pull runs.  
This former is simply EQ all the way to NPT (700-1000 PS +), then a 5 PS run 
for the bound, then unbound system.  Energy differences are taken as the 
difference between averidges for the entire final run (ie a single number not a 
graph)  Basically, I woundered according to the paper listed below, if anyone 
knows of a rule of thumb for how many replicates a person should do to publish 
which represents the entire distribution of calculated Free energies (total) 
and for pull runs to satisfy reviewiers?  I asume around 20 or so.

The paper:
Biophys J. 2008 October 15; 95(8): 3575–3590.
Protein-Protein Interaction Investigated by Steered Molecular Dynamics: The 
TCR-pMHC Complex, Michel A. Cuendet and Olivier Michielin

The publication does each one around 157 times (ie 157 individual, unique 
starting point trajectories).

My other questions, are if anyone has pointers, suggestions or critiques, etc...

Freundlishen Grüsse

Stephan Watkins
-- 
NEU: FreePhone - 0ct/min Handyspartarif mit Geld-zurück-Garantie!   
Jetzt informieren: http://www.gmx.net/de/go/freephone
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Link to Intel MKL (fftw) via cmake options

[Szilárd Páll]

> --- [CMakeCache.txt] -
>
> ...
>
> //Flags used by the compiler during all build types
> CMAKE_CXX_FLAGS:STRING=' -msse2 -ip -funroll-all-loops -std=gnu99  '
>
> //Flags used by the compiler during release builds.
> CMAKE_CXX_FLAGS_RELEASE:STRING=-mtune=itanium2 -mtune=core2  -O3 -DNDEBUG
>
> //Flags used by the compiler during all build types
> CMAKE_C_FLAGS:STRING=' -msse2 -ip -funroll-all-loops -std=gnu99  '
>
> //Flags used by the compiler during release builds.
> CMAKE_C_FLAGS_RELEASE:STRING=-mtune=itanium2 -mtune=core2  -O3 -DNDEBUG
>
> ...
>
> 
>
> These are obviously the wrong flags for the detected architecture,
> sse2 is no longer available and so are the the mtune architectures.

Indeed, some of those flags are wrong (CXX -std=gnu99), others simply
outdated (-mtune=itanium2). There are plans to correct these issues
for 4.6, but let's agree on the fact that they are not show-stoppers
(FYI you won't get more than a few percent speedup with the right
compiler options, the most I've seen is ~5%.)

If you want to get rid of them, the solution is pretty simple: just
remove the offending options and pick new ones if you think they work
better for you.

However, I'm not sure what do you mean by "sse2 is no longer
available"? Of course it is, both the Intel Compiler and the majority
of current processors support it. Also, -mtune=core2 is perfectly
valid as is -msse2.

>   CMAKE_CXX_FLAGS:STRING=' -msse3 -ip -funroll-all-loops -std=gnu99 '

As Mark said, SSE3 won't help you in any noticeable way.


> But the install is broken. On `make install-mdrun`, the scripts would
> remove any library from "src/gmxlib/CMakeFiles/CMakeRelink.dir"
> and bail out with the error below. Even if you copy the libraries
> by hand to CMakeRelink.dir/, the'll get removed by make install-mdrun
> before trying to link with them.

Now that is a bug. I'd appreciate if you could enter it in
redmine.gromacs.org withe all details on how to reproduce it!

Cheers,
--
Szilárd
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Spherical constraint (spherical force)

[Mikhail Stukan]

Dear gmx-user,

I would like to simulate an isolated  drop of water (without PBC). To  prevent 
water molecules form evaporation I would like to create a spherical constraint 
around the system. In recent article in PNAS (Caleman, Hub, van Maaren, van der 
Spoel,  v. 108, 6838 (2011)) where the authors considered similar system it is 
mentioned that:
"To avoid such evaporation, we applied a spherical flat-bottom quadratic 
potential acting on the water. That potential was implemented as an additional 
force F pointing toward the COM of the droplet..."

Could anybody give a hint how this approach can be realized in GROMACS? I 
looked through the manual, but did  not find clear answer how to implement such 
a force.

Thank you very much in advance.
Mikhail


=
Dr Mikhail Stukan
Schlumberger Dhahran Carbonate Research Center,
Dhahran Techno Valley  - KFUPM,
P.O. Box 39011, Dammam / Doha Camp  31942,
Kingdom of Saudi Arabia
Tel: +966 3 331 6182
Fax:+966 3 330 0845
mstu...@slb.com

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

Re: [gmx-users] Simulation of membrane protein

[James Starlight]

Ok, James thank you

It seems that I should to wite some script for too many iterations e.g

perl inflategro.pl minimized1.gro 0.95 DPPC 0 shrinked1.gro 5 area_shrink1.dat

grompp -f minim.mdp -c shrinked1.gro -p topol.top -o minimized2.tpr

mdrun -v -deffnm minimized2

perl inflategro.pl minimized2.gro 0.95 DPPC 0 shrinked2.gro 5 area_shrink1.dat

grompp -f minim.mdp -c shrinked2.gro -p topol.top -o minimized3.tpr

mdrun -v -deffnm minimized2

..

perl inflategro.pl minimized20.gro 0.95 DPPC 0 shrinked20.gro 5 area_shrink1.dat

grompp -f minim.mdp -c shrinked20.gro -p topol.top -o minimized21.tpr

mdrun -v -deffnm minimized21

Does this action sequence correct? So as the consequence I need to
find operator wich stop the script untill defined value of S per lipid
will be reached



Thanks again

James

2011/10/17 Justin A. Lemkul 

>
>
> James Starlight wrote:
>
>>
>> James,
>>
>> As the consequence the correct orientation of the peptide in the membrane
>> as well as futher solvation are caused many questions :)
>>
>>
>> Firsly, following by tutorial guide I've done orientation of KALP peptide
>> in the membrane by
>>
>> 1- perl inflategro.pl  confout.gro 0.95 DPPC 0
>> system_shrink1.gro 5 area_shrink1.dat
>> 2- minimization
>> 3- perl inflategro.pl  system.gro 4 DPPC 14
>> system_inflated.gro 5 area.dat
>>
>>
>>
>>
>> 4- minimization
>>
>> after six iterations of the  3rd and 4th steps I've obtained 6,5 nm^2
>> value for the area per lipid
>>
>>
> The tutorial suggests at least 26 or so iterations.  Your APL value is 100
> times larger than it should be.
>
>
>  Next I've done solvation of my protein ( including big vdv radii for
>> carbons )
>>
>>
>>
>> Finally my sytem is consisted of 7 atoms. I think that it's too big
>> ammount of water molecules for such small protein like KALP
>>
>>
> Yes, because your membrane is not correctly packed.
>
>
>  so its seems that i've done some mistakes-
>> 1- During shrinking of my peptide- I think that obtained structure (
>> http://www.sendspace.com/**file/wenkf4)
>> consist of too big distances beetween peptides so it should be futher
>> shrinked.
>>
>>
> Correct.
>
>
>
>>
>> But how many iterations must be? I've found in the tutorial that 65 A^2 is
>> good value for that system. But maybe I've used wrong parametries in the pl
>> program?
>>
>>
> No, you just haven't done enough iterations.  See above.  Your value is 6.5
> nm^2 , which is 6500 A^2.
>
>
>  2- Or maybe too many waters are moved within the membrane in spite of
>> increased VDV radius for carbon atoms. So what I should do for the excluding
>> all unnecessary water from my structure?
>>
>>
>>
> Ignore this for now.  Your system simply isn't built correctly.
>
>
>
>> E.g I want to simulate hydrophobic effect. What length of that simulation
>> must be ?
>>
>
> Perhaps tens of ns.
>
>
>  How I can evaluate the ammount of water before and after simulations?
>>
>
> Visualization.
>
>
>  Finally, What other options of Genbox could I use for preventing insertion
>> of water into my membrane ?
>>
>>
>>
> None.  A better starting model is required.
>
> -Justin
>
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Spherical constraint (spherical force)

[Mark Abraham]

On 17/10/2011 11:41 PM, Mikhail Stukan wrote:


Dear gmx-user,

I would like to simulate an isolated  drop of water (without PBC). To  
prevent water molecules form evaporation I would like to create a 
spherical constraint around the system. In recent article in PNAS 
(Caleman, Hub, van Maaren, van der Spoel,  v. 108, 6838 (2011)) where 
the authors considered similar system it is mentioned that:


"To avoid such evaporation, we applied a spherical flat-bottom 
quadratic potential acting on the water. That potential was 
implemented as an additional force F pointing toward the COM of the 
droplet..."


Could anybody give a hint how this approach can be realized in 
GROMACS? I looked through the manual, but did  not find clear answer 
how to implement such a force.





I think the only way to do something like this in GROMACS is with a COM 
virtual site and such a distance restraint from each water molecule to 
that virtual site.


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

Re: [gmx-users] Simulation of membrane protein

[Justin A. Lemkul]

James Starlight wrote:

Ok, James thank you

It seems that I should to wite some script for too many iterations e.g

perl inflategro.pl  minimized1.gro 0.95 DPPC 0 
shrinked1.gro 5 area_shrink1.dat

grompp -f minim.mdp -c shrinked1.gro -p topol.top -o minimized2.tpr

mdrun -v -deffnm minimized2

perl inflategro.pl  minimized2.gro 0.95 DPPC 0 
shrinked2.gro 5 area_shrink1.dat

grompp -f minim.mdp -c shrinked2.gro -p topol.top -o minimized3.tpr

mdrun -v -deffnm minimized2

..

perl inflategro.pl  minimized20.gro 0.95 DPPC 0 
shrinked20.gro 5 area_shrink1.dat

grompp -f minim.mdp -c shrinked20.gro -p topol.top -o minimized21.tpr

mdrun -v -deffnm minimized21



All of which can be done in a for-loop instead of typing it out manually.


Does this action sequence correct? So as the consequence I need to find 
operator wich stop the script untill defined value of S per lipid will be 
reached



Yes.  You can read that value from the screen or from the area.dat file that 
inflategro.pl prints.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Spherical constraint (spherical force)

[Jochen Hub]

Hi Mikhail,

we hard-coded the flat-bottom potential into bondfree.c which is in 
src/gmxlib. I send you the source file in a separate e-mail.


