[gmx-users] how can I get the .top file??

[Kiwoong Kim]

Dear members of gromacs



Let you know that I'm a beginner of Gromacs.



I am trying to simulate the diffusion problem on some zeolite structure. 
(especially ZSM-22)



>From the manual, I knew that the three files are required to get the .tpr 
>input file.

I got the .pdb file of my concerned zeolite (zsm-22) but it is  impossible to 
get .top file by using the pdb2gmx because the .pdb file  is just coornate file.



Therefore, my question is how can I get the .top file??

I already tried the g_x2top -f zeo.pdb -o out.top -ff oplsaa 

but errors were shown 



"Can not find forcefield for atom "



please let me know how to do it



Thx.






Kiwoong, Kim.
No. 409/Ricci Hall/Dept. of Chemical & Biomolecular Engineering/
Sogang University/Sinsoo-Dong/Mapo-Gu/Seoul 121-742/ Korea
(office) +82-2-705-8477
(CP) +82-10-8714-2208
(fax) +82-2-3272-0319
(E-mail) ki...@sogang.ac.kr

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[gmx-users] About implicit wall...

[Kiwoong Kim]

Dear members of gromacs



Hi, I'm a beginner of gromacs.



I want to simulate the diffusion problem when the particle diffuses into the 
cylinder pore which has the implicit wall (with some atoms).



The diffusing particle has to be updated during the integration step but the 
particle on the implicit wall must not be updated.

Hence, I don't know how I can do this kind of thing. 

Is there any function to handle the implicit wall that must be rigid and not to 
be updated ? 



Thx. 







Kiwoong, Kim.
No. 409/Ricci Hall/Dept. of Chemical & Biomolecular Engineering/
Sogang University/Sinsoo-Dong/Mapo-Gu/Seoul 121-742/ Korea
(office) +82-2-705-8477
(CP) +82-10-8714-2208
(fax) +82-2-3272-0319
(E-mail) ki...@sogang.ac.kr

<>-- 
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Re: [gmx-users] Normal Mode Analysis

[James Starlight]

I've found that in general ussage of cutt-offs beetwen 0.8-1.2 nm might
provide good results.

But now I have some problems with minimization of my initial structure

Firstly, I've performed steep minimization ( emtool=1000,  emstep  =
0.01 ) and than CG minimization (emtool=1,  emstep  = 0.001) but as the
result I've obtain that my struucture didnt minimize properly.
Is there any different strategies for the minimization for the ANM ?

In addition I'd like to know about conditions of such normal mode
simulations. Does this procedure require in the PBC ? ( I've performed all
steps including energy minimization in vacuu)


James

2011/10/25 Mark Abraham 

>  On 25/10/2011 3:30 AM, James Starlight wrote:
>
> I understand this but I've not been able found such information. I dont
> need in the most accurately  parametries for all cutt-offs of my system but
> I want to gain inside into the basic cutt- offs worked with the Normal mode
> analysis.
>
>
> The cut-offs are particular to the force field, not the manner in which the
> force field is used (EM vs MD vs whatever). There are literature references
> in the GROMACS manual, and also in the published work that you have been
> reading because it has objectives similar to yours. (hint, hint)
>
>
> E.g I've found that PME is not worked here.
>
>
> PME does work here. Last time you were apparently mis-matching files...
>
>
> So I must to constrain my system with simplest cuttoffs. Could you provide
> me with the simple example e.g cutt of for interaction beetwen C-alpha atoms
> only etc?
>
>
> You can't do that, and shouldn't even if you could.
>
> Mark
>
>
>
> James
>
>
>
>>  These are particular to the force field involved, not the software.
>> Please consult the appropriate literature, and see what others have used for
>> similar work.
>>
>>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
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[gmx-users] orientation restraints in binding free energy calculation

[Chunxia Gao]

Dear gmx-users:

I read some research articles of calculating the binding free energy, still I 
can not figure out how to get the orientational parameters. 

If I have the crystal structure of ligand bound protein, so I need to choose 
three anchor atoms in the protein and three anchor atoms in the ligand 
respectively? 

How to define these three atoms in ligand and protein, can I choose them 
arbitrarily? and then define one distance, two angles and three torsions?

After I have the reference orientation, what should I do?

Millions of thanks for answering my questions.

Regards
Chunxia

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Re: [gmx-users] Gromacs inquiries

[Justin A. Lemkul]

cuong nguyen wrote:

Dear Mark,

I used to put ten molecules of hexanol in a box 5 5 1 with the 
instruction "genbox -ci hexanol.gro -nmol 10 -box 5 5 1 -o layer.gro -p 
hexanol.top". However, now I want to fill up the box 4 4 4 with hexanol 
molecules.
If I change the number 10 in the instruction to 1000 or 1, it will 
run well but I do not know if this box is full.

