Re: [gmx-users] ZN2+ qtot 1.233e-06 ?

[Mark Abraham]

On 01/27/11, Chih-Ying Lin   wrote:
> 
> 
> 
> 
> Hi
> I issued "pdb2gmx with G45a3 force field" on the "bovine carbonic anhydrase" 
> 
> 
> From the .top value, the ZN+2 is given qtot 1.233e-06 ..
> 
> 
> 
>   2611       ZN2+    257     ZN     ZN   1137          2      65.37   ; qtot 
> 1.233e-06
> 
> 
> I am confused with the charges.
> Isn't ZN+2 carrying +2 charges ??
> 
> 

It is - look at the column headings higher up. See 
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for why the 
total charge doesn't look nice.

Mark
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Re: [gmx-users] Re: change in the secondary structure after simulation

[Mark Abraham]

On 01/27/11, bharat gupta   wrote:
> I actually don't understand exactly what u are asking .. since I am not an 
> expert with gromacs.. 
> 

Please leave the old context for the discussion in future emails. Only you are 
paying so much attention to your work that you can be sure of remembering 
things :-)

If your simulation started with these strands unfolded, then your problem is 
somewhere else. However, you have to be able to tell us what was the initial 
conformation, and when your "first trajectory frame" (per last email) happened 
in the simulation.

Mark


> 
> 
> I don't know when is was written .. Here are some lines from the log files of 
> simulation ...
> 
> Statistics over 151 steps using 31 frames
> 
> 
>    Energies (kJ/mol)
>           Angle    Proper Dih. Ryckaert-Bell.          LJ-14     Coulomb-14
>     7.35090e+03    4.37413e+02    3.60104e+03    5.26705e+03    2.58894e+04
> 
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
>     1.05399e+05   -2.92853e+03   -6.79288e+05   -1.07015e+05   -6.41286e+05
>     Kinetic En.   Total Energy    Temperature Pres. DC (bar) Pressure (bar)
> 
>     1.03484e+05   -5.37802e+05    3.3e+02   -2.37485e+02    1.02890e+00
>    Constr. rmsd
>     0.0e+00
> 
> 
>           Box-X          Box-Y          Box-Z
>     7.42618e+00    7.42618e+00    7.42618e+00
> 
> 
> 
>    Total Virial (kJ/mol)
>     3.44183e+04    3.40020e+01   -1.17357e+01
>     3.42160e+01    3.45369e+04   -2.46337e+01
>    -1.16644e+01   -2.48479e+01    3.44949e+04
> 
> 
> 
>    Pressure (bar)
>     1.99809e+00    9.48448e-02    4.57909e-01
>     7.74354e-02    4.97824e-01    1.84797e+00
>     4.52125e-01    1.86535e+00    5.90776e-01
> 
> 
> 
>    Total Dipole (D)
>    -1.86272e+02    4.46310e+01    2.08554e+02
> 
> 
>       T-Protein  T-non-Protein
>     2.99904e+02    3.00013e+02
> 
> 
> 
> 
>   M E G A - F L O P S   A C C O U N T I N G
> 
> 
> 
> 
> 
> There were in total 1502 frames (as shown in VMD )... 
> 
> 
> I don't know about how it compared with the coordinates of the structure that 
> I gave to grompp
> 
> 
> 
> 
> 
> 
> Pls guide
> 
> 
> 
> 
> 
> 
> 
> -- 
> 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, +82-51-583-8343Mobile no. - 010-5818-3680
> E-mail : monu46...@yahoo.com
> 
> 
> 
> 
> 
> 
>
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[gmx-users] ZN2+ qtot 1.233e-06 ?

[Chih-Ying Lin]

 Hi
 I issued "pdb2gmx with G45a3 force field" on the "bovine carbonic
anhydrase"


 From the .top value, the ZN+2 is given qtot 1.233e-06 ..



   2611   ZN2+257 ZN ZN   1137  2  65.37   ;
qtot 1.233e-06


 I am confused with the charges.
 Isn't ZN+2 carrying +2 charges ??


>From Mark =>
It is - look at the column headings higher up. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmeticfor why the
total charge doesn't look nice.


However,
qtot 1.233e-06  ~ 0  isn't it away from +2 charges too much?
Or, it is the tolerable ?


Thank you
Lin
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Re: [gmx-users] ZN2+ qtot 1.233e-06 ?

[Mark Abraham]

On 27/01/2011 7:23 PM, Chih-Ying Lin wrote:


 Hi
 I issued "pdb2gmx with G45a3 force field" on the "bovine carbonic 
anhydrase"



 From the .top value, the ZN+2 is given qtot 1.233e-06 ..



   2611   ZN2+257 ZN ZN   1137  2  65.37   
; qtot 1.233e-06



 I am confused with the charges.
 Isn't ZN+2 carrying +2 charges ??