The patch will replace all position restraints by a flatt-bottom 
spherical potential with a flat radius of 1.4nm. If you want a different 
radius you'll have to change the bondfree.c, look for the posre 
function. It's a quite dirty inflexible hack, but it was good enough for 
us. So you cannot have normal position restraints and the flat-bottom 
restraints at the same time.


Note that you must define the reference position of all the position 
restraint potentials with the -r option of grompp. E.g., if your droplet 
is at the origin, you need a gro/pdb file with all coordinates set to 
0,0,0 to be used with the -r option. The position restraints are defined 
as usual in the [ position_restraints ] sections in the topology.


I hope this helps, please let us know if something is unclear.

Jochen

On 10/17/11 Oct 17,2:41 PM, Mikhail Stukan wrote:


Dear gmx-user,

I would like to simulate an isolated  drop of water (without PBC). To  
prevent water molecules form evaporation I would like to create a 
spherical constraint around the system. In recent article in PNAS 
(Caleman, Hub, van Maaren, van der Spoel,  v. 108, 6838 (2011)) where 
the authors considered similar system it is mentioned that:


"To avoid such evaporation, we applied a spherical flat-bottom 
quadratic potential acting on the water. That potential was 
implemented as an additional force F pointing toward the COM of the 
droplet..."


Could anybody give a hint how this approach can be realized in 
GROMACS? I looked through the manual, but did  not find clear answer 
how to implement such a force.


Thank you very much in advance.

Mikhail

=

Dr Mikhail Stukan

Schlumberger Dhahran Carbonate Research Center,

Dhahran Techno Valley  - KFUPM,

P.O. Box 39011, Dammam / Doha Camp  31942,

Kingdom of Saudi Arabia

Tel: +966 3 331 6182

Fax:+966 3 330 0845
mstu...@slb.com 






--
---
Dr. Jochen Hub
Computational and Systems Biology
Dept. of Cell&  Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4715056 Fax: +46-18-511755
http://xray.bmc.uu.se/~jochen/index.html
---

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

Re: [gmx-users] High temperature Simulation

[Kavyashree M]

Hello,

The set pressure should reflect whatever system you are trying to model.
>

This statement is not very clear to me.. But when the mdout.mdp file after
grompp
during energy minimization is examined it says -

gen-vel  = no
gen-temp = 300
gen-seed = 173529

Even though I have not assigned any velocities in em.mdp file. Thats the
reason why got this doubt about temperature during energy minimization.

Thank you
With Regards
Kavya


>
> -Justin
>
>  Thank you
>> With Regards
>> Kavya
>>
>> On Mon, Oct 17, 2011 at 3:29 PM, bipin singh > bipinel...@gmail.com>> wrote:
>>
>>As far as I know we do energy minimization at room temperature only.
>>Only during equilibration
>>(NVT and NPT) we use high temperature for maintaining proper density
>>before starting the final production run.
>>
>>On Mon, Oct 17, 2011 at 15:15, Kavyashree M >> wrote:
>> > Dear users,
>> >
>> > For simulating a protein at high temperature (more than 300K,
>> > less than 400K) using OPLSAA forcefield, what are the parameters
>> > other than Temperature that need to be taken care of?
>> > Does the energy minimization step also needs to be done at high
>> > temperature? (here my aim is not to simulate an unfolding event)
>> > I have a reference -
>> > Biophysical Journal Volume 94 June 2008 –4453
>> >
>> > Any other references or suggestions will be helpful.
>> >
>> > Thanking you
>> > With Regards
>> > M. Kavyashree
>> >
>> >
>> > --
>> > gmx-users mailing listgmx-users@gromacs.org
>>
>>
>> > 
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users
>> > Please search the archive at
>> > 
>> http://www.gromacs.org/**Support/Mailing_Lists/Searchbefore
>>  posting!
>> > Please don't post (un)subscribe requests to the list. Use the
>> > www interface or send it to gmx-users-requ...@gromacs.org
>>> >.
>>
>> > Can't post? Read 
>> http://www.gromacs.org/**Support/Mailing_Lists
>> >
>>
>>
>>
>>--
>>---
>>Regards,
>>Bipin Singh
>>--
>>gmx-users mailing listgmx-users@gromacs.org
>>
>>
>>
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users
>>Please search the archive at
>>
>> http://www.gromacs.org/**Support/Mailing_Lists/Searchbefore
>>  posting!
>>Please don't post (un)subscribe requests to the list. Use the
>>www interface or send it to gmx-users-requ...@gromacs.org
>>> >.
>>
>>Can't post? Read 
>> http://www.gromacs.org/**Support/Mailing_Lists
>>
>>
>>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] trjconv:solute at the center

[Nilesh Dhumal]

Justin,

I have 26 solute atoms and 3302 solvent atoms in my sytems (total 3328
atoms).


1. trjconv -f 3.trr -s 3.tpr -pbc mol -b 400 -e 600 -dt 1 -n 500-1.ndx  -o
4-600.xtc
here I choose group 0:system (3328 atoms)

2. trjconv -f 4-600.xtc -s 3.tpr  -n 500-1.ndx -center  -o 4-600-1.xtc

 For Centering I choose group: solute (26 atoms)
 For output I choose group : Solvent (3302 atoms)


3. trjconv -f 4-600-1.xtc -s 3.tpr  -dump 500  -o 500-11.pdb

Here I choose the group: 0 (system).

I am geting for error for last command.

Fatal error:
Index[3302] 3303 is larger than the number of atoms in the trajectory file
(3302).

It look that there are no solute atoms in trajectory file.

Nilesh


On Mon, October 17, 2011 7:25 am, Justin A. Lemkul wrote:
>

>
> Nilesh Dhumal wrote:
>
>> Hello,
>>
>>
>> I have system with solute is surrounded by 256 solvent molecules. I run
>>  the simulation for 20 ns. I save the snap shot at 500 ps using
>> following command.
>>
>> trjconv -f 3.trr -s 3.tpr -n 500-1.ndx -b 500.0 -e 501.0 -dt 1.0 -pbc
>> nojump -center   -o 500-11.pdb
>>
>> I tried to keep the solute at the center box. In visualization, the
>> solute is not at center , its close to box edges.
>>
>> How can I keep the solute at the center.
>>
>>
>>
>
> You're doing too many things at once.  Split the trjconv operation:
>
>
> 1. Run trjconv -pbc mol on the whole trajectory
> 2. Run trjconv -center on the output of (1)
> 3. Run trjconv -dump 500 on the output of (2)
>
>
> -Justin
>
>
>> I am using Gromacs 4.0.7 version.
>>
>>
>> Thanks
>>
>>
>> Nilesh
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>
> --
> 
>
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read
> http://www.gromacs.org/Support/Mailing_Lists
>
>
>


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

Re: [gmx-users] High temperature Simulation

[Justin A. Lemkul]

Kavyashree M wrote:

Hello,

The set pressure should reflect whatever system you are trying to model.


This statement is not very clear to me.. But when the mdout.mdp file 
after grompp

during energy minimization is examined it says -

gen-vel  = no
gen-temp = 300
gen-seed = 173529

Even though I have not assigned any velocities in em.mdp file. Thats the
reason why got this doubt about temperature during energy minimization.



I don't see the connection to my comment about pressure, but I'll address this 
anyway.  There is no temperature during EM.  Hence with "gen-vel = no" then no 
velocities are generated.  The settings for gen-temp and gen-seed are defaults 
that are assigned when none are provided in the input .mdp file.


I seem to recall that a pressure term is written during EM, but it is largely 
meaningless.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] trjconv:solute at the center

[Justin A. Lemkul]

Nilesh Dhumal wrote:

Justin,

I have 26 solute atoms and 3302 solvent atoms in my sytems (total 3328
atoms).


1. trjconv -f 3.trr -s 3.tpr -pbc mol -b 400 -e 600 -dt 1 -n 500-1.ndx  -o
4-600.xtc
here I choose group 0:system (3328 atoms)

2. trjconv -f 4-600.xtc -s 3.tpr  -n 500-1.ndx -center  -o 4-600-1.xtc

 For Centering I choose group: solute (26 atoms)
 For output I choose group : Solvent (3302 atoms)


3. trjconv -f 4-600-1.xtc -s 3.tpr  -dump 500  -o 500-11.pdb

Here I choose the group: 0 (system).

I am geting for error for last command.

Fatal error:
Index[3302] 3303 is larger than the number of atoms in the trajectory file
(3302).

It look that there are no solute atoms in trajectory file.



In step 2, you chose to save only the solvent.

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] High temperature Simulation

[Kavyashree M]

Hello,

Yes, I have come across that but If the temperature is below
the boiling point its fine. But if it crosses the boiling temperature
in order keep the water as liquid isnt it necessary to increase the
pressure. I understand that the water models do not exactly predict
the transition temperature. So in what way does this behaviour of water
effect the simulation of a protein?