Please help me to change this instruction.



You can find out whether your box is full in several ways.  The first, and most 
direct, method is to open the new coordinate file in the visualization software 
of your choice and see if the molecules fill the box.  If there are voids, then 
add more.  The other option is to set a very high value of molecules to be 
added, and genbox will add until it cannot any more.  The latter method may be 
somewhat time-consuming, so choose a sensible value, even if it is higher than 
what you may want (e.g., try 5000 instead of 500).


-Justin


Thanks a lot.

Regards,

Cuong

2011/10/26 Mark Abraham >


On 26/10/2011 1:46 PM, cuong nguyen wrote:

Dear,

Thanks a lot for useful software. I am trying to generate a box
(4 4 4) with full hexanol molecules inside. I have used the
instruction "genbox -ci hexanol.GRO -box 4 4 4 -o layer.gro -p
hexanol.top", however it has not been successful.


Unfortunately we can't help if we don't know what is in your -ci box
(also, it's probably best not to use capitalized filename
extensions), or why you think the procedure was not successful.
Please consider the advice here http://www.gromacs.org/Support__.

Mark
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--
Nguyen Van Cuong
PhD student - Curtin University of Technology
Mobile: (+61) 452213981
 



--


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] how can I get the .top file??

[Justin A. Lemkul]

Kiwoong Kim wrote:

Dear members of gromacs

Let you know that I'm a beginner of Gromacs.

I am trying to simulate the diffusion problem on some zeolite structure. 
(especially ZSM-22)


 >From the manual, I knew that the three files are required to get the 
.tpr input file.
I got the .pdb file of my concerned zeolite (zsm-22) but it is 
impossible to get .top file by using the pdb2gmx because the .pdb file 
is just coornate file.


Therefore, my question is how can I get the .top file??
I already tried the g_x2top -f zeo.pdb -o out.top -ff oplsaa
but errors were shown

"Can not find forcefield for atom "

please let me know how to do it



The force fields in Gromacs are most directly suited to biomolecular systems, so 
their applicability for other materials may be limited.  In any case, the .n2t 
file read by g_x2top is obviously not suited for what you want to do.  You can 
add parameters in the .n2t file, per the following information:


http://www.gromacs.org/Documentation/File_Formats/.n2t_File

Depending on the complexity of the structure, you may or may not be successful.

-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] difference between restrained and constrained

[shahab shariati]

Dear gromacs users

I want to know what is difference between restrained EM and restrained EM or
between constrained MD and constrained MD.

any help will highly appreciated.
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Re: [gmx-users] difference between restrained and constrained

[Justin A. Lemkul]

shahab shariati wrote:

Dear gromacs users

I want to know what is difference between restrained EM and restrained EM or
between constrained MD and constrained MD.

any help will highly appreciated.


http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints

-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] Normal Mode Analysis

[Mark Abraham]

On 26/10/2011 7:54 PM, James Starlight wrote:
I've found that in general ussage of cutt-offs beetwen 0.8-1.2 nm 
might provide good results.


But now I have some problems with minimization of my initial structure

Firstly, I've performed steep minimization ( emtool=1000,  emstep  
= 0.01 ) and than CG minimization (emtool=1,  emstep  = 0.001) but 
as the result I've obtain that my struucture didnt minimize properly.

Is there any different strategies for the minimization for the ANM ?


We don't know the sense in which it "didn't minimize properly," so 
there's not much point us guessing.




In addition I'd like to know about conditions of such normal mode 
simulations. Does this procedure require in the PBC ? ( I've performed 
all steps including energy minimization in vacuu)


Whether not PBC represents useful boundary conditions depends on what 
conditions you are trying to model - whether possible periodicity 
artefacts or boundary artefacts are more likely to affect your results.


It does sound like you would benefit from reading some good textbook 
material on molecular simulation :)


Mark




James

2011/10/25 Mark Abraham >


On 25/10/2011 3:30 AM, James Starlight wrote:

I understand this but I've not been able found such information.
I dont need in the most accurately  parametries for all cutt-offs
of my system but I want to gain inside into the basic cutt- offs
worked with the Normal mode analysis.


The cut-offs are particular to the force field, not the manner in
which the force field is used (EM vs MD vs whatever). There are
literature references in the GROMACS manual, and also in the
published work that you have been reading because it has
objectives similar to yours. (hint, hint)



E.g I've found that PME is not worked here. 


PME does work here. Last time you were apparently mis-matching
files...



So I must to constrain my system with simplest cuttoffs. Could
you provide me with the simple example e.g cutt of for
interaction beetwen C-alpha atoms only etc?


