[gmx-users] flexiblity

[shiva birgani]

Dear all
I have simulated two different proteins (A and B). I need to compare their
flexibility. RMSF help to examine their flexibilty individually, but I want
to campare them with each other.
Do anybody know a solution to this? Would you please help me in this regard?

Regards
Shiva
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Re: [gmx-users] Fwd: Simulation of protein with phosphate ion...

[Francesco Oteri]

Dear bharat,
you can try Phosfinder (http://phosfinder.bio.uniroma2.it). It is a 
website that predict phosphate binding site on protein stucture.


The paper url is:http://www.ncbi.nlm.nih.gov/pubmed/21622655


Il 31/05/2011 02:06, bharat gupta ha scritto:

thanks ...

On Mon, May 30, 2011 at 5:03 PM, Justin A. Lemkul > wrote:




bharat gupta wrote:

Well, mine is a beta-barrel protein called Green Fluorescent
Protein. In such a case the movement of ion is very important.
As the ion in side the barrel can quench the fluorescence.
That's what I want to track..


You can probably address this with the methods I've described.
 That's likely all that anyone can offer.  Spend some time looking
through the literature at the many kinds of systems that have been
addressed using SMD and/or umbrella sampling and come up with a
coherent plan to address your system based on what you find.


-Justin

-- 



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


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Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com 



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Re: [gmx-users] Fwd: Simulation of protein with phosphate ion...

[bharat gupta]

Ya , I have tried with this server, but I am getting those residues whose
side chains are present inside the barrel. Then in no way phosphate ion can
bind to the barrel, as per the protein design rules..

On Tue, May 31, 2011 at 1:33 AM, Francesco Oteri
wrote:

>  Dear bharat,
> you can try Phosfinder (http://phosfinder.bio.uniroma2.it). It is a
> website that predict phosphate binding site on protein stucture.
>
> The paper url is: http://www.ncbi.nlm.nih.gov/pubmed/21622655
>
>
> Il 31/05/2011 02:06, bharat gupta ha scritto:
>
> thanks ...
>
> On Mon, May 30, 2011 at 5:03 PM, Justin A. Lemkul  wrote:
>
>>
>>
>> bharat gupta wrote:
>>
>>> Well, mine is a beta-barrel protein called Green Fluorescent Protein. In
>>> such a case the movement of ion is very important. As the ion in side the
>>> barrel can quench the fluorescence. That's what I want to track..
>>>
>>
>>  You can probably address this with the methods I've described.  That's
>> likely all that anyone can offer.  Spend some time looking through the
>> literature at the many kinds of systems that have been addressed using SMD
>> and/or umbrella sampling and come up with a coherent plan to address your
>> system based on what you find.
>>
>>
>> -Justin
>>
>> --
>> 
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> 
>> --
>> gmx-users mailing listgmx-users@gromacs.org
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>>
>
>
>
> --
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343
> Mobile no. - 010-5818-3680
> E-mail : monu46...@yahoo.com
>
>
>
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-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com
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Re: [gmx-users] flexiblity

[Justin A. Lemkul]

shiva birgani wrote:

Dear all
I have simulated two different proteins (A and B). I need to compare 
their flexibility. RMSF help to examine their flexibilty individually, 
but I want to campare them with each other.

Do anybody know a solution to this? Would you please help me in this regard?



Is it not just a matter of comparing the RMSF between the two proteins?

-Justin

--


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


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[gmx-users] Re: need help

[Justin A. Lemkul]

Please post all Gromacs-related questions to the gmx-users list.  I am not a 
private help service.  I am CC'ing the message to the list and would ask that 
all further discussion be posted there.


The plot you showed was simply hydrogen bonds between some molecule and FAD, 
which can easily be produced with g_hbond.  Have a thorough look through the 
Gromacs manual, Appendix D, for the capabilities of Gromacs programs.


-Justin

Babajaan nawaz wrote:

**
*
*
*Dear *Justin i had successfully followed your manual and i applied the 
protocols in our work, i need one more fovour from you, i need this type 
of graph (ligand interaction with specfic residues), for this which 
command i had to use.

Untitled-3 copy.jpg

Thaking you 


B. Babajan


--


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


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[gmx-users] how to cite gromacs?