Thank you
With Regards
kavya

On Mon, Oct 17, 2011 at 5:13 PM, bipin singh  wrote:

> Well,as I found in literatures people have used same( 1 atm) pressure
> at high temperature simulations(NPT simulations).
> with different water models.As most of the force field parameters are
> determined generally at 300K and 1 atm.
> What would be the the possible drawbacks of using the same pressure(or
> even high pressure) at different temperatures(300K-400K ranges) for a
> given force field.
>
> On Mon, Oct 17, 2011 at 17:04, Justin A. Lemkul  wrote:
> >
> >
> > Kavyashree M wrote:
> >>
> >> Thank you,
> >>
> >> What about the pressure that need to be used at that temperature
> >> (for a system of a protein in tip4p water)
> >>
> >
> > The set pressure should reflect whatever system you are trying to model.
> >
> > -Justin
> >
> >> Thank you
> >> With Regards
> >> Kavya
> >>
> >> On Mon, Oct 17, 2011 at 3:29 PM, bipin singh  >> > wrote:
> >>
> >>As far as I know we do energy minimization at room temperature only.
> >>Only during equilibration
> >>(NVT and NPT) we use high temperature for maintaining proper density
> >>before starting the final production run.
> >>
> >>On Mon, Oct 17, 2011 at 15:15, Kavyashree M  >>> wrote:
> >> > Dear users,
> >> >
> >> > For simulating a protein at high temperature (more than 300K,
> >> > less than 400K) using OPLSAA forcefield, what are the parameters
> >> > other than Temperature that need to be taken care of?
> >> > Does the energy minimization step also needs to be done at high
> >> > temperature? (here my aim is not to simulate an unfolding event)
> >> > I have a reference -
> >> > Biophysical Journal Volume 94 June 2008 –4453
> >> >
> >> > Any other references or suggestions will be helpful.
> >> >
> >> > Thanking you
> >> > With Regards
> >> > M. Kavyashree
> >> >
> >> >
> >> > --
> >> > gmx-users mailing listgmx-users@gromacs.org
> >>
> >> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> > Please search the archive at
> >> > http://www.gromacs.org/Support/Mailing_Lists/Search before
> posting!
> >> > Please don't post (un)subscribe requests to the list. Use the
> >> > www interface or send it to gmx-users-requ...@gromacs.org
> >>.
> >> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >> >
> >>
> >>
> >>
> >>--
> >>---
> >>Regards,
> >>Bipin Singh
> >>--
> >>gmx-users mailing listgmx-users@gromacs.org
> >>
> >>http://lists.gromacs.org/mailman/listinfo/gmx-users
> >>Please search the archive at
> >>http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >>Please don't post (un)subscribe requests to the list. Use the
> >>www interface or send it to gmx-users-requ...@gromacs.org
> >>.
> >>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >>
> >
> > --
> > 
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > MILES-IGERT Trainee
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > 
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > Please don't post (un)subscribe requests to the list. Use the www
> interface
> > or send it to gmx-users-requ...@gromacs.org.
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
>
>
>
> --
> ---
> Regards,
> Bipin Singh
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Ma

Re: [gmx-users] High temperature Simulation

[Kavyashree M]

Hello,

I am sorry those were two different questions..  I wanted to know what
this statement actually mean?
"The set pressure should reflect whatever system you are trying to model."

Thank you
With Regards
Kavya

>
> I don't see the connection to my comment about pressure, but I'll address
> this anyway.  There is no temperature during EM.  Hence with "gen-vel = no"
> then no velocities are generated.  The settings for gen-temp and gen-seed
> are defaults that are assigned when none are provided in the input .mdp
> file.
>
> I seem to recall that a pressure term is written during EM, but it is
> largely meaningless.
>
> -Justin
>
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] High temperature Simulation

[Justin A. Lemkul]

Kavyashree M wrote:

Hello,

I am sorry those were two different questions..  I wanted to know what
this statement actually mean?
"The set pressure should reflect whatever system you are trying to model."



You haven't fully explained what exactly you're trying to do yet, so I'm taking 
a stab in the dark.  Let's say you're trying to simulate a benchtop experiment 
with a protein in solution over a heating mantle at 350 K.  The pressure is 1 
atm under such circumstances (NPT).  Now let's say you want to simulate the 
behavior of a protein solution in a bomb calorimeter (constant volume) at 350 K. 
 The pressure is not likely to be 1 atm under such circumstances (but then too, 
you'd use NVT instead of NPT, but maybe after NPT equilibration at whatever the 
necessary pressure is).  Without a fully detailed description of what you'd like 
to accomplish, I'm going to stop guessing.


You've asked a lot of scattered questions about different topics, which makes it 
less efficient for people to help you and less clear for you to understand what 
we're trying to communicate back, even if it is somewhat generic.


-Justin


Thank you
With Regards
Kavya


I don't see the connection to my comment about pressure, but I'll
address this anyway.  There is no temperature during EM.  Hence with
"gen-vel = no" then no velocities are generated.  The settings for
gen-temp and gen-seed are defaults that are assigned when none are
provided in the input .mdp file.

I seem to recall that a pressure term is written during EM, but it
is largely meaningless.

-Justin


-- 
==__==


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin


==__==
-- 
gmx-users mailing listgmx-users@gromacs.org


http://lists.gromacs.org/__mailman/listinfo/gmx-users

Please search the archive at
http://www.gromacs.org/__Support/Mailing_Lists/Search
 before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org
.
Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists





--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] trjconv:solute at the center

[Nilesh Dhumal]

In 2nd step I choose system instaed of solvent.

 I could not make the solute at the center.

Thanks
NIlesh

On Mon, October 17, 2011 11:05 am, Justin A. Lemkul wrote:
>

>
> Nilesh Dhumal wrote:
>
>> Justin,
>>
>>
>> I have 26 solute atoms and 3302 solvent atoms in my sytems (total 3328
>> atoms).
>>
>>
>> 1. trjconv -f 3.trr -s 3.tpr -pbc mol -b 400 -e 600 -dt 1 -n 500-1.ndx
>> -o
>> 4-600.xtc
>> here I choose group 0:system (3328 atoms)
>>
>> 2. trjconv -f 4-600.xtc -s 3.tpr  -n 500-1.ndx -center  -o 4-600-1.xtc
>>
>>
>> For Centering I choose group: solute (26 atoms)
>> For output I choose group : Solvent (3302 atoms)
>>
>>
>>
>> 3. trjconv -f 4-600-1.xtc -s 3.tpr  -dump 500  -o 500-11.pdb
>>
>>
>> Here I choose the group: 0 (system).
>>
>>
>> I am geting for error for last command.
>>
>>
>> Fatal error:
>> Index[3302] 3303 is larger than the number of atoms in the trajectory
>> file (3302).
>>
>>
>> It look that there are no solute atoms in trajectory file.
>>
>>
>
> In step 2, you chose to save only the solvent.
>
>
> -Justin
>
>
> --
> 
>
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read
> http://www.gromacs.org/Support/Mailing_Lists
>
>
>


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

Re: [gmx-users] High temperature Simulation

[Kavyashree M]

Ok, The protein I am going to simulate is from a hyperthermophilic organism
which lives in deep oceanic thermal vents. so in the deep vents the pressure
will be enormous. even though I do not have much information about the
magnitude of pressure in that site and inside the cell of that organism.. I
may
be able to get some rough estimate of pressure..

So I wanted to simulate this protein at a temperature near 90 or 100 deg C.

Thank you
With Regards
Kavya

On Mon, Oct 17, 2011 at 8:45 PM, Justin A. Lemkul  wrote:

>
>
> Kavyashree M wrote:
>
>> Hello,
>>
>> I am sorry those were two different questions..  I wanted to know what
>> this statement actually mean?
>> "The set pressure should reflect whatever system you are trying to model."
>>
>>
> You haven't fully explained what exactly you're trying to do yet, so I'm
> taking a stab in the dark.  Let's say you're trying to simulate a benchtop
> experiment with a protein in solution over a heating mantle at 350 K.  The
> pressure is 1 atm under such circumstances (NPT).  Now let's say you want to
> simulate the behavior of a protein solution in a bomb calorimeter (constant
> volume) at 350 K.  The pressure is not likely to be 1 atm under such
> circumstances (but then too, you'd use NVT instead of NPT, but maybe after
> NPT equilibration at whatever the necessary pressure is).  Without a fully
> detailed description of what you'd like to accomplish, I'm going to stop
> guessing.
>
> You've asked a lot of scattered questions about different topics, which
> makes it less efficient for people to help you and less clear for you to
> understand what we're trying to communicate back, even if it is somewhat
> generic.
>
> -Justin
>
>  Thank you
>> With Regards
>> Kavya
>>
>>
>>I don't see the connection to my comment about pressure, but I'll
>>address this anyway.  There is no temperature during EM.  Hence with
>>"gen-vel = no" then no velocities are generated.  The settings for
>>gen-temp and gen-seed are defaults that are assigned when none are
>>provided in the input .mdp file.
>>
>>I seem to recall that a pressure term is written during EM, but it
>>is largely meaningless.
>>
>>-Justin
>>
>>
>>-- ==**__==
>>
>>
>>Justin A. Lemkul
>>Ph.D. Candidate
>>ICTAS Doctoral Scholar
>>MILES-IGERT Trainee
>>Department of Biochemistry
>>Virginia Tech
>>Blacksburg, VA
>>jalemkul[at]vt.edu  | (540) 231-9080
>>
>> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin
>>
>> 
>> >
>>
>>==**__==
>>
>>-- gmx-users mailing listgmx-users@gromacs.org
>>
>>
>> http://lists.gromacs.org/__**mailman/listinfo/gmx-users
>>
>>
>> 
>> >
>>Please search the archive at
>>
>> http://www.gromacs.org/__**Support/Mailing_Lists/Search
>>
>>
>> >
>> before posting!
>>Please don't post (un)subscribe requests to the list. Use the www
>>interface or send it to gmx-users-requ...@gromacs.org
>>> >.
>>Can't post? Read 
>> http://www.gromacs.org/__**Support/Mailing_Lists
>>
>> 
>> >
>>
>>
>>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support

Re: [gmx-users] trjconv:solute at the center

[Justin A. Lemkul]

Nilesh Dhumal wrote:

In 2nd step I choose system instaed of solvent.

 I could not make the solute at the center.



Don't use -b and -e when running trjconv.  I have found that PBC routines are 
not always correctly applied when parsing out sections of the trajectory.  This 
can affect your ability to center the molecule.


-Justin


Thanks
NIlesh

On Mon, October 17, 2011 11:05 am, Justin A. Lemkul wrote:


Nilesh Dhumal wrote:


Justin,


I have 26 solute atoms and 3302 solvent atoms in my sytems (total 3328
atoms).