You can't do that, and shouldn't even if you could.

Mark




James



These are particular to the force field involved, not the
software. Please consult the appropriate literature, and see
what others have used for similar work.




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Re: [gmx-users] About implicit wall...

[Mark Abraham]

On 26/10/2011 6:47 PM, Kiwoong Kim wrote:

Dear members of gromacs

Hi, I'm a beginner of gromacs.

I want to simulate the diffusion problem when the particle diffuses 
into the cylinder pore which has the implicit wall (with some atoms).


I don't understand the sense in which it could be an implicit wall, and 
be comprised of atoms...


The diffusing particle has to be updated during the integration step 
but the particle on the implicit wall must not be updated.

Hence, I don't know how I can do this kind of thing.
Is there any function to handle the implicit wall that must be rigid 
and not to be updated ?


GROMACS can freeze atoms in their initial position, or use positional 
restraints to allow them some freedom - check out the manual.


Mark



Thx.





	Kiwoong, Kim. No. 409/Ricci Hall/Dept. of Chemical & Biomolecular 
Engineering/ Sogang University/Sinsoo-Dong/Mapo-Gu/Seoul 121-742/ 
Korea (office) +82-2-705-8477 (CP) +82-10-8714-2208 (fax) 
+82-2-3272-0319 (E-mail) ki...@sogang.ac.kr







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Re: [gmx-users] Normal Mode Analysis

[James Starlight]

Mark hello,

2011/10/26 Mark Abraham 

>
>  We don't know the sense in which it "didn't minimize properly," so there's
> not much point us guessing.
>
>
> The output value for Epot was -2.0 after steep minimization and -2.5 after
CG. Also as the consequense after both energy minimization runs the system
told me that the system have not been minimized completely or the step size
was too short ( I've changd the step size from 0.01 in both directions as
well as EMtool from 1000 to 0.1 but that results were unchanged )

Also during diagonalization of the Hessian the system told me that lowest
six modes were not zero's in their frequensies. It's also could indicate
that I've analyzed not properly minimized structure



By the way I've heard that there is possible way to extract Normal Modes
from MD trajectories directly. E.g I've simulated my protein and obtain trr
file and want to extract from that trajectory all eigenvectors ( modes)
separately. Might it be realized in Gromacs and via what program should I do
it?

James
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Re: [gmx-users] Gromacs inquiries

[Mark Abraham]

On 26/10/2011 5:18 PM, cuong nguyen wrote:

Dear Mark,

I used to put ten molecules of hexanol in a box 5 5 1 with the 
instruction "genbox -ci hexanol.gro -nmol 10 -box 5 5 1 -o layer.gro 
-p hexanol.top". However, now I want to fill up the box 4 4 4 with 
hexanol molecules.
If I change the number 10 in the instruction to 1000 or 1, it will 
run well but I do not know if this box is full.

Please help me to change this instruction.


It probably can't be full. genbox -ci does not generate a close packing, 
so the first part of your procedure isn't useful, as you would have 
learned from reading genbox -h. See 
http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation for a 
sound workflow.


Mark



Thanks a lot.

Regards,

Cuong

2011/10/26 Mark Abraham >


On 26/10/2011 1:46 PM, cuong nguyen wrote:

Dear,

Thanks a lot for useful software. I am trying to generate a
box (4 4 4) with full hexanol molecules inside. I have used
the instruction "genbox -ci hexanol.GRO -box 4 4 4 -o
layer.gro -p hexanol.top", however it has not been successful.


Unfortunately we can't help if we don't know what is in your -ci
box (also, it's probably best not to use capitalized filename
extensions), or why you think the procedure was not successful.
Please consider the advice here http://www.gromacs.org/Support.

Mark
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--
Nguyen Van Cuong
PhD student - Curtin University of Technology
Mobile: (+61) 452213981





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Re: [gmx-users] Normal Mode Analysis

[Mark Abraham]

On 26/10/2011 11:04 PM, James Starlight wrote:

Mark hello,

2011/10/26 Mark Abraham >



We don't know the sense in which it "didn't minimize properly," so
there's not much point us guessing.


The output value for Epot was -2.0 after steep minimization and -2.5 
after CG. Also as the consequense after both energy minimization runs 
the system told me that the system have not been minimized completely 
or the step size was too short ( I've changd the step size from 0.01 
in both directions as well as EMtool from 1000 to 0.1 but that results 
were unchanged )


Also during diagonalization of the Hessian the system told me that 
lowest six modes were not zero's in their frequensies. It's also could 
indicate that I've analyzed not properly minimized structure


Or that your starting structure is not close enough to a sensible 
minimum for a local gradient-based optimizer to do the job. Look at the 
atoms with the large forces and see what you can learn.