[leila karami]

Dear gromacs users

I want to know how to cite gromacs version 4.0.7? what paper do relate to
that?
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Re: [gmx-users] how to cite gromacs?

[Justin A. Lemkul]

leila karami wrote:

Dear gromacs users

I want to know how to cite gromacs version 4.0.7? what paper do relate 
to that?





Reference 5 in the manual.  Note that information on how to cite Gromacs is 
provided on  p. iv of the manual, as well.


-Justin

--


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


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[gmx-users] Thermal_Unfolding

[shahid nayeem]

Dear Gromacs Users

I want to study thermal unfolding of protein in gromacs. One way to do is
to simulate at different temperature. What I want to do is to gradually
increase temperature after each n number of steps and collect the n' number
of frame for each temperature interval. If I can do this in gromacs then
what should be the .mdp file for such increment in temperature at regular
intervals.
Thanks for any help.
Shahid Nayeem
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Re: [gmx-users] Thermal_Unfolding

[Justin A. Lemkul]

shahid nayeem wrote:

Dear Gromacs Users

I want to study thermal unfolding of protein in gromacs. One way to do 
is to simulate at different temperature. What I want to do is to 
gradually increase temperature after each n number of steps and collect 
the n' number of frame for each temperature interval. If I can do this 
in gromacs then what should be the .mdp file for such increment in 
temperature at regular intervals.


Start with the manual.

http://manual.gromacs.org/online/mdp_opt.html#sa

-Justin

--


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


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[gmx-users] Pulling a ligand out of protein cavity

[Shay Teaching]

Dear gromacs users,

I am trying to pull a ligand out of a cavity of a membrane protein (along
the Z axis).
Problem is, that with every pull settings I have tried the ligand gets
"stuck" on the protein's center of mass. How can I make it go all the was to
the bulk water?
It always gets stuck on the COM. And I've tried using both umbrella and
constant force, so I'm getting the feeling that I'm missing something
trivial.

Here's an example of one set of pull-parameters I tried:
--->
pull = constant_force
pull_geometry= distance
pull_dim = N N Y
pull_start   = yes; define initial COM distance > 0

pull_ngroups   = 1
pull_group0= Protein
pull_group1= Ligand
;pull_rate1= -0.001; 0.01 nm per ps = 10 nm per ns
pull_k1= 1000   ; kJ mol^-1 nm^-2
<--

Can anyone help enlighten me as to what I am doing wrong?
Thanks,
-Shay

P.S.
Using gromacs 4.0.7.
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Re: [gmx-users] Pulling a ligand out of protein cavity

[Justin A. Lemkul]

Shay Teaching wrote:

Dear gromacs users,

I am trying to pull a ligand out of a cavity of a membrane protein 
(along the Z axis).
Problem is, that with every pull settings I have tried the ligand gets 
"stuck" on the protein's center of mass. How can I make it go all the 
was to the bulk water?
It always gets stuck on the COM. And I've tried using both umbrella and 
constant force, so I'm getting the feeling that I'm missing something 
trivial.


Here's an example of one set of pull-parameters I tried:
--->
pull = constant_force
pull_geometry= distance


You can only use the distance method if the distance between pull_group0 and 
pull_group1 is constantly decreasing or increasing.  If you're moving through a 
channel, you should use the position method in conjunction with an appropriate 
pull_vec1.



pull_dim = N N Y
pull_start   = yes; define initial COM distance > 0

pull_ngroups   = 1
pull_group0= Protein


You probably need a better reference group, i.e. some subset of residues that 
forms the entrance or exit from the channel, but you may be able to get away 
with this reference group if you using a more appropriate pull_geometry, as 
suggested above.


-Justin


pull_group1= Ligand
;pull_rate1= -0.001; 0.01 nm per ps = 10 nm per ns
pull_k1= 1000   ; kJ mol^-1 nm^-2
<--

Can anyone help enlighten me as to what I am doing wrong?
Thanks,
-Shay

P.S.
Using gromacs 4.0.7.