From Mark =>
It is - look at the column headings higher up. See 
http://www.gromacs.org/Documentation/Floating_Point_Arithmeticfor why 
the total charge doesn't look nice.



However,
qtot 1.233e-06  ~ 0  isn't it away from +2 charges too much?


qtot is not the atomic partial charge. Like I said last time "look at 
the column headings higher up"


Mark


Or, it is the tolerable ?


Thank you
Lin






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Re: [gmx-users] Re: Gromacs + GPU: Problems running dppc example in ftp://ftp.gromacs.org/pub/benchmarks/gmxbench-3.0.tar.gz

[Carsten Kutzner]

Hi Camilo,

On Jan 27, 2011, at 7:19 AM, Camilo Andrés Jimenez Cruz wrote:

> Sorry, abrupt sending,
> 
> the coulombtype is the same
> 
> coulombtype =  cut-off
Is your cut-off actually 0.0 then?

Carsten

> 
> and constraints =  all-bonds is the same. Any idea?
> 
> 2011/1/27 Camilo Andrés Jimenez Cruz 
> Hi all!
> 
> I am trying to run the dppc example located in 
> ftp://ftp.gromacs.org/pub/benchmarks/gmxbench-3.0.tar.gz, with the gpu 
> version of gromacs, when  I run it I get 
> 
> WARNING: OpenMM does not support leap-frog, will use velocity-verlet 
> integrator.
> 
> 
> ---
> Program mdrun_sg, VERSION 4.5.3
> Source code file: 
> /usr/src/redhat/BUILD/gromacs-4.5.3/src/kernel/openmm_wrapper.cpp, line: 555
> 
> Fatal error:
> OpenMM supports only the following methods for electrostatics: NoCutoff (i.e. 
> rcoulomb = rvdw = 0 ),Reaction-Field, Ewald or PME.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
> 
> 
> but when I compare the mdp file with the examples in 
> http://www.gromacs.org/Downloads/Installation_Instructions/Gromacs_on_GPUs 
> (impl_1nm, for example), the integrator is the same
> 
> integrator  =  md
> 
> -- 
> Camilo Andrés Jiménez Cruz
> 
> 
> 
> 
> -- 
> Camilo Andrés Jiménez Cruz
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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[gmx-users] gro to itp

[trevor brown]

Dear all,
I obtained a gro file with g_x2top for a CNT.
I deleted [commands] in t and saved it as XXX.itp
Is it true? If no, how can I convert it into .itp?

best,
trevor
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[gmx-users] proton proton exchange and constant pH simulations.

[Olga Ivchenko]

Dear gromacs users,

I want to ask if is it possible to amke proton proton exchange simulations
by now and constant pH simulations in new versions of Gromacs.

best,
Olga
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Re: [gmx-users] proton proton exchange and constant pH simulations.

[Mark Abraham]

On 27/01/2011 9:44 PM, Olga Ivchenko wrote:

Dear gromacs users,

I want to ask if is it possible to amke proton proton exchange 
simulations by now and constant pH simulations in new versions of Gromacs.


Not sure what you mean, but probably not. See recent publications from 
Lindahl group for what is possible.


Mark
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Re: [gmx-users] Re: change in the secondary structure after simulation

[Justin A. Lemkul]

Mark Abraham wrote:



On 01/27/11, *bharat gupta *  wrote:
I actually don't understand exactly what u are asking .. since I am 
not an expert with gromacs.. 


Please leave the old context for the discussion in future emails. Only 
you are paying so much attention to your work that you can be sure of 
remembering things :-)


If your simulation started with these strands unfolded, then your 
problem is somewhere else. However, you have to be able to tell us what 
was the initial conformation, and when your "first trajectory frame" 
(per last email) happened in the simulation.




I would also add that VMD does a fairly poor job sometimes of guessing secondary 
structure.  So if no beta strand was present in the very first frame, that 
doesn't necessarily mean the secondary structure wasn't stable, it just means 
VMD didn't display it properly.


-Justin


Mark



I don't know when is was written .. Here are some lines from the log 
files of simulation ...

Statistics over 151 steps using 31 frames

   Energies (kJ/mol)
  AngleProper Dih. Ryckaert-Bell.  LJ-14 
Coulomb-14
7.35090e+034.37413e+023.60104e+035.26705e+03   
 2.58894e+04
LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. 
 Potential
1.05399e+05   -2.92853e+03   -6.79288e+05   -1.07015e+05   
-6.41286e+05
Kinetic En.   Total EnergyTemperature Pres. DC (bar) Pressure 
(bar)
1.03484e+05   -5.37802e+053.3e+02   -2.37485e+02   
 1.02890e+00

   Constr. rmsd
0.0e+00

  Box-X  Box-Y  Box-Z
7.42618e+007.42618e+007.42618e+00

   Total Virial (kJ/mol)
3.44183e+043.40020e+01   -1.17357e+01
3.42160e+013.45369e+04   -2.46337e+01
   -1.16644e+01   -2.48479e+013.44949e+04

   Pressure (bar)
1.99809e+009.48448e-024.57909e-01
7.74354e-024.97824e-011.84797e+00
4.52125e-011.86535e+005.90776e-01

   Total Dipole (D)
   -1.86272e+024.46310e+012.08554e+02

  T-Protein  T-non-Protein
2.99904e+023.00013e+02


M E G A - F L O P S   A C C O U N T I N G


There were in total 1502 frames (as shown in VMD )... 