By the way I've heard that there is possible way to extract Normal 
Modes from MD trajectories directly. E.g I've simulated my protein and 
obtain trr file and want to extract from that trajectory all 
eigenvectors ( modes) separately. Might it be realized in Gromacs and 
via what program should I do it?


Sorry, we can't make guesses based on things you can't remember details 
about. Maybe you want to consider Essential Dynamics.


Mark
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[gmx-users] position restrained minimization on the one part of a system

[Atila Petrosian]

Dear all

my system contains protein + ligand+ water molecules.

protein + ligand = solute

water molecules = solvent

I want to do minimization energy in 3 steps :

step 1) on protein only

step 2) on all solute (protein + ligand)

step 3) on all system

should I use position restrained minimization energy and use define =
-DPOSRES in mdp file? if so, what is my mdp file for each of 3 steps?


# step 1:

??? please complete this section.

# step 2:

define  = -DPOSRES_WATER

# step 3:

I don't use -DPOSRES.


In posre.itp file, what is suitable value for force constant?


best regards
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Re: [gmx-users] position restrained minimization on the one part of a system

[Mark Abraham]

On 26/10/2011 11:24 PM, Atila Petrosian wrote:

Dear all

my system contains protein + ligand+ water molecules.

protein + ligand = solute

water molecules = solvent

I want to do minimization energy in 3 steps :

step 1) on protein only

step 2) on all solute (protein + ligand)

step 3) on all system

should I use position restrained minimization energy and use define =  
-DPOSRES in mdp file?


You will need some way to change which [moleculetypes] have position 
restraints during which step. The details will vary with how you've 
constructed your overall topology. IIRC, if pdb2gmx is able to treat the 
whole system in one pass, then it will write such position restraint 
files automatically. Otherwise, you will have to understand how the 
#include mechanism works and how to trigger it with define = -Dx. By 
design, it is possible to use the same .top for all three steps.



if so, what is my mdp file for each of 3 steps?


Each will use a different "define" line - check out some tutorials for 
example ideas.





# step 1:

??? please complete this section.

# step 2:

define  = -DPOSRES_WATER

# step 3:

I don't use -DPOSRES.


In posre.itp file, what is suitable value for force constant?


Whatever leads to successful equilibration. The default used by pdb2gmx 
is 1000 (whatever the units are).


Mark
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Re: [gmx-users] Normal Mode Analysis

[James Starlight]

Mark,

2011/10/26 Mark Abraham 

>
>  Or that your starting structure is not close enough to a sensible minimum
> for a local gradient-based optimizer to do the job. Look at the atoms with
> the large forces and see what you can learn.
>
So for that purpose I've done steep minimization first and only that based
on that minimized structure I did CG minimization. I changed the emtool (
from 100 to 1000) as well as step size but my structure always have not been
prorely minimized ( based on the system output ). Also I've found that there
is third L-BFGS
algorithm for
minimization. In what cases this minimization could be
helpfull?



> Sorry, we can't make guesses based on things you can't remember details
> about. Maybe you want to consider Essential Dynamics.
>

As I know the Essential dynamics is the type of the PC analysis ( in this
case the ensemble of the analysed structures is replaced by the ensemble of
the MD snapshots ). But I've heard that there is possible ways to extract
normal modes indirectly from the output trajectories.


James
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Re: [gmx-users] Normal Mode Analysis

[Justin A. Lemkul]

James Starlight wrote:

Mark,

2011/10/26 Mark Abraham >



Or that your starting structure is not close enough to a sensible
minimum for a local gradient-based optimizer to do the job. Look at
the atoms with the large forces and see what you can learn.

So for that purpose I've done steep minimization first and only that 
based on that minimized structure I did CG minimization. I changed the 
emtool ( from 100 to 1000) as well as step size but my structure always 
have not been prorely minimized ( based on the system output ). Also 
I've found that there is third L-BFGS 
 algorithm for 
minimization. In what cases this minimization could be helpfull?




You should probably be using it.

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

Note that increasing emtol from 100 to 1000 actually makes your results worse, 
since mdrun will stop when the maximum force is below 1000 kJ/mol-nm, which is 
orders of magnitude too high for NMA.


-Justin




Sorry, we can't make guesses based on things you can't remember
details about. Maybe you want to consider Essential Dynamics.


As I know the Essential dynamics is the type of the PC analysis ( in 
this case the ensemble of the analysed structures is replaced by the 
ensemble of the MD snapshots ). But I've heard that there is possible 
ways to extract normal modes indirectly from the output trajectories.