1. trjconv -f 3.trr -s 3.tpr -pbc mol -b 400 -e 600 -dt 1 -n 500-1.ndx
-o
4-600.xtc
here I choose group 0:system (3328 atoms)

2. trjconv -f 4-600.xtc -s 3.tpr  -n 500-1.ndx -center  -o 4-600-1.xtc


For Centering I choose group: solute (26 atoms)
For output I choose group : Solvent (3302 atoms)



3. trjconv -f 4-600-1.xtc -s 3.tpr  -dump 500  -o 500-11.pdb


Here I choose the group: 0 (system).


I am geting for error for last command.


Fatal error:
Index[3302] 3303 is larger than the number of atoms in the trajectory
file (3302).


It look that there are no solute atoms in trajectory file.



In step 2, you chose to save only the solvent.


-Justin


--



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin



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









--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] High temperature Simulation

[Justin A. Lemkul]

Kavyashree M wrote:

Ok, The protein I am going to simulate is from a hyperthermophilic organism
which lives in deep oceanic thermal vents. so in the deep vents the pressure
will be enormous. even though I do not have much information about the
magnitude of pressure in that site and inside the cell of that 
organism.. I may

be able to get some rough estimate of pressure..

So I wanted to simulate this protein at a temperature near 90 or 100 deg C.



I would suggest investigating what an appropriate pressure value might be 
(although I agree it's hard to say, and you may not be able to actually simulate 
at such a pressure for stability reasons), equilibrate under NPT until the 
pressure and temperature are stable, then switch to NVT to eliminate the boiling 
issue.  It is hard to say whether or not any force field or water model will 
inherently be stable for these conditions, but high temperature MD is a topic 
that is well-represented in the literature.  I'd suggest you apply proven 
methodology that makes sense in your case.


-Justin


Thank you
With Regards
Kavya

On Mon, Oct 17, 2011 at 8:45 PM, Justin A. Lemkul > wrote:




Kavyashree M wrote:

Hello,

I am sorry those were two different questions..  I wanted to
know what
this statement actually mean?
"The set pressure should reflect whatever system you are trying
to model."


You haven't fully explained what exactly you're trying to do yet, so
I'm taking a stab in the dark.  Let's say you're trying to simulate
a benchtop experiment with a protein in solution over a heating
mantle at 350 K.  The pressure is 1 atm under such circumstances
(NPT).  Now let's say you want to simulate the behavior of a protein
solution in a bomb calorimeter (constant volume) at 350 K.  The
pressure is not likely to be 1 atm under such circumstances (but
then too, you'd use NVT instead of NPT, but maybe after NPT
equilibration at whatever the necessary pressure is).  Without a
fully detailed description of what you'd like to accomplish, I'm
going to stop guessing.

You've asked a lot of scattered questions about different topics,
which makes it less efficient for people to help you and less clear
for you to understand what we're trying to communicate back, even if
it is somewhat generic.

-Justin

Thank you
With Regards
Kavya


   I don't see the connection to my comment about pressure, but I'll
   address this anyway.  There is no temperature during EM.
 Hence with
   "gen-vel = no" then no velocities are generated.  The
settings for
   gen-temp and gen-seed are defaults that are assigned when
none are
   provided in the input .mdp file.

   I seem to recall that a pressure term is written during EM,
but it
   is largely meaningless.

   -Justin


   -- ====


   Justin A. Lemkul
   Ph.D. Candidate
   ICTAS Doctoral Scholar
   MILES-IGERT Trainee
   Department of Biochemistry
   Virginia Tech
   Blacksburg, VA
   jalemkul[at]vt.edu   | (540)
231-9080
   http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

   >

   ====

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

   >
   http://lists.gromacs.org/mailman/listinfo/gmx-users


   >
   Please search the archive at
   http://www.gromacs.org/Support/Mailing_Lists/Search


   > before
posting!
   Please don't post (un)subscribe requests to the list. Use the www
   interface or send it to gmx-users-requ...@gromacs.org

   >.
   Can't post? Read
http://www.gromacs.org/Support/Mailing_Lists

   >



-- 
=

[gmx-users] Interaction energy

[Steven Neumann]

Dear Gmx Users,

I would like to calculate the interaction energy (LJ and
electrostatic) between each residue and my ligands (10 ligands in the
system). I would like to see what is the contribution of electrostatic and
vdW interactions between ligand and each of my residue. I thought to use
g_energy and specify each of my residues in index files but it is not
possible. Will you suggest how to do this?

Thank you,

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

Re: [gmx-users] trjconv:solute at the center

[Nilesh Dhumal]

Thanks Justin,

Still solute is not at center.

Nilesh


On Mon, October 17, 2011 11:27 am, Justin A. Lemkul wrote:
>

>
> Nilesh Dhumal wrote:
>
>> In 2nd step I choose system instaed of solvent.
>>
>>
>> I could not make the solute at the center.
>>
>>
>
> Don't use -b and -e when running trjconv.  I have found that PBC routines
> are not always correctly applied when parsing out sections of the
> trajectory.  This can affect your ability to center the molecule.
>
> -Justin
>
>
>> Thanks
>> NIlesh
>>
>>
>> On Mon, October 17, 2011 11:05 am, Justin A. Lemkul wrote:
>>
>>
>>> Nilesh Dhumal wrote:
>>>
>>>
 Justin,



 I have 26 solute atoms and 3302 solvent atoms in my sytems (total
 3328
 atoms).


 1. trjconv -f 3.trr -s 3.tpr -pbc mol -b 400 -e 600 -dt 1 -n
 500-1.ndx
 -o
 4-600.xtc
 here I choose group 0:system (3328 atoms)

 2. trjconv -f 4-600.xtc -s 3.tpr  -n 500-1.ndx -center  -o
 4-600-1.xtc



 For Centering I choose group: solute (26 atoms)
 For output I choose group : Solvent (3302 atoms)




 3. trjconv -f 4-600-1.xtc -s 3.tpr  -dump 500  -o 500-11.pdb



 Here I choose the group: 0 (system).



 I am geting for error for last command.



 Fatal error:
 Index[3302] 3303 is larger than the number of atoms in the
 trajectory file (3302).


 It look that there are no solute atoms in trajectory file.



>>> In step 2, you chose to save only the solvent.
>>>
>>>
>>>
>>> -Justin
>>>
>>>
>>>
>>> --
>>> 
>>>
>>>
>>>
>>> Justin A. Lemkul
>>> Ph.D. Candidate
>>> ICTAS Doctoral Scholar
>>> MILES-IGERT Trainee
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>>
>>>
>>> 
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-requ...@gromacs.org. Can't post?
>>> Read
>>> http://www.gromacs.org/Support/Mailing_Lists
>>>
>>>
>>>
>>>
>>
>>
>>
>
> --
> 
>
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read
> http://www.gromacs.org/Support/Mailing_Lists
>
>
>


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

[gmx-users] Re: gmx-users Digest, Vol 90, Issue 82

[Алексей Раевский]

No I need your help in any way, antechamber is not only the way I could do
it, I think...I just showed you that I tried something before I wrote you a
letter.  It is not necessary to use amber forcefield, but I don't think that
prodrg is a good choice for this task, though the only modification of the
residues in the peptide is acylation. But may be you know something! Thank
you very much?


On 17/10/2011 5:01 PM, Алексей Раевский wrote:
> Hi!
> I need an advice concerninng topology building of such substance like
> cyclosporine A. I've tried to make it with antechamber tool, cause I
> wanted to use amber99sb forcefield. But the program gave me an error
> in the begining and no results in the end after 12 hours of
> calculations ))) Can you give any suggestions for my next steps? This
> compound is a peptide chain built from acyl-adenylated amino acids
> (L-valine, L-leucine, L-alanine, L-glycine, 2-aminobutyric acid,
> 4-methylthreonine, and D-alanine).
> Thank you very much!

If you're asking for antechamber help, you're on the wrong forum.

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

Re: [gmx-users] Simulation of membrane protein

[James Starlight]

Dear Justin,

After 20 iterations I've obtained structure like this
http://www.sendspace.com/file/gyyj38


I suppose that this variat is more closely to correct form :)

But during solvation via GenBox I've obtained that error

One of the box vectors has become shorter than twice the cut-off length or
box_yy-|box_zy| or box_zz has become smaller than the cut-off.

Where I can change that cut-off distance?


James


2011/10/17 Justin A. Lemkul 

>
>
> James Starlight wrote:
>
>> Ok, James thank you
>>
>> It seems that I should to wite some script for too many iterations e.g
>>
>> perl inflategro.pl  minimized1.gro 0.95 DPPC 0
>> shrinked1.gro 5 area_shrink1.dat
>>
>>
>> grompp -f minim.mdp -c shrinked1.gro -p topol.top -o minimized2.tpr
>>
>> mdrun -v -deffnm minimized2
>>
>> perl inflategro.pl  minimized2.gro 0.95 DPPC 0
>> shrinked2.gro 5 area_shrink1.dat
>>
>>
>> grompp -f minim.mdp -c shrinked2.gro -p topol.top -o minimized3.tpr
>>
>> mdrun -v -deffnm minimized2
>>
>> ..
>>
>> perl inflategro.pl  minimized20.gro 0.95 DPPC 0
>> shrinked20.gro 5 area_shrink1.dat
>>
>>
>> grompp -f minim.mdp -c shrinked20.gro -p topol.top -o minimized21.tpr
>>
>> mdrun -v -deffnm minimized21
>>
>>
> All of which can be done in a for-loop instead of typing it out manually.
>
>
>  Does this action sequence correct? So as the consequence I need to find
>> operator wich stop the script untill defined value of S per lipid will be
>> reached
>>
>>
> Yes.  You can read that value from the screen or from the area.dat file
> that inflategro.pl prints.
>
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] topologies for POPE and DMPE

[Thomas Piggot]

Hi Pramod,

Please keep all general queries and questions on the GROMACS mailing list.

For CHARMM27, POPC can be found as an rtp entry. This means a topology 
can be generated using pdb2gmx. It is easiest if you do this using one 
POPC lipid and then make an itp from the top. A CHARMM POPC bilayer can 
be downloaded from the internet 
(http://terpconnect.umd.edu/~jbklauda/research/download.html).


