Re: [gmx-users] How To SOLVATE

[Justin Lemkul]

On 10/27/13 9:30 PM, Hari Pandey wrote:

Hi GROMACS users

can any body tell me how do I solvate fixed number of molecules in fixed 
volume: for example 100 molecule water in 14*14*14 Aungstrom^3  box.  eidt conf 
and genbox  never can do this.



genbox -maxsol 100 will put a block of no more than 100 waters in the unit cell.

genbox -ci -nmol 100 will add 100 molecules randomly within the unit cell.


One more question.
Please any body help me on following warning:

WARNING: masses and atomic (Van der Waals) radii will be determined
  based on residue and atom names. These numbers can deviate
  from the correct mass and radius of the atom type.

Volume  of input 125 (nm^3)
Massof input 967.25 (a.m.u.)
Density of input 12.8493 (g/l)
Scaling all box vectors by 0.234221
new system size :  0.050  0.055  0.037
 shift   :  1.914  1.914  1.914 (nm)
new center  :  2.500  2.500  2.500 (nm)
new box vectors :  5.000  5.000  5.000 (nm)
new box angles  :  90.00  90.00  90.00 (degrees)
new box volume  : 125.00   (nm^3)



Here mass of input is not correct. It should be 444.5



There is a warning that masses may not be correctly detected for a reason.  Are 
you using any strange atoms?  No one on this list can tell what is right without 
seeing exactly what you're doing (description of the system, commands, input 
files, etc).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] How To SOLVATE

[Hari Pandey]

Hi GROMACS users

can any body tell me how do I solvate fixed number of molecules in fixed 
volume: for example 100 molecule water in 14*14*14 Aungstrom^3  box.  eidt conf 
and genbox  never can do this.

One more question.
Please any body help me on following warning:

WARNING: masses and atomic (Van der Waals) radii will be determined
         based on residue and atom names. These numbers can deviate
         from the correct mass and radius of the atom type.

Volume  of input 125 (nm^3)
Mass    of input 967.25 (a.m.u.)
Density of input 12.8493 (g/l)
Scaling all box vectors by 0.234221
new system size :  0.050  0.055  0.037
    shift       :  1.914  1.914  1.914 (nm)
new center      :  2.500  2.500  2.500 (nm)
new box vectors :  5.000  5.000  5.000 (nm)
new box angles  :  90.00  90.00  90.00 (degrees)
new box volume  : 125.00               (nm^3)



Here mass of input is not correct. It should be 444.5

Thanks in advance

Hari
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[gmx-users] *** Extended deadline *** CfP: 4th International Workshop on Model-driven Approaches for Simulation Engineering part of the Symposium on Theory of Modeling and Simulation (SCS SpringSim 20

[Daniele Gianni]

(Please accept our apologies if you receive multiple copies of this CFP)

#
 CALL FOR PAPERS

 4th International Workshop on
Model-driven Approaches for Simulation Engineering
part of the Symposium on Theory of Modeling and Simulation
 (SCS SpringSim 2014)


#

April 13-16, 2014, Tampa, FL (USA)
http://www.sel.uniroma2.it/Mod4Sim14

#
# Papers Due: *** November 22, 2013 *** extended
# Accepted papers will be published in the conference proceedings
# and archived in the ACM Digital Library.
#

The workshop aims to bring together experts in model-based, model-driven
and software engineering with experts in simulation methods and simulation
practitioners, with the objective to advance the state of the art in
model-driven simulation engineering.

Model-driven engineering approaches provide considerable advantages to
software systems engineering activities through the provision of consistent
and coherent models at different abstraction levels. As these models are in
a machine readable form, model-driven engineering approaches can also
support the exploitation of computing capabilities for model reuse,
programming code generation, and model checking, for example.

The definition of a simulation model, its software implementation and its
execution platform form what is known as simulation engineering. As
simulation systems are mainly based on software, these systems can
similarly benefit from model-driven approaches to support automatic
software generation, enhance software quality, and reduce costs,
development effort and time-to-market.