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


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[gmx-users] position restrained minimization on the one part of a system

[Atila Petrosian]

Dear Mark

thanks for your reply

you said "if pdb2gmx is able to treat the whole system in one pass, then it
will write such position restraint
files automatically"

in my system, what pdb2gmx includes are in below:

; Include forcefield parameters
#include "amber03.ff/forcefield.itp"

; Include chain topologies
#include "complex_Protein_chain_A.itp"
#include "complex_DNA_chain_B.itp"

; Include Position restraint file
#ifdef POSRES
#include "posre_Protein_chain_A.itp"

; Include Position restraint file
#ifdef POSRES
#include "posre_Protein_chain_B.itp"

; Include water topology
#include "amber03.ff/tip3p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

; Include topology for ions
#include "amber03.ff/ions.itp"

[ system ]
; Name
complex

[ molecules ]
; Compound#mols
Protein_chain_A 1
DNA_chain_B 1
SOL3500


unfortunately, I don't know about step 1.

please guide me about that.
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[gmx-users] position restrained minimization on the one part of a system

[Atila Petrosian]

 I want to use define  = -DPOSRES_Protein_chain_A for step 1.

 is it true?
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Re: [gmx-users] Normal Mode Analysis

[Tsjerk Wassenaar]

Hi James,

Regarding PCA and NMA congruency, they are different things, unless
the energy landscape consists of a single harmonic potential well. The
principal components and the normal modes will usually correlate quite
well, but if the simulation is sampling different energy minima, there
may be quite a difference. You can easily work that out graphically
for a two dimensional energy landscape :)

Cheers,

Tsjerk

On Wed, Oct 26, 2011 at 2:57 PM, Justin A. Lemkul  wrote:
>
>
> James Starlight wrote:
>>
>> Mark,
>>
>> 2011/10/26 Mark Abraham > >
>>
>>
>>    Or that your starting structure is not close enough to a sensible
>>    minimum for a local gradient-based optimizer to do the job. Look at
>>    the atoms with the large forces and see what you can learn.
>>
>> So for that purpose I've done steep minimization first and only that based
>> on that minimized structure I did CG minimization. I changed the emtool (
>> from 100 to 1000) as well as step size but my structure always have not been
>> prorely minimized ( based on the system output ). Also I've found that there
>> is third L-BFGS 
>> algorithm for minimization. In what cases this minimization could be
>> helpfull?
>>
>
> You should probably be using it.
>
> http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis
>
> Note that increasing emtol from 100 to 1000 actually makes your results
> worse, since mdrun will stop when the maximum force is below 1000 kJ/mol-nm,
> which is orders of magnitude too high for NMA.
>
> -Justin
>
>>
>>
>>    Sorry, we can't make guesses based on things you can't remember
>>    details about. Maybe you want to consider Essential Dynamics.
>>
>>
>> As I know the Essential dynamics is the type of the PC analysis ( in this
>> case the ensemble of the analysed structures is replaced by the ensemble of
>> the MD snapshots ). But I've heard that there is possible ways to extract
>> normal modes indirectly from the output trajectories.
>>
>>
>> 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 list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>



-- 
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
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Re: [gmx-users] position restrained minimization on the one part of a system

[Justin A. Lemkul]

Atila Petrosian wrote:

 I want to use define  = -DPOSRES_Protein_chain_A for step 1.

 is it true?



Not per the topology you posted earlier.  Your only option (at this point) for 
restraining the protein is -DPOSRES, which restrains all the chains.


If you want to restrain parts of your structure, you will likely need to create 
custom posre.itp files for the different chains (or whatever merged combinations 
of them) using genrestr and perhaps custom index groups generated by make_ndx.


A trivial example of such a procedure is described in the protein-ligand 
tutorial I wrote:


http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html

-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] Adding hydrogens to united atom trajectories

[Jon Kapla]

Hi,

I'm performing united atom simulations of sugars and lipids and 
comparing calculated properties like C-H dipolar couplings and order 
parameters with corresponding results from experiments. To do this I 
need to calculate the hydrogen postitions of the hydrogens I'm 
interested in, and have previously used the gromacs protonate tool for 
this. Since some time this tool seems to be quite broken, so I've 
written my own routines for the calculations.


Now to my concern. The gromacs tool seems to have used a fixed H-C-H 
angle of 109.5 degrees when adding CH2-group hydrogens. I'm sure that 
this is an approximation as good as anything, but shouldn't a better 
approach be to let the H-C-H angle vary with the corresponding C-C-C or 
C-C-O angle?


I've done some searching regarding this, and I've found these two articles

 MASTRYUKOV, V.; OSINA, E. Journal of Molecular Structure. 1977, 36, 
127-132.