Cheers

Tom

ram bio wrote:

Dear Dr.Tom,

This is in response to the your message regarding the lipid bilayers
for MD simulation. I have a protein and ligand complex to be simulated
in lipid bilayer. Do, you have POPC structure and itp files
parameterised by CHARMM 27 FF.

Regards,

Pramod

On Mon, Oct 17, 2011 at 12:07 PM, Thomas Piggot  wrote:

Hi Roy,

PE lipids are less frequently used than PC ones and there are fewer
topologies available. Also it has been shown that using the Berger PC lipid
topologies (the most frequently used united-atom PC lipids) and simply
changing the CH3 atoms in the head group to H is not a good approach for PE
(de Vries et al. DOI: 10.1021/jp0366926 is I think the first mention of
this).

Other PE topologies I am aware of are either the all-atom CHARMM (27 or 36)
lipids or there are two united-atom GROMOS PE topologies:

The first is the GROMOS43A1-S3 force field which has a POPE topology (you
can download this from the contributions section on the GROMACS website). I
have simulated a POPE membrane using these parameters before with no
problems.

The second (and here is a shameless plug for some of my work, sorry!) is a
GROMOS53A6 based PE described in a paper we have just got accepted into J.
Phys. Chem B (http://dx.doi.org/10.1021/jp207013v). The supplementary
information for this paper (which is not yet available) has an
analysis/validation of POPE and DPPE membrane using these parameters which
are based upon the PC topologies of Kukol (DOI: 10.1021/ct8003468) and
Chandrasekhar (DOI: 10.1007/s00249-002-0269-4). If you (or anyone else) wish
to use these PE topologies send me an email off-list and I can let you have
them. I have not tested DMPE yet but I would imagine it should be similar to
DPPE and you can also make a DMPE bilayer from a DPPE one by simply removing
two CH2 groups from each lipid tail and equilibrating the new membrane.

Cheers

Tom

Roy Lee wrote:

Dear all,


I would like to simulate my protein in a lipid bilayer using gromacs
4.5.4, and a forcefield of gromos96. However i don't have the topologies
files for lipid bilayer for POPE and DMPE. Anybody knows where can i get the
topologies file for POPE and DMPE ?


Any help is much appreciated.


Thanks a lot!


Roy


--
Dr Thomas Piggot
University of Southampton, UK.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface
or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists



--
Dr Thomas Piggot
University of Southampton, UK.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Interaction energy

[Justin A. Lemkul]

Steven Neumann wrote:

Dear Gmx Users,
 
I would like to calculate the interaction energy (LJ and 
electrostatic) between each residue and my ligands (10 ligands in the 
system). I would like to see what is the contribution of electrostatic 
and vdW interactions between ligand and each of my residue. I thought to 
use g_energy and specify each of my residues in index files but it is 
not possible. Will you suggest how to do this?
 


For such information, you have to specify these groups as energygrps in the .mdp 
file.  You can rerun the trajectory using mdrun -rerun and a new .tpr file 
specifying these groups, but depending on the output frequency, the result may 
not be as accurate as you'd like.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Simulation of membrane protein

[Justin A. Lemkul]

James Starlight wrote:

Dear Justin,

After 20 iterations I've obtained structure like this 
http://www.sendspace.com/file/gyyj38



I suppose that this variat is more closely to correct form :)



I can't access the file, so I don't know.  20 iterations still doesn't sound 
like enough for the tutorial system, unless you shrunk faster than what was 
recommended.



But during solvation via GenBox I've obtained that error

One of the box vectors has become shorter than twice the cut-off length 
or box_yy-|box_zy| or box_zz has become smaller than the cut-off.


Where I can change that cut-off distance?



There is no reason that your system should be this small to trigger this error. 
 The box dimensions should be on the order of 6 nm.  genbox uses a search 
radius for deleting overlapping molecules.  Perhaps the value you have set in 
vdwradii.dat for C radii is too large for genbox to function properly.  Without 
more detail, I can't suggest anything else.  The procedure in the tutorial 
should work; I've run through it dozens of times.  Please pay careful attention 
to all of the values specified in all of the necessary files and commands.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] trjconv:solute at the center

[Justin A. Lemkul]

Nilesh Dhumal wrote:

Thanks Justin,

Still solute is not at center.



Is your reference frame (i.e. the .tpr file) centered?  If not, centering likely 
won't work as desired.  I assumed that it was centered, per normal system 
building procedures.


-Justin


Nilesh


On Mon, October 17, 2011 11:27 am, Justin A. Lemkul wrote:


Nilesh Dhumal wrote:


In 2nd step I choose system instaed of solvent.


I could not make the solute at the center.



Don't use -b and -e when running trjconv.  I have found that PBC routines
are not always correctly applied when parsing out sections of the
trajectory.  This can affect your ability to center the molecule.

-Justin



Thanks
NIlesh


On Mon, October 17, 2011 11:05 am, Justin A. Lemkul wrote:



Nilesh Dhumal wrote:



Justin,



I have 26 solute atoms and 3302 solvent atoms in my sytems (total
3328
atoms).


1. trjconv -f 3.trr -s 3.tpr -pbc mol -b 400 -e 600 -dt 1 -n
500-1.ndx
-o
4-600.xtc
here I choose group 0:system (3328 atoms)

2. trjconv -f 4-600.xtc -s 3.tpr  -n 500-1.ndx -center  -o
4-600-1.xtc



For Centering I choose group: solute (26 atoms)
For output I choose group : Solvent (3302 atoms)




3. trjconv -f 4-600-1.xtc -s 3.tpr  -dump 500  -o 500-11.pdb



Here I choose the group: 0 (system).



I am geting for error for last command.



Fatal error:
Index[3302] 3303 is larger than the number of atoms in the
trajectory file (3302).


It look that there are no solute atoms in trajectory file.




In step 2, you chose to save only the solvent.



-Justin



--




Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




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








--



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin



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









--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] trjconv:solute at the center

[Tsjerk Wassenaar]

Hey :)

The reference plays no role in centering. But I guess that Nilesh expects
centering of the solute w.r.t. to the solvent, or is looking at the wrong
center (tric/rect).

Cheers,

Tsjerk

On Oct 17, 2011 7:06 PM, "Justin A. Lemkul"  wrote:

Nilesh Dhumal wrote: > > Thanks Justin, > > Still solute is not at center. >

Is your reference frame (i.e. the .tpr file) centered?  If not, centering
likely won't work as desired.  I assumed that it was centered, per normal
system building procedures.

-Justin

> Nilesh > > > On Mon, October 17, 2011 11:27 am, Justin A. Lemkul wrote: >
>> Nilesh Dhumal wrote...
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] REMD and GBSA

[Ben Reynwar]

On Fri, Oct 14, 2011 at 9:11 AM, Mark Abraham  wrote:
> On 14/10/2011 10:12 AM, Ben Reynwar wrote:
>>
>> Hi gromacs list,
>>
>> I'm about to start some REMD simulations using generalized Born
>> solvent on a protein of about 5000 atoms.  I have two questions, the
>> first of which is about gromacs, the second more about REMD in
>> general.
>>
>> (1)
>> I'm getting some pretty ugly energy drift (300K->500K in 1 ns) for an
>> NVE MD test simulation using a 2 fs time step.  It goes away if I use
>> 1 fs, however I was under the impression that 2 fs is normally OK.  I
>> was wondering whether that could be caused by the use of the cut-off
>> method which is required with the coloumb and VdW interactions when
>> using GBSA?  Or perhaps I'm doing something else wrong.  I'll include
>> the mdp file I'm using at the bottom of the email in case anyone feels
>> like pointing out my foolishness to me.
>
> Drift is normal if you use 2fs with hbond constraints. all-bond constraints
> are necessary for 2fs.
>
Great. Thank you.

>>
>> (2)
>> I've been analyzing some data from an REMD simulation by my
>> predecessor and see very slow replica flow rates.  They are about two
>> orders of magnitude smaller than the idealized rate of the exchange
>> attempt frequency multiplied by the acceptance fraction (exchanges are
>> attempted every 2 ps with a 0.4 acceptance fraction).  If I look at
>> the energy distribution for a given replica/temperature combination
>> over a time scale of around 1 ns, it is clearly shifted from the
>> average energy distribution for that temperature.  The timescale for
>> changes in this energy shift is around 10 ns.  My current theory for
>> the slow rate of replica flow is that the slow fluctuations in the
>> energy of the protein are limiting replica flow, since a replica with
>> lower than average energy will tend to remain at the bottom of the
>> temperature range, while those with higher than average energies will
>> tend to remain at the top.  Has anyone else observed this kind of
>> behavior?  Is my reasoning wrong in any obvious way?
>
> A replica with "lower than average energy" *for that temperature* will tend
> to drift down the temperature ladder in favour of another.
>
> One can observe blockages in replica flow. If all the replicas below a given
> temperature are in regions of configuration space that cannot access PE high
> enough to have a significant chance of exchanging above that temperature,
> then flow does not occur (and vice-versa, of course). If one were to sample
> a FES that had two minima that should be sampled in a 2:1 ratio, but started
> from a 1:1 ratio and did not have a high enough temperature range to cross
> the barrier, then the exchange acceptance rate can look good when nothing
> useful is occurring - the observation will necessarily be that these minima
> are equally likely. The two groups are actually engaging in disjoint flow,
> and one needs to look at metrics other than the acceptance rate to observe
> it. The only way to deal with such a bottleneck is to have replicas at a
> high enough temperature that both groups can exchange to those temperatures
> - only now can barrier crossing occur. These kinds of phenomena can
> certainly occur over short time scales in localized regions of configuration
> and temperature space.
>
> Mark
>

Do you know if anyone has done any studies looking at replica flow in
well-defined, comparatively low-dimensional landscapes to get a
qualitative feel for these kinds of effects?  It would be interesting
to see what effect replica exchange settings can have on replica flow
beyond the simple random walk models, when you take into account the
fact that different regions of configuration space could have
different potential energy distributions for the same temperature.