--


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


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Re: [gmx-users] GTG to GAG with amber FF99SB force field

[yaolisha]

Hi Tsjerk,
   Thank you for the response. I am sorry for the bad email structure  
which was messed up when I copy it from microsoft word to my email  
editor.
   The error message from gromacs i think comes from the multiplicity  
of HA-CA-CB-OH dihedral. In amber ff99sb force field, this dihedral  
angle has a mixed multiplicity. It has a multiplicity of 3 for the  
rotation around CA-CB bond axis, and a mulitiplicity of 1 with energy  
minimium at HA-CA-CB-OH equal to 0 degree. To this kind of dihedral, I  
don't know how to build a mixed muliplicity dihedral angle potential.


Best,
Lishan


Hi Lishan,

Your mail would be a bit more readable with more structure...

Anyway, it says in the manual you can't do perturbation on the
multiplicity. That makes sense, because interpolation from 1 to 3

goes

through a whole series of rational numbers, but you can't have
non-integer periods... If you must, you first have to remove the
dihedral, i.e. bring the amplitude to 0, and then raise again to the
other function.

Cheers,

Tsjerk

On Mon, May 30, 2011 at 3:15 AM,   wrote:

Dear Gromacs users: I use gromacs.4-5-3 to calculate the free

energy changes

for the GTG to GAG alchemy process, where charge annihilation is

performed

first followed by soft core VDW calculation. When doing the soft

core VDW

calculation, I see this error message ?Fatal error: [ file

gtg_vdw.top, line

314 ]: Proper Dih. multiplicity can not be perturbed

1.00!=3.00?.

Line 314 has the following content ?17 16 18 24 9? The atoms with

VDW radius

and well depth changes include 20 CT 3 THR CG2 20 -0. 12.01 CTD

0.0

12.01 ; qtot 0.0439 21 HC 3 THR HG21 21 0. 1.008 HCD 0.0 1.008;

qtot

0.1081 22 HC 3 THR HG22 22 0. 1.008 HCD 0.0 1.008; qtot 0.1723

23 HC 3

THR HG23 23 0. 1.008 HCD 0.0 1.008; qtot 0.2365 24 OH 3 THR OG1

24

-0. 16 OHD 0.0 16 ; qtot -0.4396 25 HO 3 THR HG1 25 0.

1.008 HOD 0.0

1.008; qtot -0.0294 Atom types CTD, HCD, OHD, HOD are defined in a

separate

file and included in the topology file. My question is how to solve

this

problem and a related question is whether the overall setup is

correct.

Best, Lishan


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Re: [gmx-users] Pulling a ligand out of protein cavity

[Shay Teaching]

Thanks for you prompt reply - I'll try that and post back.
-SA

On Tue, May 31, 2011 at 4:46 PM, Justin A. Lemkul  wrote:

>
>
> Shay Teaching wrote:
>
>> Dear gromacs users,
>>
>> I am trying to pull a ligand out of a cavity of a membrane protein (along
>> the Z axis).
>> Problem is, that with every pull settings I have tried the ligand gets
>> "stuck" on the protein's center of mass. How can I make it go all the was to
>> the bulk water?
>> It always gets stuck on the COM. And I've tried using both umbrella and
>> constant force, so I'm getting the feeling that I'm missing something
>> trivial.
>>
>> Here's an example of one set of pull-parameters I tried:
>> --->
>> pull = constant_force
>> pull_geometry= distance
>>
>
> You can only use the distance method if the distance between pull_group0
> and pull_group1 is constantly decreasing or increasing.  If you're moving
> through a channel, you should use the position method in conjunction with an
> appropriate pull_vec1.
>
>
>  pull_dim = N N Y
>> pull_start   = yes; define initial COM distance > 0
>>
>> pull_ngroups   = 1
>> pull_group0= Protein
>>
>
> You probably need a better reference group, i.e. some subset of residues
> that forms the entrance or exit from the channel, but you may be able to get
> away with this reference group if you using a more appropriate
> pull_geometry, as suggested above.
>
> -Justin
>
>
>  pull_group1= Ligand
>> ;pull_rate1= -0.001; 0.01 nm per ps = 10 nm per ns
>> pull_k1= 1000   ; kJ mol^-1 nm^-2
>> <--
>>
>> Can anyone help enlighten me as to what I am doing wrong?
>> Thanks,
>> -Shay
>>
>> P.S.
>> Using gromacs 4.0.7.
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>
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[gmx-users] forgetten password

[Hyunjin Kim]

Hi,

I forgot my password to access the mailing list site.
What should I do to fix this?

