Re: [gmx-users] Question about gromacs mailing list

[Alessandra Villa]

Hi,

On Thu, Feb 6, 2020 at 4:02 AM Amit Kumar  wrote:

> Dear gromacs users,
> After subscribing to the gromacs mailing list I am getting only daily
> digest, I am not getting a question-answer thread, so posting my question
> once I cannot reply in the thread.
>
>
You have probably selected "digest mode" when you enrolled in the
mailing-list. You could change this setting by login to the subscription
page.
To do that use the link you find in the welcome email that you got once you
enrolled.
In your case should be something like

https://maillist.sys.kth.se/mailman/options/gromacs.org_gmx-users/ak543714%40gmail.com


Best regards
Alessandra
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[gmx-users] Question about gromacs mailing list and configurational entropy

[Amit Kumar]

Dear gromacs users,
After subscribing to the gromacs mailing list I am getting only daily
digest, I am not getting a question-answer thread, so posting my question
once I cannot reply in the thread.

I have also asked previously this question and got a reply from David van
der Spoel too and after that, I am getting a value of schlitter's entropy
but getting only one value of schlitter's value while I want it for every
frame to plot time vs entropy graph.
So can you tell me what is happening and how to troubleshoot this?

Thank You
Amit Kumar
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Re: [gmx-users] Question about Gromacs

[David van der Spoel]

Den 2019-08-26 kl. 20:53, skrev Najla Hosseini:

Dear David,

Hope you are doing well.
I am Gromacs user and I need to change the partial charge of molecules 
in force field or itp file as a function of distance during the run in 
Gromacs. Is it possible? How I should do that?
Please pose your questions on the mailing list, however this is not 
possible to dynamically.


If not, I should use two itp file with a condition for finishing one 
of them and starting the new tpr file based on another itp file, how I 
should do that?


Thank you so much.
I really appreciate your consideration and time.

Best Regards, Najla

--
/*Kind Regards,
*/
/*Najla *
/



--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se

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[gmx-users] question about Gromacs 5.0.4 build

[Susan Chacko]

Hi all,

I had installed Gromacs 5.0.4  on a Centos6 system a few years ago, and 
it was fine. We recently migrated our systems to Centos7, where Gromacs 
2018 was installed, also without problems.  A user requested the old 
Gromacs 5.0.4 on the Centos7 system to complete a project.


I worked through the identical install process, but of course with a 
newer compiler. The build of Gromacs went fine, but when I got to 'make 
check', one of the tests gave an error.



->  13 - SelectionUnitTests (Failed)
[ RUN  ] SelectionCollectionDataTest.HandlesCharge
/usr/local/src/gromacs/gromacs-5.0.4/src/testutils/refdata.cpp:868: Failure
Value of: strValue
  Actual: "6"
Expected: refStrValue
Which is: "5"
Google Test trace:
/usr/local/src/gromacs/gromacs-5.0.4/src/testutils/refdata.cpp:861: Checking 
'/Compiled/Selection1/Atoms/Length'
/usr/local/src/gromacs/gromacs-5.0.4/src/gromacs/selection/tests/selectioncollection.cpp:312:
 Checking selection "charge < 0.5"
/usr/local/src/gromacs/gromacs-5.0.4/src/testutils/refdata.cpp:575: Failure
Failed
Reference data item not found
Google Test trace:
/usr/local/src/gromacs/gromacs-5.0.4/src/testutils/refdata.cpp:861: Checking 
'/Compiled/Selection1/Atoms/[5]'
/usr/local/src/gromacs/gromacs-5.0.4/src/gromacs/selection/tests/selectioncollection.cpp:312:
 Checking selection "charge < 0.5"
[  FAILED  ] SelectionCollectionDataTest.HandlesCharge (1 ms)


The build completed ok, and the user reports that all their tests ran 
fine. Here are the differences between the compiles:


Centos6: Intel compiler 2015.1.133, OpenMPI 1.8.4, instruction set AVX256

Centos7: Intel compiler 2017.4.196, OpenMPI 2.1.2, instruction set SSE4.1

The cmake versions were also different, but that seems minor.

Does anyone have any thoughts about the error above? Should I try 
rebuilding with GCC? Is the Gromacs that I built safe to use :-)?