Cheers,
Ben

>>
>> Cheers,
>> Ben
>>
>> ; An energy drift simulation of TaHSP.
>>
>> ; 7.3.2 Preprocssing
>> ; --
>> ; defines pass to the preprocessor
>> define =
>>
>> ; 7.3.3 Run Control
>> ; -
>> ; group(s) for center of mass motion removal
>> comm_grps = System
>> ; Use the MD integrator (as opposed to minimization).
>> integrator = md
>> ; maximum number of steps to integrate
>> nsteps = 1
>> ; remove center of mass translation and rotation around centre of mass
>> comm_mode = Angular
>> ; [ps] time step for integration
>> dt = 0.002
>> ; [steps] frequency of mass motion removal
>> nstcomm = 10
>> ; [ps] starting time for run
>> tinit = 0
>>
>> ; 7.3.8 Output Control
>> ; 
>> ; [steps] freq to write velocities to trajectory
>> nstvout = 0
>> ; [steps] freq to write energies to log file
>> nstlog = 100
>> ; Write to energy file frequently.
>> nstenergy = 100
>> ; group(s) to write to xtc trajectory
>> xtc_grps = System
>> ; [real] precision to write xtc trajectory
>> xtc_precision = 1000
>> ; [steps] freq to write coordinates to xtc trajectory
>> nstxtcout = 1000
>> ; [steps] freq to write coordinates to

RE: [gmx-users] lipid membrane slicing

[Poojari, Chetan]

Hi Justin,

Using make_ndx  on the trajectory file (output from trjorder), and listing out 
different lipids i did see the lipids arranged based on the distance from 
protein.

Now i want to choose lipids within 0.5nm from protein for my analysis. As in 
the index file the lipids are listed based on distance, I am not sure which 
lipid numbers fall within 0.5 nm range.

Please can i know if i can get information about the distance between 1st lipid 
listed in index file and the protein, then the 2nd lipid and protein and so on.


Kind Regards,
chetan


From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: 14 October 2011 12:44
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] lipid membrane slicing

Poojari, Chetan wrote:
> Thank you Justin, Igor  for your suggestions.
>
> I tried with trjorder and below is the command i used:
>
> trjorder -f  *.xtc -s  *.tpr -n order.ndx -na 50 -da 0 -r 0.5 -o ordered.xtc
>
> I choose protein as my reference group and lipids as the group of molecules
> to be ordered,  -na 50 : no of atoms in lipid molecule and cut-off distance
> of 0.5nm from protein.
>
> As i understood from trjorder description, the above command i have used
> should order lipids within 0.5nm from the protein and this information will
> be outputted into new xtc file i am writing. Using the new xtc file with
> g_order i should be able to calculate order parameter for lipids within 0.5nm
> from protein. Please can I know if I am right with the understanding of the
> trjorder description.
>
>

All the lipids are ordered, not just the ones within 0.5 nm.  The -r option is
only useful in conjunction with -shell, for printing the molecules within the
specified distance.  Here, it's not doing anything.

> Is it possible to order the lipids away from the protein using trjorder, so
> that i can calculate the order parameter for lipids away from protein as
> well. If so please can I know how can i set distance away from protein.
>
>

Use index groups specifying different lipids.  They are ordered in the
trajectory by distance, so as the molecule number (and thus atom indices)
increase, so too does that molecule's distance from the protein.

-Justin

>
> Kind Regards, chetan
>
>
>  From: gmx-users-boun...@gromacs.org
> [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul
> [jalem...@vt.edu] Sent: 11 October 2011 23:24 To: Discussion list for GROMACS
> users Subject: Re: [gmx-users] lipid membrane slicing
>
> Igor Marques wrote:
>> chetan,
>>
>> i'm not sure about the use of -sl option in g_order.
>>
>> however, for the purpose you mentioned, i'd suggest you to: create two
>> different trajectories, using trjconv and an index file grouping lipids
>> closer to the protein and lipids away from the protein. then, you should be
>> able to analyse each trajcetory and get the order parameters for each group
>> of lipids.
>>
>
> This is more easily accomplished with trjorder.
>
> -Justin
>
>> good luck, igor
>>
>>
>> Igor Marques
>>
>>
>> On Tue, Oct 11, 2011 at 6:20 PM, Poojari, Chetan > > wrote:
>>
>> Hi,
>>
>> I have protein completely inserted into lipid membrane and would like to
>> study order parameter around the protein as well as away from the protein.
>>
>> For this I would like to slice my membrane into parts.
>>
>> I tried the following command:
>>
>> g_order -s *.tpr -f *.xtc -n sn1.ndx -d z -od deuter_sn1.xvg -sl 2
>>
>> The output i get from this is as same as the one where i dont use -sl 2
>> flag and it also doesnt show the different parts it has used for order
>> parameter calculation.
>>
>> Please can I know how to slice my lipid membrane so that i can study order
>> parameter for each part separately.
>>
>>
>> Kind Regards, chetan
>>
>> 
>>
>> 
>>  Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft:
>> Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B
>> 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher
>> Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke
>> (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M.
>> Schmidt
>> 
>>
>> 
>>  -- gmx-users mailing listgmx-users@gromacs.org
>> 
>> http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the
>> archive at http://www.gromacs.org/Support/Mailing_Lists/Search before
>> posting! Please don't post (un)subscribe requests to the 

Re: [gmx-users] lipid membrane slicing

[Justin A. Lemkul]

Poojari, Chetan wrote:

Hi Justin,

Using make_ndx  on the trajectory file (output from trjorder), and listing out 
different lipids i did see the lipids arranged based on the distance from 
protein.

Now i want to choose lipids within 0.5nm from protein for my analysis. As in 
the index file the lipids are listed based on distance, I am not sure which 
lipid numbers fall within 0.5 nm range.



g_select can tell you this.


Please can i know if i can get information about the distance between 1st lipid 
listed in index file and the protein, then the 2nd lipid and protein and so on.




Either use g_select or measure distances with g_dist.

-Justin


Kind Regards,
chetan


From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: 14 October 2011 12:44
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] lipid membrane slicing

Poojari, Chetan wrote:

Thank you Justin, Igor  for your suggestions.

I tried with trjorder and below is the command i used:

trjorder -f  *.xtc -s  *.tpr -n order.ndx -na 50 -da 0 -r 0.5 -o ordered.xtc

I choose protein as my reference group and lipids as the group of molecules
to be ordered,  -na 50 : no of atoms in lipid molecule and cut-off distance
of 0.5nm from protein.

As i understood from trjorder description, the above command i have used
should order lipids within 0.5nm from the protein and this information will
be outputted into new xtc file i am writing. Using the new xtc file with
g_order i should be able to calculate order parameter for lipids within 0.5nm
from protein. Please can I know if I am right with the understanding of the
trjorder description.




All the lipids are ordered, not just the ones within 0.5 nm.  The -r option is
only useful in conjunction with -shell, for printing the molecules within the
specified distance.  Here, it's not doing anything.


Is it possible to order the lipids away from the protein using trjorder, so
that i can calculate the order parameter for lipids away from protein as
well. If so please can I know how can i set distance away from protein.




Use index groups specifying different lipids.  They are ordered in the
trajectory by distance, so as the molecule number (and thus atom indices)
increase, so too does that molecule's distance from the protein.

-Justin


Kind Regards, chetan


 From: gmx-users-boun...@gromacs.org
[gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul
[jalem...@vt.edu] Sent: 11 October 2011 23:24 To: Discussion list for GROMACS
users Subject: Re: [gmx-users] lipid membrane slicing

Igor Marques wrote:

chetan,

i'm not sure about the use of -sl option in g_order.

however, for the purpose you mentioned, i'd suggest you to: create two
different trajectories, using trjconv and an index file grouping lipids
closer to the protein and lipids away from the protein. then, you should be
able to analyse each trajcetory and get the order parameters for each group
of lipids.


This is more easily accomplished with trjorder.

-Justin


good luck, igor


Igor Marques


On Tue, Oct 11, 2011 at 6:20 PM, Poojari, Chetan mailto:c.pooj...@fz-juelich.de>> wrote:

Hi,

I have protein completely inserted into lipid membrane and would like to
study order parameter around the protein as well as away from the protein.

For this I would like to slice my membrane into parts.

I tried the following command:

g_order -s *.tpr -f *.xtc -n sn1.ndx -d z -od deuter_sn1.xvg -sl 2

The output i get from this is as same as the one where i dont use -sl 2
flag and it also doesnt show the different parts it has used for order
parameter calculation.

Please can I know how to slice my lipid membrane so that i can study order
parameter for each part separately.


Kind Regards, chetan




 Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft:
Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B
3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke
(stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M.
Schmidt



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

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

[gmx-users] Updating charges on-the-fly

[J. Nathan Scott]

Hello fellow GMX users,

I've been digging in the archives and haven't yet found a good response to
this question, so I thought I'd ask again, since I see from a post just last
month others are still interested in this subject as well. Is it possible in
Gromacs to periodically update/change the charges on a given molecule or
residue during the course of a simulation?

What I am envisioning is having a production simulation running, and then
every "x" amount of time, the current checkpoint file gets read and
processed by an external routine that calculates charges on the residue or
molecule of interest, which are then fed back into Gromacs to continue the
run. Is it possible to execute an external program from within a Gromacs
simulation? I know this functionality must be in there somewhere, since
Gromacs can communicate with external QM software, but I'm not sure if a
charge modification scheme could make use of the same built-in I/O methods.

Is such a scheme possible? I realize an alternative method would be to stop
the run, do some calculation to recalculate the charges, and then perhaps
use some simple code to modify the .top file directly, and finally grompp
out a new tpr file and continue the run. Lather, rinse, repeat. I'm guessing
this could be rather slow because of needing to call grompp over and over
and the need to continually restart the simulation.

For what it's worth, my interest lies mainly in excited state chromophores
and I'd be using modified ZINDO code to calculate charges every x number of
steps. This calculation is *very* fast, even for large chromophores,
therefore my focus on other performance bottlenecks.

I would be extremely grateful for any feedback on this subject, particularly
from anyone who has done a similar thing successfully and cares to share any
tips or code.