Thanks.


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[gmx-users] number of molecules generated during pdb2gmx

[Hyunjin Kim]

Hi,

I included a small organic moelcule using separating .itp and .rtp files
in charmm36.
If I ran pdb2gmx to generate top file, it generated properly.
However, although I included 256 molecules, it still treated them as one
molecule as follows:


[ molecules ]
; Compound#mols
Orgainic 1

If I correct it manually, then it built the following error:
---
Program grompp, VERSION 4.5.4
Source code file: grompp.c, line: 523

Fatal error:
number of coordinates in coordinate file (thf.gro, 3328)
 does not match topology (thf.top, 851968)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

It looks 256 molucules are considered as one molecule. Can I treat them
each residue as one molecule as the water case?
I have searched for this on your web, but I can not find the proper way to
fix this.

Thanks for your help.


Hyunjin.




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Re: [gmx-users] forgetten password

[Justin A. Lemkul]

Hyunjin Kim wrote:

Hi,

I forgot my password to access the mailing list site.
What should I do to fix this?



You can get a password reminder at:

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

-Justin

--


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


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Re: [gmx-users] number of molecules generated during pdb2gmx

[Justin A. Lemkul]

Hyunjin Kim wrote:

Hi,

I included a small organic moelcule using separating .itp and .rtp files
in charmm36.
If I ran pdb2gmx to generate top file, it generated properly.
However, although I included 256 molecules, it still treated them as one
molecule as follows:


[ molecules ]
; Compound#mols
Orgainic 1

If I correct it manually, then it built the following error:
---
Program grompp, VERSION 4.5.4
Source code file: grompp.c, line: 523

Fatal error:
number of coordinates in coordinate file (thf.gro, 3328)
 does not match topology (thf.top, 851968)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

It looks 256 molucules are considered as one molecule. Can I treat them
each residue as one molecule as the water case?
I have searched for this on your web, but I can not find the proper way to
fix this.



If you have an .itp file already, running pdb2gmx is unnecessary.  Make a simple 
topology with a text editor, generically:


#include "forcefield.itp"
#include "molecule.itp"

[ system ]
my system

[ molecules ]
MOL 256

-Justin

--


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


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[gmx-users] Recommended way to run production using the same conditions as equilibration

[Andrew DeYoung]

Hi,

In molecular dynamics I have learned that there are three main phases:
energy minimization, equilibration (say, 2 ns in duration), and
production/dynamics (say, 3 ns in duration).  Suppose that I want my
production run to use the same conditions as equilibration.  What is the
best way to do this?

I can think of two conceptual ways to approach this:
(1) Do one long 5 ns run.  Then, when doing analysis, ignore the frames
corresponding to the initial 2 ns, using the -b option found in most of the
Gromacs trajectory analysis programs to consider only the final 3 ns.

(2) Do equilibration and production in separate runs.  This way, doing
analysis is perhaps more foolproof:  I don't need to worry about always
neglecting the initial 2 ns, and the initial time I consider is always,
conveniently, t = 0 ps.  

>From looking at various Gromacs tutorials, it seems that approach (2) is
recommended.  But now, even within approach (2), there are at least two
options.  One option is to feed the checkpoint file from equilibration into
the grompp part of production.  For example, 

EQUILIBRATION: 
[equilibration has been prepared using grompp]
mdrun -deffnm npt-eq -cpo npt-eq.cpt
PRODUCTION:
grompp -f npt-md.mdp -c npt-eq.gro -t npt-eq.cpt -p water.top -o npt-md.tpr
-po npt-mdout.mdp
mdrun -deffnm npt-md

where I have used the -cpo option in mdrun of equilibration and fed this
resulting checkpoint file to grompp of production, using -t.  Is this
correct?

Or, I could eliminate the grompp step of production (since my production run
uses the same parameters as in equilibration) and feed the checkpoint file
directly to mdrun of production:

EQUILIBRATION: 
mdrun -deffnm npt-eq -cpo npt-eq.cpt
PRODUCTION:
mdrun -deffnm npt-md -cpi npt-eq.cpt

where I have used -cpi in mdrun of production to feed in the checkpoint
file.  (In contrast to grompp, there is no -t option in mdrun.)  Is this
correct?  My concern here is that, in the entry for mdrun in the Gromacs
manual, it says that for the option -cpi, "By default the output will be
appending to the existing output files."  But since I have specified output
file names using -deffnm npt-md, will the trajectory indeed be written to
npt-md files, or will it be appended to the npt-eq files, from which the
checkpoint file originated?  