Similarly to systems and software engineering, simulation engineering can
exploit the capabilities of model-driven approaches by increasing the
abstraction level in simulation model specifications and by automating the
derivation of simulator code. Further advantages can be gained by using
modeling languages, such as UML and SysML – but not exclusively those. For
example, modeling languages can be used for descriptive modeling (to
describe the system to be simulated), for analytical modeling (to specify
analytically the simulation of the same system), and for implementation
modeling (to define the respective simulator).

A partial list of topics of interest includes:

* model-driven simulation engineering processes
* requirements modeling for simulation
* domain specific languages for modeling and simulation
* model transformations for simulation model building
* model transformations for simulation model implementation
* model-driven engineering of distributed simulation systems
* relationship between metamodeling standards (e.g., MOF, Ecore) and
distributed simulation standards (e.g., HLA, DIS)
* metamodels for simulation reuse and interoperability
* model-driven technologies for different simulation paradigms (discrete
event simulation, multi-agent simulation, sketch-based * simulation, etc.)
* model-driven methods and tools for performance engineering of simulation
systems
* simulation tools for model-driven software performance engineering
* model-driven technologies for simulation verification and validation
* model-driven technologies for data collection and analysis
* model-driven technologies for simulation visualization
* Executable UML
* Executable Architectures
* SysML / Modelica integration
* Simulation Model Portability and reuse
* model-based systems verification and validation
* simulation for model-based systems engineering

To stimulate creativity, however, the workshop maintains a wider scope and
welcomes contributions offering original perspectives on model-driven
engineering of simulation systems.

+++
On-Line Submissions and Publication
+++

We invite paper submissions in three forms:

1. Full paper (max 8 pages), describing innovative research results. These
papers are eligible for the best paper award and may be invited for an
extended version in a special issue of the SCS SIMULATION journal.
2. Work-in-progress paper (max 6 pages), describing novel research ideas
and promising work that have not yet been fully evaluated.
3. Short paper (max 6 pages), describing industrial and hands-on experience
on any relevant area (i.e. military, government, space, etc.).

All the papers must be submitted through the SCS conference management
systems (http://www.softconf.com/scs/DEVS14/) and select the Mod4Sim track.
The submissions must be in PDF format and conform to the SCS conference
template (Word template is available at
http://www.scs.org/upload/documents/templates/ConferenceSubmissionWORDTemplate.doc,
guidelines are available at
http://www.scs.org/PDFs/formattingkit.pdf). All the submitted papers mu

Re: [gmx-users] pbc problem

[Mark Abraham]

To make this clear, center the trajectory on the water and watch the time
evolution in some visualization program.

Mark


On Sun, Oct 27, 2013 at 5:08 PM, Justin Lemkul  wrote:

>
>
> On 10/27/13 12:05 PM, shahab shariati wrote:
>
>> Dear Tsjerk Wassenaar
>>
>> Very very thanks for your reply.
>>
>> I used trjconv -pbc mol.
>>
>> pbc problem was solved only for lipid molecules.
>>
>> When I see new trajectory by vmd, there are some problesm about drug
>> molecule.
>>
>> https://www.dropbox.com/s/**xq4s6az17buhvb8/images-2.docx
>>
>> If I show my system as 4 regions, my system before equilibration is as
>> fallows:
>>
>> region (1): water + drug
>> region (2): top leaflet of bilayer
>> region (3): bottom leaflet of bilayer
>> region (4): water
>>
>> After equilibration, drug molecule exits region (1) and enters region (4),
>> alternately.
>>
>> On the other hand, drug molecule is in region (1)in some frames and is
>> in region (4) in other frames.
>>
>> Please tell me how to fix it? Is this issue (about drug molecule) pbc
>> problem?
>>
>>
> As has already been stated several times, there is no problem at all.  The
> outcome is completely normal, and there are not discrete regions (1) and
> (4). It is a continuous block of water via PBC.  The molecule can freely
> diffuse throughout it.
>
> -Justin
>
> --
> ==**
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul@outerbanks.umaryland.**edu  |
> (410) 706-7441
>
> ==**
>
> --
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Re: [gmx-users] pbc problem

[Justin Lemkul]

On 10/27/13 12:05 PM, shahab shariati wrote:

Dear Tsjerk Wassenaar

Very very thanks for your reply.

I used trjconv -pbc mol.

pbc problem was solved only for lipid molecules.