 Dakkouri, M. Journal of Molecular Structure. 1997, 413-414, 133-152.

stating the following empirical relationship between the angles (the 
second article is citing the first) as an approximation of the angle 
correlations fitted from diffraction data:


HCH=126.1-0.175*CCX

A C-C-O angle of 113 degrees would with this relation give a H-C-H angle 
of 106.3 degrees.


Does anyone have any thoughts about this?

Regards
Jon Kapla

--
_

Jon Kapla
  Division of Physical Chemistry
  Dpt. of Materials and Environmental Chemistry (MMK)
  Arrhenius Laboratory
  Stockholm University
  SE-106 91 Stockholm
Pos:PhD Student
Phone:  +46 8 16 11 79 (office)
Phone:  +46 70 304 19 89 (cell)
E-mail: jon.ka...@mmk.su.se
_

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[gmx-users] position restrained minimization on the one part of a system

[Atila Petrosian]

Dear Justin

thanks for your attention

I deleted posre.itp file which pdb2gmx was created (containing all solute).I
made a posre.itp (containing only protein) by genrestr.

now if I use define = -DPOSRES, gromacs use from my posre.itp. is it true?
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Re: [gmx-users] position restrained minimization on the one part of a system

[Mark Abraham]

On 27/10/2011 12:28 AM, Atila Petrosian wrote:

Dear Mark

thanks for your reply

you said "if pdb2gmx is able to treat the whole system in one pass, 
then it will write such position restraint

files automatically"

in my system, what pdb2gmx includes are in below:

; Include forcefield parameters
#include "amber03.ff/forcefield.itp"

; Include chain topologies
#include "complex_Protein_chain_A.itp"
#include "complex_DNA_chain_B.itp"

; Include Position restraint file
#ifdef POSRES
#include "posre_Protein_chain_A.itp"

; Include Position restraint file
#ifdef POSRES
#include "posre_Protein_chain_B.itp"


This is the kind of thing to which I was referring, but it appears you 
have edited your .top and removed the #endif lines that should match the 
#ifdef. Start again with pdb2gmx to generate a new .top, and then you 
will be able to choose your "define = -DPOSRES_xxx" to use position 
restraints on whichever part of the system you want with no need to ever 
touch a .top or .itp file.


Mark



; Include water topology
#include "amber03.ff/tip3p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

; Include topology for ions
#include "amber03.ff/ions.itp"

[ system ]
; Name
complex

[ molecules ]
; Compound#mols
Protein_chain_A 1
DNA_chain_B 1
SOL3500


unfortunately, I don't know about step 1.

please guide me about that.




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Re: [gmx-users] position restrained minimization on the one part of a system

[Justin A. Lemkul]

Atila Petrosian wrote:

Dear Justin

thanks for your attention

I deleted posre.itp file which pdb2gmx was created (containing all 
solute).I made a posre.itp (containing only protein) by genrestr.


now if I use define = -DPOSRES, gromacs use from my posre.itp. is it true?



Assuming you have constructed your topology correctly, yes.  Note the advice 
Mark has just sent, 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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Re: [gmx-users] Normal Mode Analysis

[James Starlight]

Justin,


I've forced with the problem that I could not prorerly minimized my system
in the NMA conditions. Even in STEEP minimizaation I could not obtain Epot
value lower than +3.00 with that parametries ( I've used KALP peptide as a
test input )

; Parameters describing what to do, when to stop and what to save
integrator= steep
emtol= 1  ; Stop minimization when the maximum force < 1.0
kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps= 500  ; Maximum number of (minimization) steps to
perform



; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist= 1; Frequency to update the neighbor list and long
range forces
ns_type= grid; Method to determine neighbor list (simple,
grid)
rlist= 1.2; Cut-off for making neighbor list (short range
forces)
coulombtype= Shift
rcoulomb= 1.0
rcoulomb_switch= 0.0
vdwtype = Shift
rvdw= 1.0
rvdw_switch = 0.0

Than I've tried to futher minimized this structure via  l-bfgs algorithm by

integrator= l-bfgs
dt  =  0.01
emtol= 0.001 ;
emstep  = 0.1  ; Energy step size
nsteps= 5000  ; Maximum number of (minimization) steps
to perform

but Epot was still big.

What I've done wrong ?
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[gmx-users] Center of simulation box

[zhenlong li]

Dear all,

In my simulation, when the simulation box shrinks, the center of box always
shift towards the origin even if the center motion is set to removed every
timestep.
I just wonder if there is an anticipated center position for a given
simulation box in gromacs. The box type is dodecahedron in my simulation.

My problem is how to make sure a group of atoms, such as proteins,  sit at
the center of the simulation box after the simulation box become stable.
Current, as the center of the box floats, it is very difficult to maintain
it by position restraint of the center group.