If both of these options are correct, which is preferable?

Thank you very much.

Andrew DeYoung
Carnegie Mellon University

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Re: [gmx-users] Recommended way to run production using the same conditions as equilibration

[Justin A. Lemkul]

Andrew DeYoung wrote:

Hi,

In molecular dynamics I have learned that there are three main phases:
energy minimization, equilibration (say, 2 ns in duration), and
production/dynamics (say, 3 ns in duration).  Suppose that I want my
production run to use the same conditions as equilibration.  What is the
best way to do this?

I can think of two conceptual ways to approach this:
(1) Do one long 5 ns run.  Then, when doing analysis, ignore the frames
corresponding to the initial 2 ns, using the -b option found in most of the
Gromacs trajectory analysis programs to consider only the final 3 ns.

(2) Do equilibration and production in separate runs.  This way, doing
analysis is perhaps more foolproof:  I don't need to worry about always
neglecting the initial 2 ns, and the initial time I consider is always,
conveniently, t = 0 ps.  



If the conditions for equilibration and production are identical, then either 
approach works.  Most workflows separate equilibration and production due to the 
use of restraints, different T or P coupling schemes, etc.  But if all you're 
doing is extending the same ensemble, then the choice here between 1 and 2 makes 
no difference.



From looking at various Gromacs tutorials, it seems that approach (2) is

recommended.  But now, even within approach (2), there are at least two
options.  One option is to feed the checkpoint file from equilibration into
the grompp part of production.  For example, 

EQUILIBRATION: 
[equilibration has been prepared using grompp]

mdrun -deffnm npt-eq -cpo npt-eq.cpt
PRODUCTION:
grompp -f npt-md.mdp -c npt-eq.gro -t npt-eq.cpt -p water.top -o npt-md.tpr
-po npt-mdout.mdp
mdrun -deffnm npt-md

where I have used the -cpo option in mdrun of equilibration and fed this
resulting checkpoint file to grompp of production, using -t.  Is this
correct?



Yes.  See, for instance:

http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Changing_.mdp_file_options.

and

http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Exact_vs_binary_identical_continuation


Or, I could eliminate the grompp step of production (since my production run
uses the same parameters as in equilibration) and feed the checkpoint file
directly to mdrun of production:

EQUILIBRATION: 
mdrun -deffnm npt-eq -cpo npt-eq.cpt

PRODUCTION:
mdrun -deffnm npt-md -cpi npt-eq.cpt

where I have used -cpi in mdrun of production to feed in the checkpoint
file.  (In contrast to grompp, there is no -t option in mdrun.)  Is this
correct?  My concern here is that, in the entry for mdrun in the Gromacs
manual, it says that for the option -cpi, "By default the output will be
appending to the existing output files."  But since I have specified output
file names using -deffnm npt-md, will the trajectory indeed be written to
npt-md files, or will it be appended to the npt-eq files, from which the
checkpoint file originated?  



They will be written to npt-md.xtc/log/etc.  When supplying -deffnm, the use of 
any other flag for input or output overrides the name in -deffnm, so you can use 
the previous checkpoint file, even if it has a different name.  You can also get 
around the appending problem by using -noappend.



If both of these options are correct, which is preferable?



Whichever one makes sense to you.  I tend to go with the grompp/mdrun combo. 
That offers you the ability to change .mdp options for I/O purposes, remove 
restraints, etc.


-Justin

--


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


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[gmx-users] unit of ekrot and ektrans

[Swarnendu Tripathi]

Hello everybody,

I have a question ragarding the unit of translational and rotational energy.
I am using the gromacs-4.0.7 version and it gives these units in the
ektran.xvg and ekrot.xvg as "kJ mol\S-1\N" after I used the command" g_traj
-f traj.trr -s topol.trr -ekt ektrans.xvg -ekr ekrot.xvg.
I was expecting the unit of these quantitites in the unit of energy "kJ/mol"
in gromacs. Any suggestions to convert these to right unit?