When I see new trajectory by vmd, there are some problesm about drug
molecule.

https://www.dropbox.com/s/xq4s6az17buhvb8/images-2.docx

If I show my system as 4 regions, my system before equilibration is as
fallows:

region (1): water + drug
region (2): top leaflet of bilayer
region (3): bottom leaflet of bilayer
region (4): water

After equilibration, drug molecule exits region (1) and enters region (4),
alternately.

On the other hand, drug molecule is in region (1)in some frames and is
in region (4) in other frames.

Please tell me how to fix it? Is this issue (about drug molecule) pbc
problem?



As has already been stated several times, there is no problem at all.  The 
outcome is completely normal, and there are not discrete regions (1) and (4). 
It is a continuous block of water via PBC.  The molecule can freely diffuse 
throughout it.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
--
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[gmx-users] pbc problem

[shahab shariati]

Dear Tsjerk Wassenaar

Very very thanks for your reply.

I used trjconv -pbc mol.

pbc problem was solved only for lipid molecules.

When I see new trajectory by vmd, there are some problesm about drug
molecule.

https://www.dropbox.com/s/xq4s6az17buhvb8/images-2.docx

If I show my system as 4 regions, my system before equilibration is as
fallows:

region (1): water + drug
region (2): top leaflet of bilayer
region (3): bottom leaflet of bilayer
region (4): water

After equilibration, drug molecule exits region (1) and enters region (4),
alternately.

On the other hand, drug molecule is in region (1)in some frames and is
in region (4) in other frames.

Please tell me how to fix it? Is this issue (about drug molecule) pbc
problem?

Best wishes
-- 
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Re: [gmx-users] error in umbralla sampling step 6

[Justin Lemkul]

On 10/27/13 11:23 AM, sunyeping wrote:



Yeping Sun
Institute of Microbiology, Chinese Academy of Sciences
--
发件人：Justin Lemkul 
发送时间：2013年10月27日(星期日) 20:27
收件人：gromacs 
主　题：Re: 答复: [gmx-users] error in umbralla sampling step 6


Please keep the discussion on the list.

On 10/27/13 5:09 AM, sunyeping wrote:

Dear professor Lemkul,

For warning 1:
I use the npt_umbrella.mdp file you provided in step 6 in the umbralla sampling
tutorial. You told us to start by running a brief NPT equilibration in each
window using this mdp file. If Parrinello-Rahman pressure coupling should be
used, why did you put it in the mdp file?



I know the tutorial system is robust enough that it won't matter.  That is not
necessarily true for whatever other system you come up with.  Be careful when
extrapolating something that works in a tutorial with something that is
untested.  The general logic is the same (you need to equilibrate for a little
while first), but you have to think a bit about the proper settings.  There is
also no guarantee that the length of time I set in the tutorial simulation
processes (equilibration, SMD, and umbrella sampling) will necessarily be
sufficient for whatever you're doing.


For warning 2:
I check the gro files using vmd but I cann't find any molecule broken? How can I
find the brroken molecule?


The only way to find them is to look.  I have no special advice for this.


I add -pbc whole option to the  trjconv as following:

trjconv -s pull.tpr -f traj.xtc -o conf.gro -sep -pbc whole

then It seems that the problemis solved. Is that a correct wayyou mean to solve 
the problem?



Then clearly something was broken across PBC, which means there is no real 
problem.

-Justin



In case that something was broken across PBC, why there is no real problem? Do 
you mean molecule breaking will not affect the simulation result?



We use the term "broken" very loosely.  The molecule is still intact from a 
topological standpoint.  It is only "broken" in the way that we see it.  The 
dynamics of a given molecule are the same if the molecule is "intact" in the 
"center" of the box (also a misnomer in a periodic system) or "broken" and a 
boundary.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] mdrun cpt

[Justin Lemkul]

On 10/27/13 9:37 AM, Pavan Ghatty wrote:

Hello All,

Is there a way to make mdrun put out .cpt file with the same frequency as a
.xtc or .trr file. From here
http://www.gromacs.org/Documentation/How-tos/Doing_Restarts I see that we
can choose how often (time in mins) the .cpt file is written. But clearly
if the frequency of output of .cpt (frequency in mins) and .xtc (frequency
in simulation steps) do not match, it can create problems during analysis;
especially in the event of frequent crashes. Also, I am not storing .trr
file since I dont need that precision.
I am using Gromacs 4.6.1.