-- 
--
J. Nathan Scott, Ph.D.
Postdoctoral Fellow
Department of Chemistry and Biochemistry
Montana State University
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] trjconv:solute at the center

[Nilesh Dhumal]

Ya, I want to center solute w.r.t to the solvent.

I have more question, if I want to save the coordinates of a snapshot with
no pbc effect, can I use -pbc nojump in trjconv.

nilesh

On Mon, October 17, 2011 1:34 pm, Tsjerk Wassenaar wrote:
> Hey :)
>
>
> The reference plays no role in centering. But I guess that Nilesh expects
>  centering of the solute w.r.t. to the solvent, or is looking at the
> wrong center (tric/rect).
>
> Cheers,
>
>
> Tsjerk
>
>
> On Oct 17, 2011 7:06 PM, "Justin A. Lemkul"  wrote:
>
>
> Nilesh Dhumal wrote: > > Thanks Justin, > > Still solute is not at
> center. >
>
> Is your reference frame (i.e. the .tpr file) centered?  If not, centering
>  likely won't work as desired.  I assumed that it was centered, per
> normal system building procedures.
>
> -Justin
>
>
>> Nilesh > > > On Mon, October 17, 2011 11:27 am, Justin A. Lemkul wrote:
>> >
>>
>>> Nilesh Dhumal wrote...
>>>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read
> http://www.gromacs.org/Support/Mailing_Lists


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

Re: [gmx-users] Simulation of membrane protein

[James Starlight]

Justin

>
>>
> I can't access the file, so I don't know.  20 iterations still doesn't
> sound like enough for the tutorial system, unless you shrunk faster than
> what was recommended.


20 iteration was a simple example. It means that many iterations produced
more accuracy results in comparison to previous one :)
Its only one not understood for me.
After 20 iterations I've obtained S per lipid value= 0.2 nm^2. It's equal to
2 A^2 ( 1A=0.1 nm) http://en.wikipedia.org/wiki/Angstrom
Why you told in the tutorial that experimental value was 65 A^2 ?

>
>
>>
>   Perhaps the value you have set in vdwradii.dat for C radii is too large
> for genbox to function properly.
>

It seems that this is true because I've defined vdv radii as 0.4 instead of
0.375. Could the differense in the 0.015 result in the error?



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

[gmx-users] box dimension

[Nilesh Dhumal]

Hello,

I have saved the coordinates of snapshot from trajectory in pdb file.

The dimesnion of box in pdb file are
32.805   32.805   32.805  90.00  90.00  90.00 P 1

I am trying to find  atoms close to center of box.

there are  atoms whose distance from center is more that ~17 A. My center
coordinates are 0.0 0.0 0.0.

How is it possible?

I am using Gromacs 4.0.7 version.

Thanks

Nilesh











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

Re: [gmx-users] Simulation of membrane protein

[Justin A. Lemkul]

James Starlight wrote:

Justin



I can't access the file, so I don't know.  20 iterations still
doesn't sound like enough for the tutorial system, unless you shrunk
faster than what was recommended.


20 iteration was a simple example. It means that many iterations 
produced more accuracy results in comparison to previous one :)


OK, please be literal in the future.  Providing incorrect or inaccurate 
information slows you down on your goal to getting a resolution and makes people 
less likely to help you.



Its only one not understood for me.
After 20 iterations I've obtained S per lipid value= 0.2 nm^2. It's 
equal to 2 A^2 ( 1A=0.1 nm) http://en.wikipedia.org/wiki/Angstrom


I am familiar with this unit conversion.  0.2 nm^2 is, however, 20 A^2 (mind the 
square term).



Why you told in the tutorial that experimental value was 65 A^2 ?



Because it is.  Different techniques give slightly different results, but 
generally 0.62 - 0.65 nm^2 is an accepted value for the APL of DPPC.


If you have achieved 0.2 nm^2, you have greatly overcompressed your box.  Either 
you did far more shrinking steps than is called for, or you scaled down much too 
quickly.  The procedure of 26 shrinks with a 0.95 scaling factor produces a very 
reproducible result.  You should stick to it.






  Perhaps the value you have set in vdwradii.dat for C radii is too
large for genbox to function properly. 



It seems that this is true because I've defined vdv radii as 0.4 instead 
of 0.375. Could the differense in the 0.015 result in the error?





Likely the error comes from the fact that your box is extremely small, but I 
would also advise you to not make ad hoc changes to the values shown in the 
tutorial.  They are there for a reason.  I have found that a 0.4 nm carbon 
radius gives undesirable result (an overall lack of sufficient hydration).


Check your box dimensions in the last shrunken .gro file you produced.  If the 
x/y dimensions are any less than 6 nm or so, you've gone too far.  In fact, you 
should be aiming to reproduce whatever the box dimensions were of the original 
DPPC membrane.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] trjconv:solute at the center

[Tsjerk Wassenaar]

Hi Nilesh,

To center the solute with respect to the solvent, first center the
solute in the box, and then put the solvent in the box. Mind that that
involves two passes of trjconv.

If 'no pbc effect' means no wrapping over the boundaries, yes you can
use -dump with -pbc nojump to save a snapshot. trjconv will go over
the frames and 'unwrap' the frames before the snapshot you want.

Hope it helps,

Tsjerk

On Mon, Oct 17, 2011 at 9:18 PM, Nilesh Dhumal  wrote:
> Ya, I want to center solute w.r.t to the solvent.
>
> I have more question, if I want to save the coordinates of a snapshot with
> no pbc effect, can I use -pbc nojump in trjconv.
>
> nilesh
>
> On Mon, October 17, 2011 1:34 pm, Tsjerk Wassenaar wrote:
>> Hey :)
>>
>>
>> The reference plays no role in centering. But I guess that Nilesh expects
>>  centering of the solute w.r.t. to the solvent, or is looking at the
>> wrong center (tric/rect).
>>
>> Cheers,
>>
>>
>> Tsjerk
>>
>>
>> On Oct 17, 2011 7:06 PM, "Justin A. Lemkul"  wrote:
>>
>>
>> Nilesh Dhumal wrote: > > Thanks Justin, > > Still solute is not at
>> center. >
>>
>> Is your reference frame (i.e. the .tpr file) centered?  If not, centering
>>  likely won't work as desired.  I assumed that it was centered, per
>> normal system building procedures.
>>
>> -Justin
>>
>>
>>> Nilesh > > > On Mon, October 17, 2011 11:27 am, Justin A. Lemkul wrote:
>>> >
>>>
 Nilesh Dhumal wrote...

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



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] solvents in gmx

[Yao Yao]

Hi Gmxers,

Is there a way I can check all the kinds of solvents in gromacs? Apart from 
water, ethanol, ...,
are there any Glycerol, Treholose, 

Thanks,

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

Re: [gmx-users] solvents in gmx

[Justin A. Lemkul]

Yao Yao wrote:

Hi Gmxers,

Is there a way I can check all the kinds of solvents in gromacs? Apart 
from water, ethanol, ...,

are there any Glycerol, Treholose, 



There likely aren't many.  Anything available would be in the force field 
subdirectory for whatever force field you want.  Others may be available on the 
User Contributions section of the Gromacs website.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] REMD and GBSA

[Mark Abraham]

On 18/10/2011 4:58 AM, Ben Reynwar wrote:

On Fri, Oct 14, 2011 at 9:11 AM, Mark Abraham  wrote:

On 14/10/2011 10:12 AM, Ben Reynwar wrote:

Hi gromacs list,

I'm about to start some REMD simulations using generalized Born
solvent on a protein of about 5000 atoms.  I have two questions, the
first of which is about gromacs, the second more about REMD in
general.

(1)
I'm getting some pretty ugly energy drift (300K->500K in 1 ns) for an
NVE MD test simulation using a 2 fs time step.  It goes away if I use
1 fs, however I was under the impression that 2 fs is normally OK.  I
was wondering whether that could be caused by the use of the cut-off
method which is required with the coloumb and VdW interactions when
using GBSA?  Or perhaps I'm doing something else wrong.  I'll include
the mdp file I'm using at the bottom of the email in case anyone feels
like pointing out my foolishness to me.

Drift is normal if you use 2fs with hbond constraints. all-bond constraints
are necessary for 2fs.


Great. Thank you.


(2)
I've been analyzing some data from an REMD simulation by my
predecessor and see very slow replica flow rates.  They are about two
orders of magnitude smaller than the idealized rate of the exchange
attempt frequency multiplied by the acceptance fraction (exchanges are
attempted every 2 ps with a 0.4 acceptance fraction).  If I look at
the energy distribution for a given replica/temperature combination
over a time scale of around 1 ns, it is clearly shifted from the
average energy distribution for that temperature.  The timescale for
changes in this energy shift is around 10 ns.  My current theory for
the slow rate of replica flow is that the slow fluctuations in the
energy of the protein are limiting replica flow, since a replica with
lower than average energy will tend to remain at the bottom of the
temperature range, while those with higher than average energies will
tend to remain at the top.  Has anyone else observed this kind of
behavior?  Is my reasoning wrong in any obvious way?

A replica with "lower than average energy" *for that temperature* will tend
to drift down the temperature ladder in favour of another.

One can observe blockages in replica flow. If all the replicas below a given
temperature are in regions of configuration space that cannot access PE high
enough to have a significant chance of exchanging above that temperature,
then flow does not occur (and vice-versa, of course). If one were to sample
a FES that had two minima that should be sampled in a 2:1 ratio, but started
from a 1:1 ratio and did not have a high enough temperature range to cross
the barrier, then the exchange acceptance rate can look good when nothing
useful is occurring - the observation will necessarily be that these minima
are equally likely. The two groups are actually engaging in disjoint flow,
and one needs to look at metrics other than the acceptance rate to observe
it. The only way to deal with such a bottleneck is to have replicas at a
high enough temperature that both groups can exchange to those temperatures
- only now can barrier crossing occur. These kinds of phenomena can
certainly occur over short time scales in localized regions of configuration
and temperature space.

Mark


Do you know if anyone has done any studies looking at replica flow in
well-defined, comparatively low-dimensional landscapes to get a
qualitative feel for these kinds of effects?  It would be interesting
to see what effect replica exchange settings can have on replica flow
beyond the simple random walk models, when you take into account the
fact that different regions of configuration space could have
different potential energy distributions for the same temperature.