Thank you,

-Swarnendu
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Re: [gmx-users] unit of ekrot and ektrans

[Dommert Florian]

On Tue, 2011-05-31 at 15:31 -0400, Swarnendu Tripathi wrote:
> Hello everybody,
> 
> I have a question ragarding the unit of translational and rotational
> energy. I am using the gromacs-4.0.7 version and it gives these units
> in the ektran.xvg and ekrot.xvg as "kJ mol\S-1\N" after I used the
> command" g_traj -f traj.trr -s topol.trr -ekt ektrans.xvg -ekr
> ekrot.xvg.
> I was expecting the unit of these quantitites in the unit of energy
> "kJ/mol" in gromacs. Any suggestions to convert these to right unit?
> 

\S-1\N is just a xmgrace command for a superscript. Plot ektrans.xvg and
ekrot.xvg with xmgrace and check which unit appears at the axes labels.

/Flo

> Thank you,
> 
> -Swarnendu 
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-- 
Florian Dommert
Dipl. - Phys.

Institute for Computational Physics
University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

EMail: domm...@icp.uni-stuttgart.de
Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert

Tel.: +49 - (0)711 - 68563613
Fax.: +49 - (0)711 - 68563658


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Re: [gmx-users] unit of ekrot and ektrans

[Swarnendu Tripathi]

Thanks. I got it.

I was using gnuplot before.

-Swarnendu

On Tue, May 31, 2011 at 3:45 PM, Dommert Florian <
domm...@icp.uni-stuttgart.de> wrote:

> On Tue, 2011-05-31 at 15:31 -0400, Swarnendu Tripathi wrote:
> > Hello everybody,
> >
> > I have a question ragarding the unit of translational and rotational
> > energy. I am using the gromacs-4.0.7 version and it gives these units
> > in the ektran.xvg and ekrot.xvg as "kJ mol\S-1\N" after I used the
> > command" g_traj -f traj.trr -s topol.trr -ekt ektrans.xvg -ekr
> > ekrot.xvg.
> > I was expecting the unit of these quantitites in the unit of energy
> > "kJ/mol" in gromacs. Any suggestions to convert these to right unit?
> >
>
> \S-1\N is just a xmgrace command for a superscript. Plot ektrans.xvg and
> ekrot.xvg with xmgrace and check which unit appears at the axes labels.
>
> /Flo
>
> > Thank you,
> >
> > -Swarnendu
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> > www interface or send it to gmx-users-requ...@gromacs.org.
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
> --
> Florian Dommert
> Dipl. - Phys.
>
> Institute for Computational Physics
> University Stuttgart
>
> Pfaffenwaldring 27
> 70569 Stuttgart
>
> EMail: domm...@icp.uni-stuttgart.de
> Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
>
> Tel.: +49 - (0)711 - 68563613
> Fax.: +49 - (0)711 - 68563658
>
> --
> gmx-users mailing listgmx-users@gromacs.org
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[gmx-users] Dreiding force field in Gromacs ?

[Sanku M]

Hi,

  I was wondering whether Gromacs can be used to perform simulation using 
Dreiding force field developed by Goddard and co-workers ( J.Phys.Chem. 
,94,8897,1990). If someone can share some experience in porting this force 
field 
in gromacs, that will be very helpful.

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Re: [gmx-users] implicit solvent LINCS errors

[Michael Daily]

The following mdp file produces a successful dynamics run out to 100K 
steps / 200 ps.  What I discovered is this:


Using the md integrator, it is necessary to turn off pressure coupling.  
However, pressure coupling works with sd (Langevin) integrator.