What problems are you experiencing?  There is no need for .cpt frequency to be 
the same as .xtc frequency, because any duplicate frames should be handled 
elegantly when appending.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] error in umbralla sampling step 6

[sunyeping]

Yeping Sun
Institute of Microbiology, Chinese Academy of Sciences
--
发件人：Justin Lemkul 
发送时间：2013年10月27日(星期日) 20:27
收件人：gromacs 
主　题：Re: 答复: [gmx-users] error in umbralla sampling step 6


Please keep the discussion on the list.

On 10/27/13 5:09 AM, sunyeping wrote:
> Dear professor Lemkul,
>
> For warning 1:
> I use the npt_umbrella.mdp file you provided in step 6 in the umbralla 
> sampling
> tutorial. You told us to start by running a brief NPT equilibration in each
> window using this mdp file. If Parrinello-Rahman pressure coupling should be
> used, why did you put it in the mdp file?
>

I know the tutorial system is robust enough that it won't matter.  That is not 
necessarily true for whatever other system you come up with.  Be careful when 
extrapolating something that works in a tutorial with something that is 
untested.  The general logic is the same (you need to equilibrate for a little 
while first), but you have to think a bit about the proper settings.  There is 
also no guarantee that the length of time I set in the tutorial simulation 
processes (equilibration, SMD, and umbrella sampling) will necessarily be 
sufficient for whatever you're doing.

> For warning 2:
> I check the gro files using vmd but I cann't find any molecule broken? How 
> can I
> find the brroken molecule?

The only way to find them is to look.  I have no special advice for this.

> I add -pbc whole option to the  trjconv as following:
>
> trjconv -s pull.tpr -f traj.xtc -o conf.gro -sep -pbc whole
>
> then It seems that the problemis solved. Is that a correct wayyou mean to 
> solve the problem?
>

Then clearly something was broken across PBC, which means there is no real 
problem.

-JustinIn case that something was broken across PBC, why there is no real 
problem? Do you mean molecule breaking will not affect the simulation result?

-- 
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] pbc problem

[Tsjerk Wassenaar]

Hi Shahab,

What about running trjconv -pbc mol with a .tpr as input file?

Cheers,

Tsjerk


On Sun, Oct 27, 2013 at 3:24 PM, shahab shariati
wrote:

> Dear Justin
>
> I attached images related to before (em2.gro) and after equilibration.
>
>
> https://www.dropbox.com/s/yjkyj5ycshvp20u/images.docx
> --
> gmx-users mailing listgmx-users@gromacs.org
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>



-- 
Tsjerk A. Wassenaar, Ph.D.
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[gmx-users] pbc problem

[shahab shariati]

Dear Justin

I attached images related to before (em2.gro) and after equilibration.


https://www.dropbox.com/s/yjkyj5ycshvp20u/images.docx
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[gmx-users] mdrun cpt

[Pavan Ghatty]

Hello All,

Is there a way to make mdrun put out .cpt file with the same frequency as a
.xtc or .trr file. From here
http://www.gromacs.org/Documentation/How-tos/Doing_Restarts I see that we
can choose how often (time in mins) the .cpt file is written. But clearly
if the frequency of output of .cpt (frequency in mins) and .xtc (frequency
in simulation steps) do not match, it can create problems during analysis;
especially in the event of frequent crashes. Also, I am not storing .trr
file since I dont need that precision.
I am using Gromacs 4.6.1.

Thank you,
Pavan
-- 
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[gmx-users] pbc problem

[shahab shariati]

Dear Justin

Please check this trajectory file (1.xtc) being smaller than 0.xtc.

https://www.dropbox.com/s/9qd2l37qyfqvpox/1.xtc
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Re: [gmx-users] pbc problem

[Justin Lemkul]

On 10/27/13 8:16 AM, shahab shariati wrote:

Dear Justin

I want to study translocation of drug molecule in lipid bilayer.

My gro file after minimization is em2.gro.