See for example Walter Nadler, Jan H. Meinke, and Ulrich H. E. Hansmann 
"Folding proteins by first-passage-times-optimized replica exchange", 
PHYSICAL REVIEW E 78, 061905, 2008 (and related work)


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

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] box dimension

[Mark Abraham]

On 18/10/2011 7:05 AM, Nilesh Dhumal wrote:

Hello,

I have saved the coordinates of snapshot from trajectory in pdb file.

The dimesnion of box in pdb file are
32.805   32.805   32.805  90.00  90.00  90.00 P 1

I am trying to find  atoms close to center of box.

there are  atoms whose distance from center is more that ~17 A. My center
coordinates are 0.0 0.0 0.0.

How is it possible?


Molecules diffuse across periodic boundaries during the simulation. 
While computing interactions, mdrun corrects for periodicity on the fly, 
but does not trouble itself to guess what manner of post-processing you 
would like to do. There is a suggested trjconv workflow on the the 
GROMACS website. I suggest you try it.


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

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Updating charges on-the-fly

[Mark Abraham]

On 18/10/2011 5:40 AM, J. Nathan Scott wrote:

Hello fellow GMX users,

I've been digging in the archives and haven't yet found a good 
response to this question, so I thought I'd ask again, since I see 
from a post just last month others are still interested in this 
subject as well. Is it possible in Gromacs to periodically 
update/change the charges on a given molecule or residue during the 
course of a simulation?


Not currently, but it would not be hard to do.

What I am envisioning is having a production simulation running, and 
then every "x" amount of time, the current checkpoint file gets read 
and processed by an external routine that calculates charges on the 
residue or molecule of interest, which are then fed back into Gromacs 
to continue the run. Is it possible to execute an external program 
from within a Gromacs simulation? I know this functionality must be in 
there somewhere, since Gromacs can communicate with external QM 
software, but I'm not sure if a charge modification scheme could make 
use of the same built-in I/O methods.


GROMACS is a normal C program, and can execute an external program. 
Obviously this will still be inefficient if GROMACS was running in 
parallel, since you have to have an I/O phase before and after the 
external program and probably the other processors cannot do anything 
useful. You would then have to re-distribute the charge vector over any 
GROMACS parallel nodes.




Is such a scheme possible? I realize an alternative method would be to 
stop the run, do some calculation to recalculate the charges, and then 
perhaps use some simple code to modify the .top file directly, and 
finally grompp out a new tpr file and continue the run. Lather, rinse, 
repeat. I'm guessing this could be rather slow because of needing to 
call grompp over and over and the need to continually restart the 
simulation.


This would be slower still, but reliable and easy for proving the method.



For what it's worth, my interest lies mainly in excited state 
chromophores and I'd be using modified ZINDO code to calculate charges 
every x number of steps. This calculation is *very* fast, even for 
large chromophores, therefore my focus on other performance bottlenecks.


Ideally, GROMACS code would be linked with ZINDO and call the correct 
function directly. This shouldn't be too bad since you merely need an 
array of coordinates (and some other data which can be hard-coded 
somehow) as input, and the charges out. You should probably get one or 
other of the crude hacks working first, to judge how much value the 
speed-up might have.


Mark



I would be extremely grateful for any feedback on this subject, 
particularly from anyone who has done a similar thing successfully and 
cares to share any tips or code.


--
--
J. Nathan Scott, Ph.D.
Postdoctoral Fellow
Department of Chemistry and Biochemistry
Montana State University




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

Re: [gmx-users] acylation of peptide

[Mark Abraham]

On 18/10/2011 2:57 AM, ???  wrote:
No I need your help in any way, antechamber is not only the way I 
could do it, I think...I just showed you that I tried something before 
I wrote you a letter.  It is not necessary to use amber forcefield, 
but I don't think that prodrg is a good choice for this task, though 
the only modification of the residues in the peptide is acylation. But 
may be you know something! Thank you very much?


If the atom types and interactions for the acylated peptide can be found 
in a regular force field, then the simplest approach is to create a new 
residue for the force field of interest using a text editor, following 
the instructions on the GROMACS website. Knowledge of chapter 5 of the 
manual will be essential.


Mark




On 17/10/2011 5:01 PM, ???  wrote:
> Hi!
> I need an advice concerninng topology building of such substance like
> cyclosporine A. I've tried to make it with antechamber tool, cause I
> wanted to use amber99sb forcefield. But the program gave me an error
> in the begining and no results in the end after 12 hours of
> calculations ))) Can you give any suggestions for my next steps? This
> compound is a peptide chain built from acyl-adenylated amino acids
> (L-valine, L-leucine, L-alanine, L-glycine, 2-aminobutyric acid,
> 4-methylthreonine, and D-alanine).
> Thank you very much!

If you're asking for antechamber help, you're on the wrong forum.

Mark




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

Re: [gmx-users] box dimension

[Nilesh Dhumal]

I used -pbc nojump to remove pbc effect.

 trjconv 3.trr  -s 3.tpr -pbc nojump -o 500-11.pdb

Basically I want to find the conformer close to center of box.

Nilesh

On Mon, October 17, 2011 6:36 pm, Mark Abraham wrote:
> On 18/10/2011 7:05 AM, Nilesh Dhumal wrote:
>
>> Hello,
>>
>>
>> I have saved the coordinates of snapshot from trajectory in pdb file.
>>
>>
>> The dimesnion of box in pdb file are
>> 32.805   32.805   32.805  90.00  90.00  90.00 P 1
>>
>>
>> I am trying to find  atoms close to center of box.
>>
>>
>> there are  atoms whose distance from center is more that ~17 A. My
>> center coordinates are 0.0 0.0 0.0.
>>
>> How is it possible?
>>
>
> Molecules diffuse across periodic boundaries during the simulation.
> While computing interactions, mdrun corrects for periodicity on the fly,
> but does not trouble itself to guess what manner of post-processing you
> would like to do. There is a suggested trjconv workflow on the the GROMACS
> website. I suggest you try it.
>
> Mark
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read
> http://www.gromacs.org/Support/Mailing_Lists
>
>
>


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

Re: [gmx-users] box dimension

[Mark Abraham]

On 18/10/2011 11:48 AM, Nilesh Dhumal wrote:

I used -pbc nojump to remove pbc effect.


Please read trjconv -h about -pbc nojump. If molecules can't jump, then 
they must diffuse. You can't have both.


Mark



  trjconv 3.trr  -s 3.tpr -pbc nojump -o 500-11.pdb

Basically I want to find the conformer close to center of box.

Nilesh

On Mon, October 17, 2011 6:36 pm, Mark Abraham wrote:

On 18/10/2011 7:05 AM, Nilesh Dhumal wrote:


Hello,


I have saved the coordinates of snapshot from trajectory in pdb file.


The dimesnion of box in pdb file are
32.805   32.805   32.805  90.00  90.00  90.00 P 1


I am trying to find  atoms close to center of box.


there are  atoms whose distance from center is more that ~17 A. My
center coordinates are 0.0 0.0 0.0.

How is it possible?


Molecules diffuse across periodic boundaries during the simulation.
While computing interactions, mdrun corrects for periodicity on the fly,
but does not trouble itself to guess what manner of post-processing you
would like to do. There is a suggested trjconv workflow on the the GROMACS
website. I suggest you try it.

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







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

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] some problems when using g_membed

[mircial]

Dear All:

I am using g_membed command to insert a protein into a membrane  
bilayer, however, when I run the following command:


g_membed -f input.tpr -p topology.top -xyinit 0.1 -xyend 1.0 -nxy 1000

I encountered the following errors:

Program g_membed, VERSION 4.5.4
Source code file: constr.c, line: 176

Fatal error:
Too many LINCS warnings (3270)
If you know what you are doing you can adjust the lincs warning  
threshold in your mdp file

or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


Does this mean that there is some un-reasonable physical positions?  
How can I set the environment variable GMX_MAXCONSTRWARN to -1 or how  
can I avoid this error?


Thanks very much for your time and your kind!

Best Regards

R.-X. G.

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

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] do Shell Molecular Dynamics with GROMACS

[杜波]

how can i do if i want to do Shell Molecular Dynamics(Drude ) with
GROMACS VERSION 4.0.7?


I only find you should set "emtol: (1.0) niter: (20) fcstep: (0)
[ps2]" in *.mdp file .(GROMACS_4.0 manual)
But  how i can write the *.gro and *.top ? Are they smae with the
traditional MD?

And i can not find any more information on the web :
 http://www.gromacs.org/Special:Search?search=shell&qid=0&ns=main&path=

thanks!!
regards,
Bo Du
Department of Polymer Science and Engineering,
School of Chemical Engineering and technology,
Tianjin University, Weijin Road 92, Nankai District 300072,
Tianjin City P. R. China
Tel/Fax: +86-22-27404303
E-mail: 2008d...@gmail.com
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] some problems when using g_membed

[Mark Abraham]

On 18/10/2011 2:08 PM, mirc...@sjtu.edu.cn wrote:
> Dear All:
>
> I am using g_membed command to insert a protein into a membrane
> bilayer, however, when I run the following command:
>
> g_membed -f input.tpr -p topology.top -xyinit 0.1 -xyend 1.0 -nxy 1000
>
> I encountered the following errors:
>
> Program g_membed, VERSION 4.5.4
> Source code file: constr.c, line: 176
>
> Fatal error:
> Too many LINCS warnings (3270)
> If you know what you are doing you can adjust the lincs warning
> threshold in your mdp file
> or set the environment variable GMX_MAXCONSTRWARN to -1,
> but normally it is better to fix the problem
> For more information and tips for troubleshooting, please check the
> GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
> Does this mean that there is some un-reasonable physical positions?
> How can I set the environment variable GMX_MAXCONSTRWARN to -1 or how
> can I avoid this error?

g_membed is a modified version of mdrun. As such, see
http://www.gromacs.org/Documentation/Terminology/Blowing_Up

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