All suggestions much appreciated,

Susan

--
Susan Chacko, Ph.D.
HPC @ NIH Staff

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Re: [gmx-users] Question about GROMACS

[Mark Abraham]

Hi,

Yes, the deform .mdp option is intended to do these kinds of things, but I
don't think there is more documentation than you can see here
http://manual.gromacs.org/documentation/5.1.2/user-guide/mdp-options.html#non-equilibrium-md,
so look for a publication that reports using it.

Mark

On Tue, Feb 16, 2016 at 10:58 AM  wrote:

>
>  Dear All
>
> I have a quick question about GROMACS. Is there any chance to exert
> different types of loading such as torsional or bending or linear tension
> loading on simulation box in GROMACS ?
>
> Best wishes
>
> Ali khourshaei shargh (khourshaeisha...@mech.sharif.edu)
> Department of Mechanical Engineering
> Sharif University of Technology, Tehran, Iran
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> posting!
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[gmx-users] Question about GROMACS

[khourshaeishargh]

 Dear All

I have a quick question about GROMACS. Is there any chance to exert
different types of loading such as torsional or bending or linear tension
loading on simulation box in GROMACS ?

Best wishes

Ali khourshaei shargh (khourshaeisha...@mech.sharif.edu)
Department of Mechanical Engineering
Sharif University of Technology, Tehran, Iran
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Re: [gmx-users] question about gromacs

[Mark Abraham]

Hi,

As genrestr -h warns, you need a position restraint files per moleculetype,
not for the whole set of such molecules.

Mark


On Tue, Feb 4, 2014 at 2:39 PM, Andrew Bostick wrote:

> Hi all
>
> My system contain dopc + cholesterol + water + drug molecules.
>
> I want to do MD simulation with position restraint on dopc and cholesterol
> molecules.
>
> I used following lines to obtain posre*.itp files:
>
> genrestr -f npt.gro -n index.ndx -o posre_dopc.itp
>
> genrestr -f npt.gro -n index.ndx -o posre_chol.itp
>
> My topol.top file is as follows:
>
> ; Include forcefield parameters
> #include "gromos-43a1-s3_lipid.ff/forcefield.itp"
>
> #include "cholesterol.itp"
> #ifdef POSRES_chol
> #include "posre_chol.itp"
> #endif
>
> #include "dopc.itp"
> #ifdef POSRES_dopc
> #include "posre_dopc.itp"
> #endif
>
> #include "gromos-43a1-s3_lipid.ff/spc.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct   fcxfcyfcz
>11   1000   1000   1000
> #endif
>
> #include "drug.itp"
>
> [ system ]
> ; Name
> dopc/chol/drug/sol
>
> [ molecules ]
> ; Compound#mols
> CHOL26
> DOPC   102
> drg   1
> SOL   4677
>
> When I used grompp, I encountered error:
>
> Fatal error:
> [ file posre_chol.itp, line 34 ]:
> Atom index (30) in position_restraints out of bounds (1-29).
> This probably means that you have inserted topology section
> "position_restraints" in a part belonging to a different molecule than you
> intended to. In that case move the "position_restraints" section to the
> right molecule.
>
> I check the GROMACS website at http://www.gromacs.org/Documentation/Errors
> .
> in my opinion my topol.top file is true.
>
> How to fix this error.
>
> Any help will highly appreciated.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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>
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Re: [gmx-users] question about gromacs

[Justin Lemkul]

On 2/4/14, 8:43 AM, Andrew Bostick wrote:

I used following line in mdp file:

define  = -DPOSRES_dopc -DPOSRES_chol

Is my manner true?



To do what?  That will trigger the #include statements in the topology, but the 
error message shown below indicates that you have not correctly created those 
.itp files.


-Justin



On Tue, Feb 4, 2014 at 5:09 PM, Andrew Bostick wrote:


Hi all

My system contain dopc + cholesterol + water + drug molecules.

I want to do MD simulation with position restraint on dopc and cholesterol
molecules.