After NPT-MD simulation, I obtained npt.gro and 0.xtc files.

When I see trajectory by vmd, there are some things abnormal.

I guess there is pbc problem.

I attached these 3 files. Please after viewing them, tell me is my guess
true.

If yes, please guide me how to fix it. If no, please tell me what is
problem?

https://www.dropbox.com/s/d0hppxdngj7xwst/em2.gro

https://www.dropbox.com/s/gnqf6fuxwwj0zzt/npt.gro

https://www.dropbox.com/s/w899y86mhp0ysbo/0.xtc



Images are better, especially ones that don't have to be downloaded.  I'm not 
going to download a potentially large .xtc file, sorry.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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Re: 答复: [gmx-users] error in umbralla sampling step 6

[Justin Lemkul]

Please keep the discussion on the list.

On 10/27/13 5:09 AM, sunyeping wrote:

Dear professor Lemkul,

For warning 1:
I use the npt_umbrella.mdp file you provided in step 6 in the umbralla sampling
tutorial. You told us to start by running a brief NPT equilibration in each
window using this mdp file. If Parrinello-Rahman pressure coupling should be
used, why did you put it in the mdp file?



I know the tutorial system is robust enough that it won't matter.  That is not 
necessarily true for whatever other system you come up with.  Be careful when 
extrapolating something that works in a tutorial with something that is 
untested.  The general logic is the same (you need to equilibrate for a little 
while first), but you have to think a bit about the proper settings.  There is 
also no guarantee that the length of time I set in the tutorial simulation 
processes (equilibration, SMD, and umbrella sampling) will necessarily be 
sufficient for whatever you're doing.



For warning 2:
I check the gro files using vmd but I cann't find any molecule broken? How can I
find the brroken molecule?


The only way to find them is to look.  I have no special advice for this.


I add -pbc whole option to the  trjconv as following:

trjconv -s pull.tpr -f traj.xtc -o conf.gro -sep -pbc whole

then It seems that the problemis solved. Is that a correct wayyou mean to solve 
the problem?



Then clearly something was broken across PBC, which means there is no real 
problem.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] pbc problem

[shahab shariati]

Dear Justin

I want to study translocation of drug molecule in lipid bilayer.

My gro file after minimization is em2.gro.

After NPT-MD simulation, I obtained npt.gro and 0.xtc files.

When I see trajectory by vmd, there are some things abnormal.

I guess there is pbc problem.

I attached these 3 files. Please after viewing them, tell me is my guess
true.

If yes, please guide me how to fix it. If no, please tell me what is
problem?

https://www.dropbox.com/s/d0hppxdngj7xwst/em2.gro

https://www.dropbox.com/s/gnqf6fuxwwj0zzt/npt.gro

https://www.dropbox.com/s/w899y86mhp0ysbo/0.xtc

Best wishes
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[gmx-users] RE:Requests

[lloyd riggs]

 

>You are not allowed to post to this mailing list, and your message has
>been automatically rejected. If you think that your messages are
>being rejected in error, contact the mailing list owner at
>gmx-developers...

 

Sorry I was trying to post this to the "Feature suggestion/request" site on gromacs mailserver, however this has been changed in recent months.  I thus do not know how to post such a thing now without joining the developer mail site (I would at present not be such a person, and would not like to see such a thing bogged down with user help mails/spam).

 

I was just attempting to run this by some developers.  In the past two years I have run into several materials based work which would benifit from electric currents, or electomagnetic fields (external broad range in setting).  In the recent science there was a nice piece about this applied to liquid droplets with particles, or doped secoundary chemistry (oils, polymers, complex small molecule/metal adducts and/or nano bead polymers...), which primarily work through external magnetic field altering the surface chemistry, and retaining the effects after fields are removed.  This can also be applied to electromagentic induced crystalization at atomic level, multi layered liquid interfaces...etc.

 

In any case this might be an area where simulations would play a large part if effects from external fields, or even free electrons (currents applied in layers, surfaces or the entire unit cell) could be modeled sufficiently.  Meaning probably a good lab funding source and interesting work.

 

Sorry about any spelling areas.

 

Sincerely,

 

Stephan Watkins, (now PhDd)

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