Mike

---

; title and include files
title= 1EX6-S35P_md1
;cpp  = cpp
;include  = 
-I/home/yoo2/myusr/gromacs-3.3.3/share/gromacs/top/ -I./

define   =
; integrator and input/output setting up
;integrator   = md
integrator = sd

nsteps   = 100 ; 2 ns
dt   = 0.002
nstxout  = 5000
nstvout  = 5000
nstenergy= 500
nstxtcout= 500
nstlog   = 500
xtc_grps = System
energygrps   = System
comm_mode= Linear

;implicit solvent
implicit_solvent = GBSA
gb_algorithm = OBC
gb_saltconc = 0.15 ; note - this feature is not functional yet
rgbradii = 2.0 ; need larger cut-off than atomistic models

; neighbor searching and vdw/pme setting up
nstlist  = 10
ns_type  = grid
pbc  = xyz
;rlist= 1.4
rlist= 2.0

;coulombtype  = pme
coulombtype  = Cut-Off
fourierspacing   = 0.1
pme_order= 6
;rcoulomb = 1.4
rcoulomb = 2.0

;vdwtype  = switch
vdwtype  = Cut-Off
rvdw_switch  = 1.0
;rvdw = 1.2
rvdw = 2.0

; cpt control
tcoupl   = v-rescale
tc-grps  = System
tau_t= 0.4
ref_t= 300.0
Pcoupl   = parrinello-rahman
pcoupltype   = isotropic
tau_p= 1.0
compressibility  = 4.5e-5
ref_p= 1.0

; velocity & temperature control
gen_vel  = yes
gen_temp = 300.0
annealing= no
constraints  = hbonds
constraint_algorithm = lincs
morse= no

---


On 5/30/11 8:45 PM, Michael D. Daily wrote:
Thanks for the recommendations everyone.  I tried all of the mdp 
changes recommended by Justin (increase rlist, rvdw, etc to 2.0; 
change T-coupling to v-scale, and eliminate P-coupling).  When I 
increased the distance cutoffs, it ran about 30 ps then crashed 
instead of crashing immediately.  Only when I also turned off 
P-coupling did it keep running long-term (now it's up to 500K+ steps / 
1 ns), so apparently the problem was a lack of control of system 
volume.  Reducing the timestep from 2 fs to 1fs did not work by itself 
and was not necessary ultimately to get it to run.


Josh, thanks for the physical explanation of why the protein might 
explode.  My starting structure was a minimized xtal structure so I 
wouldn't call it "extended."  I'll try again with 4.5.4 before I scale 
this up any further.


Mike


On 5/30/2011 8:02 PM, Mark Abraham wrote:

On 31/05/2011 10:54 AM, Justin A. Lemkul wrote:



Joshua L. Phillips wrote:
I've found that I often get LINCS warnings like this when starting 
from

highly extended conformations when using implicit solvent. The GBSA
surface tension combined with the lack of viscosity (due to the 
absence
of explicit water) allows the protein to change conformation much 
faster

than LINCS likes by default.

Normally, I just run a short vacuum simulation (keep the same settings
as Justin suggested but set GBSA = No) to let the system relax a 
little

more before starting a GBSA run (EM is often just not enough). Usually
only about 50ps. Also, doing this with position restraints can help 
slow
down the collapse, and usually results in just enough collapse that 
the

following GBSA run will satisfy the default LINCS settings.

Another option might be to run a short simulation with GBSA turned on,
but using Langevin dynamics to include some additional friction that
should slow down the initial collapse.



That's generally a good idea.  We often use the sd integrator when 
doing GBSA calculations.



Also, you could fudge with the environment variables associated with
LINCS, but this seems a little dangerous compared to the above two
suggestions.



I wouldn't say "a little dangerous," I'd say "very dangerous" :)  If 
the constraints are failing, it's not necessarily (or usually) their 
fault.  The system is unstable, and trying to just override this 
will give you a trajectory, but you should be concerned that this 
trajectory is being ruled by spurious forces.



I would be interested in peoples' opinions and suggestions on how to
handle this issue as it is quite common when starting from highly
extended structures using GBSA. Some proteins are more susceptible 
than

others...



Reducing the timestep is a good option.  If the dynamics are 
occurring so fast tha

Re: [gmx-users] implicit solvent LINCS errors

[Joshua L. Phillips]

Thanks for the suggestions. I can see how a smaller dt would probably be
the most general approach to use as it should work with just about any
reasonable combination of settings.