I used following lines to obtain posre*.itp files:

genrestr -f npt.gro -n index.ndx -o posre_dopc.itp

genrestr -f npt.gro -n index.ndx -o posre_chol.itp

My topol.top file is as follows:

; Include forcefield parameters
#include "gromos-43a1-s3_lipid.ff/forcefield.itp"

#include "cholesterol.itp"
#ifdef POSRES_chol
#include "posre_chol.itp"
#endif

#include "dopc.itp"
#ifdef POSRES_dopc
#include "posre_dopc.itp"
#endif

#include "gromos-43a1-s3_lipid.ff/spc.itp"

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

#include "drug.itp"

[ system ]
; Name
dopc/chol/drug/sol

[ molecules ]
; Compound#mols
CHOL26
DOPC   102
drg   1
SOL   4677

When I used grompp, I encountered error:

Fatal error:
[ file posre_chol.itp, line 34 ]:
Atom index (30) in position_restraints out of bounds (1-29).
This probably means that you have inserted topology section
"position_restraints" in a part belonging to a different molecule than you
intended to. In that case move the "position_restraints" section to the
right molecule.

I check the GROMACS website at http://www.gromacs.org/Documentation/Errors.
in my opinion my topol.top file is true.

How to fix this error.

Any help will highly appreciated.







--
==

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
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] question about gromacs

[Andrew Bostick]

I used following line in mdp file:

define  = -DPOSRES_dopc -DPOSRES_chol

Is my manner true?


On Tue, Feb 4, 2014 at 5:09 PM, Andrew Bostick wrote:

> Hi all
>
> My system contain dopc + cholesterol + water + drug molecules.
>
> I want to do MD simulation with position restraint on dopc and cholesterol
> molecules.
>
> I used following lines to obtain posre*.itp files:
>
> genrestr -f npt.gro -n index.ndx -o posre_dopc.itp
>
> genrestr -f npt.gro -n index.ndx -o posre_chol.itp
>
> My topol.top file is as follows:
>
> ; Include forcefield parameters
> #include "gromos-43a1-s3_lipid.ff/forcefield.itp"
>
> #include "cholesterol.itp"
> #ifdef POSRES_chol
> #include "posre_chol.itp"
> #endif
>
> #include "dopc.itp"
> #ifdef POSRES_dopc
> #include "posre_dopc.itp"
> #endif
>
> #include "gromos-43a1-s3_lipid.ff/spc.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct   fcxfcyfcz
>11   1000   1000   1000
> #endif
>
> #include "drug.itp"
>
> [ system ]
> ; Name
> dopc/chol/drug/sol
>
> [ molecules ]
> ; Compound#mols
> CHOL26
> DOPC   102
> drg   1
> SOL   4677
>
> When I used grompp, I encountered error:
>
> Fatal error:
> [ file posre_chol.itp, line 34 ]:
> Atom index (30) in position_restraints out of bounds (1-29).
> This probably means that you have inserted topology section
> "position_restraints" in a part belonging to a different molecule than you
> intended to. In that case move the "position_restraints" section to the
> right molecule.
>
> I check the GROMACS website at http://www.gromacs.org/Documentation/Errors.
> in my opinion my topol.top file is true.
>
> How to fix this error.
>
> Any help will highly appreciated.
>
>
>
>
>
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[gmx-users] question about gromacs

[Andrew Bostick]

Hi all

My system contain dopc + cholesterol + water + drug molecules.

I want to do MD simulation with position restraint on dopc and cholesterol
molecules.

I used following lines to obtain posre*.itp files:

genrestr -f npt.gro -n index.ndx -o posre_dopc.itp

genrestr -f npt.gro -n index.ndx -o posre_chol.itp

My topol.top file is as follows:

; Include forcefield parameters
#include "gromos-43a1-s3_lipid.ff/forcefield.itp"

#include "cholesterol.itp"
#ifdef POSRES_chol
#include "posre_chol.itp"
#endif

#include "dopc.itp"
#ifdef POSRES_dopc
#include "posre_dopc.itp"
#endif

#include "gromos-43a1-s3_lipid.ff/spc.itp"

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

#include "drug.itp"

[ system ]
; Name
dopc/chol/drug/sol

[ molecules ]
; Compound#mols
CHOL26
DOPC   102
drg   1
SOL   4677

When I used grompp, I encountered error:

Fatal error:
[ file posre_chol.itp, line 34 ]:
Atom index (30) in position_restraints out of bounds (1-29).
This probably means that you have inserted topology section
"position_restraints" in a part belonging to a different molecule than you
intended to. In that case move the "position_restraints" section to the
right molecule.

I check the GROMACS website at http://www.gromacs.org/Documentation/Errors.
in my opinion my topol.top file is true.

How to fix this error.

Any help will highly appreciated.
-- 
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