Thank you in advance for any suggestions!

with best wishes
Zhenlong
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Re: [gmx-users] Center of simulation box

[Justin A. Lemkul]

zhenlong li wrote:

Dear all,

In my simulation, when the simulation box shrinks, the center of box 
always shift towards the origin even if the center motion is set to 
removed every timestep.
I just wonder if there is an anticipated center position for a given 
simulation box in gromacs. The box type is dodecahedron in my simulation.




Yes, this is expected.  By default, a unit cell built by Gromacs will be 
centered at (x/2, y/2, z/2).


My problem is how to make sure a group of atoms, such as proteins,  sit 
at the center of the simulation box after the simulation box become stable.
Current, as the center of the box floats, it is very difficult to 
maintain it by position restraint of the center group.




If you are applying periodic boundary conditions, there is no such thing as a 
center (since the system is infinite).  While it may be a useful convention for 
visualization purposes, there is no effect on the calculation itself.


-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] Normal Mode Analysis

[Justin A. Lemkul]

James Starlight wrote:

Justin,


I've forced with the problem that I could not prorerly minimized my 
system in the NMA conditions. Even in STEEP minimizaation I could not 
obtain Epot value lower than +3.00 with that parametries ( I've used 
KALP peptide as a test input )




The Epot value is less significant than Fmax (which is what is set in the .mdp 
file, anyway).  What Fmax do you achieve?  Real copied and pasted output would 
be useful.



; Parameters describing what to do, when to stop and what to save
integrator= steep   
emtol= 1  ; Stop minimization when the maximum force < 1.0 
kJ/mol/nm

emstep  = 0.01  ; Energy step size
nsteps= 500  ; Maximum number of (minimization) 
steps to perform




; Parameters describing how to find the neighbors of each atom and how 
to calculate the interactions
nstlist= 1; Frequency to update the neighbor list and 
long range forces
ns_type= grid; Method to determine neighbor list 
(simple, grid)
rlist= 1.2; Cut-off for making neighbor list (short 
range forces)
coulombtype= Shift   
rcoulomb= 1.0

rcoulomb_switch= 0.0
vdwtype = Shift
rvdw= 1.0
rvdw_switch = 0.0   


Than I've tried to futher minimized this structure via  l-bfgs algorithm by

integrator= l-bfgs
dt  =  0.01
emtol= 0.001 ;
emstep  = 0.1  ; Energy step size
nsteps= 5000  ; Maximum number of (minimization) 
steps to perform


but Epot was still big.

What I've done wrong ?


Are you using single- or double-precision?

-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] Normal Mode Analysis

[James Starlight]

I've used double precision. Today I'll copied output because it's done on
lab comp but from the output log I've found that minimization was not
completed ( e.g when I've calculate Normal Modes with that minimized
structure I've obtain message that my system was not minimized properly )

2011/10/26 Justin A. Lemkul 

>
>
> James Starlight wrote:
>
>> Justin,
>>
>>
>> I've forced with the problem that I could not prorerly minimized my system
>> in the NMA conditions. Even in STEEP minimizaation I could not obtain Epot
>> value lower than +3.00 with that parametries ( I've used KALP peptide as a
>> test input )
>>
>>
> The Epot value is less significant than Fmax (which is what is set in the
> .mdp file, anyway).  What Fmax do you achieve?  Real copied and pasted
> output would be useful.
>
>
>  ; Parameters describing what to do, when to stop and what to save
>> integrator= steep   emtol= 1  ; Stop minimization when
>> the maximum force < 1.0 kJ/mol/nm
>> emstep  = 0.01  ; Energy step size
>> nsteps= 500  ; Maximum number of (minimization) steps
>> to perform
>>
>>
>>
>> ; Parameters describing how to find the neighbors of each atom and how to
>> calculate the interactions
>> nstlist= 1; Frequency to update the neighbor list and long
>> range forces
>> ns_type= grid; Method to determine neighbor list (simple,
>> grid)
>> rlist= 1.2; Cut-off for making neighbor list (short range
>> forces)
>> coulombtype= Shift   rcoulomb= 1.0
>> rcoulomb_switch= 0.0
>> vdwtype = Shift
>> rvdw= 1.0
>> rvdw_switch = 0.0
>> Than I've tried to futher minimized this structure via  l-bfgs algorithm
>> by
>>
>> integrator= l-bfgs
>> dt  =  0.01
>> emtol= 0.001 ;
>> emstep  = 0.1  ; Energy step size
>> nsteps= 5000  ; Maximum number of (minimization) steps
>> to perform
>>
>> but Epot was still big.
>>
>> What I've done wrong ?
>>
>
> Are you using single- or double-precision?
>
> -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] query on OPLS-2005

[Sanku M]

Hi,
  I wanted to check what is actually OPLS-2005 forcefield that is recently 
being referred often for md simulation. However, I also see that whenever, 
OPLS-2005 is being referred, it cites a 2001 paper by Jorgensen on OPLS 
forcefield. So, what is actually OPLS-2005?
So, I wonder what version of OPLS forcefield is present in gromacs 4.5 series. 
Is it also so-called OPLS-2005 forcefield?
Sanku-- 
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[gmx-users] polymer chain length and density

[Juliette N.]