-- Josh

On Tue, 2011-05-31 at 11:02 +1000, Mark Abraham wrote:
> On 31/05/2011 10:54 AM, Justin A. Lemkul wrote:
> >
> >
> > Joshua L. Phillips wrote:
> >> I've found that I often get LINCS warnings like this when starting from
> >> highly extended conformations when using implicit solvent. The GBSA
> >> surface tension combined with the lack of viscosity (due to the absence
> >> of explicit water) allows the protein to change conformation much faster
> >> than LINCS likes by default.
> >>
> >> Normally, I just run a short vacuum simulation (keep the same settings
> >> as Justin suggested but set GBSA = No) to let the system relax a little
> >> more before starting a GBSA run (EM is often just not enough). Usually
> >> only about 50ps. Also, doing this with position restraints can help slow
> >> down the collapse, and usually results in just enough collapse that the
> >> following GBSA run will satisfy the default LINCS settings.
> >>
> >> Another option might be to run a short simulation with GBSA turned on,
> >> but using Langevin dynamics to include some additional friction that
> >> should slow down the initial collapse.
> >>
> >
> > That's generally a good idea.  We often use the sd integrator when 
> > doing GBSA calculations.
> >
> >> Also, you could fudge with the environment variables associated with
> >> LINCS, but this seems a little dangerous compared to the above two
> >> suggestions.
> >>
> >
> > I wouldn't say "a little dangerous," I'd say "very dangerous" :)  If 
> > the constraints are failing, it's not necessarily (or usually) their 
> > fault.  The system is unstable, and trying to just override this will 
> > give you a trajectory, but you should be concerned that this 
> > trajectory is being ruled by spurious forces.
> >
> >> I would be interested in peoples' opinions and suggestions on how to
> >> handle this issue as it is quite common when starting from highly
> >> extended structures using GBSA. Some proteins are more susceptible than
> >> others...
> >>
> >
> > Reducing the timestep is a good option.  If the dynamics are occurring 
> > so fast that the constraints can't keep up, reducing dt can help.
> 
> Agreed. Even using all-vs-all kernels, I've observed similar symptoms as 
> the OP lately with excessive rotation of v-site terminal methyl groups. 
> I can generate stable trajectories by starting my equilibration with 0.5 
> fs timesteps, and switching later.
> 
> Mark
> 
> >
> > -Justin
> >
> >> I also tend to find that version 4.5.4 is much more stable than even
> >> 4.5.3 for implicit solvent simulations.
> >>
> >> -- Josh
> >>
> >> On Mon, 2011-05-30 at 18:06 -0500, Michael D. Daily wrote:
> >>> Thanks Justin, this is very helpful.  I'll attempt these fixes 
> >>> tomorrow.
> >>>
> >>> Mike
> >>>
> >>> On 5/30/2011 5:50 PM, Justin A. Lemkul wrote:
> 
>  Michael D. Daily wrote:
> > Hi all,
> >
> > I'm trying to run implicit solvent calculations in gromacs 4.5 
> > with the charmm forcefield.  I am able to minimize successfully 
> > and compile for 
>  When troubleshooting, it is always advisable to try the latest 
>  version (4.5.4) to see if the problem is reproducible.  If a 
>  pertinent bug has been fixed, there's no use troubleshooting the 
>  broken version.
> 
> > mdrun, but soon after starting, mdrun complains about excessive 
> > rotation in LINCS (see the error printed below that).  I also 
> > include my mdp file at the bottom.  Can anyone advise me as to the 
> > possible cause of such errors, as it is difficult to diagnose 
> > given that grompp worked fine.
> >
>  For reference:
> 
>  http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
>   
> 
> 
>  If grompp worked, that just means your coordinate and topology 
>  matched and there were no internal conflicts within the .mdp file.  
>  It is no guarantee that the resulting simulation will actually 
>  work, unfortunately.
> 
> > --- lincs error ---
> >
> > Step 1, time 0.002 (ps)  LINCS WARNING
>  Typically an instant LINCS failure indicates insufficient 
>  minimization.  You said you minimized successfully, but what does 
>  this mean?  What values did you achieve for Fmax and Epot?
> 
> > relative constraint deviation after LINCS:
> > rms 0.000780, max 0.020692 (between atoms 880 and 881)
> > bonds that rotated more than 30 degrees:
> >  atom 1 atom 2  angle  previous, current, constraint length
> > 606607   36.71.0527   0.1080  0.1080
> > 614615   35.60.8972   0.1125  0.
> > 614616   75.30.1054   0.1121  0.
> > 880881   58.00.1068   0.1134  0.