Dear experts,

I have a quick and naive inquiry. I see in the molecular dynamics
simulations that density of the polymers increase slightly with increasing
degree of polymerization ( or Mw). Even for the systems having the same
total atom numbers but one with less number of chains of higher Mw. My guess
its because of the less void space in case of higher Mw chains..?!

And usually properties depending on Mw level off with no significant change
in the property of interest vs chain length.

Please kindly help!

Thanks,
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Re: [gmx-users] polymer chain length and density

[Mark Abraham]

On 27/10/2011 10:43 AM, Juliette N. wrote:

Dear experts,

I have a quick and naive inquiry. I see in the molecular dynamics 
simulations that density of the polymers increase slightly with 
increasing degree of polymerization ( or Mw). Even for the systems 
having the same total atom numbers but one with less number of chains 
of higher Mw. My guess its because of the less void space in case of 
higher Mw chains..?!


And usually properties depending on Mw level off with no significant 
change in the property of interest vs chain length.


Lengthy converged equilibrium simulations using a valid model physics 
should agree with experimental properties. So at least one of those 
conditions isn't true.


Mark
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[gmx-users] Re:polymer chain length and density

[Dr. Vitaly V. Chaban]

> Dear experts,
>
> I have a quick and naive inquiry. I see in the molecular dynamics
> simulations that density of the polymers increase slightly with increasing
> degree of polymerization ( or Mw). Even for the systems having the same
> total atom numbers but one with less number of chains of higher Mw. My guess
> its because of the less void space in case of higher Mw chains..?!

It is because the interatomic distances between chemically bonded
atoms are noticeably smaller than between the atoms of just
neighboring molecules.

I think when you come to publishing your results, you will need to
exactly specify the number of monomers in your chain. It may also be
interesting to discuss how much your properties are affected by this
length.


> And usually properties depending on Mw level off with no significant change
> in the property of interest vs chain length.




-- 
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA
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[gmx-users] convert parameters of Buckingham potential to/from LJ potential

[Kan]

Dear gmx Users,

I am trying to convert parameters of Buckingham potential to/from LJ
potential. It seems that there is tool in Gromacs, g_sigeps which is capable
of doing this. However,when I typed the following command: "./sigeps_mpi
-nice 2   -A 6159492 -B 0.019891 -C 0.002692 -qi -1.041094 -qj -1.041094",
no output of LJ came out. Since there is no example availabe, I can not
figure out how to do it correctly. I would be thankful if anyone can help
me!

Best wishes,

Kan
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Re: [gmx-users] convert parameters of Buckingham potential to/from LJ potential

[Justin A. Lemkul]

Kan wrote:

Dear gmx Users,

I am trying to convert parameters of Buckingham potential to/from LJ 
potential. It seems that there is tool in Gromacs, g_sigeps which is 
capable of doing this. However,when I typed the following command: 
"./sigeps_mpi -nice 2   -A 6159492 -B 0.019891 -C 0.002692 -qi -1.041094 
-qj -1.041094", no output of LJ came out. Since there is no example 
availabe, I can not figure out how to do it correctly. I would be 
thankful if anyone can help me!




You can't convert between Buckingham and LJ.  They are different functions.  The 
help description for g_sigeps states that it is for C6/Cn to sigma/epsilon 
conversion.  The Buckingham options are for plotting the potential only, it seems.


-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] position restrained minimization on the one part of a system

[Tsjerk Wassenaar]

Hi Atila,

> ; Include chain topologies
> #include "complex_Protein_chain_A.itp"
> #include "complex_DNA_chain_B.itp"
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre_Protein_chain_A.itp"
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre_Protein_chain_B.itp"

Aside from the missing #ifdefs that Mark mentioned, this is also
plainly wrong. The position restraints are part of the molecule
definition, so now both sets of restraints are made part of the last
moleculetype, which is the DNA chain. You'll have to have

; Include chain topologies
#include "complex_Protein_chain_A.itp"
#ifdef POSRES
#include "posre_Protein_chain_A.itp"
#endif

#include "complex_DNA_chain_B.itp"
#ifdef POSRES
#include "posre_Protein_chain_B.itp"
#endif


I note that the position restraints for chain B are called protein too...

Cheers,

Tsjerk


-- 
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
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