I don't know about how it compared with the coordinates of the 
structure that I gave to grompp




Pls guide




--
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 



--


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] gro to itp

[Justin A. Lemkul]

trevor brown wrote:

Dear all,
I obtained a gro file with g_x2top for a CNT.
I deleted [commands] in t and saved it as XXX.itp


What is [commands]?


Is it true? If no, how can I convert it into .itp?
 


A .gro file contains coordinates, while an .itp file is a topology.  They're not 
interconvertible.


The output of g_x2top is either a .top or .rtp, not a .gro, so I don't know what 
you're working with.  A .top can be converted to a .itp very easily:


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

-Justin


best,
trevor



--


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] Re: change in the secondary structure after simulation

[bharat gupta]

I generated the secondary structure profile of structure retrieved from the
last frame of the simulation ... In that profile those amino acids that are
shown as loops in VMD doesnot have any secondary structure assignment ... it
means that during simulation the structure got changed some how ... and It's
really surprising ?? ... Can u tell me where can the fault be as I am
planning to do the simulation again and this time I will check the structure
after every step .. but for that I want to know how can I save the structure
after every step say for eg. after energy minimization ..

On Thu, Jan 27, 2011 at 8:35 PM, Justin A. Lemkul  wrote:

>
>
> Mark Abraham wrote:
>
>>
>>
>> On 01/27/11, *bharat gupta *  wrote:
>>
>>> I actually don't understand exactly what u are asking .. since I am not
>>> an expert with gromacs..
>>>
>>
>> Please leave the old context for the discussion in future emails. Only you
>> are paying so much attention to your work that you can be sure of
>> remembering things :-)
>>
>> If your simulation started with these strands unfolded, then your problem
>> is somewhere else. However, you have to be able to tell us what was the
>> initial conformation, and when your "first trajectory frame" (per last
>> email) happened in the simulation.
>>
>>
> I would also add that VMD does a fairly poor job sometimes of guessing
> secondary structure.  So if no beta strand was present in the very first
> frame, that doesn't necessarily mean the secondary structure wasn't stable,
> it just means VMD didn't display it properly.
>
> -Justin
>
>  Mark
>>
>>
>>> I don't know when is was written .. Here are some lines from the log
>>> files of simulation ...
>>> Statistics over 151 steps using 31 frames
>>>
>>>   Energies (kJ/mol)
>>>  AngleProper Dih. Ryckaert-Bell.  LJ-14
>>> Coulomb-14
>>>7.35090e+034.37413e+023.60104e+035.26705e+03
>>>  2.58894e+04
>>>LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>>>  Potential
>>>1.05399e+05   -2.92853e+03   -6.79288e+05   -1.07015e+05
>>> -6.41286e+05
>>>Kinetic En.   Total EnergyTemperature Pres. DC (bar) Pressure
>>> (bar)
>>>1.03484e+05   -5.37802e+053.3e+02   -2.37485e+02
>>>  1.02890e+00
>>>   Constr. rmsd
>>>0.0e+00
>>>
>>>  Box-X  Box-Y  Box-Z
>>>7.42618e+007.42618e+007.42618e+00
>>>
>>>   Total Virial (kJ/mol)
>>>3.44183e+043.40020e+01   -1.17357e+01
>>>3.42160e+013.45369e+04   -2.46337e+01
>>>   -1.16644e+01   -2.48479e+013.44949e+04
>>>
>>>   Pressure (bar)
>>>1.99809e+009.48448e-024.57909e-01
>>>7.74354e-024.97824e-011.84797e+00
>>>4.52125e-011.86535e+005.90776e-01
>>>
>>>   Total Dipole (D)
>>>   -1.86272e+024.46310e+012.08554e+02
>>>
>>>  T-Protein  T-non-Protein
>>>2.99904e+023.00013e+02
>>>
>>>
>>> M E G A - F L O P S   A C C O U N T I N G
>>>
>>>
>>> There were in total 1502 frames (as shown in VMD )...
>>> I don't know about how it compared with the coordinates of the structure
>>> that I gave to grompp
>>>
>>> 
>>>
>>> Pls guide
>>>
>>>
>>>
>>>
>>> --
>>> 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 
>>>
>>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
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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] Re: change in the secondary structure after simulation

[Justin A. Lemkul]

bharat gupta wrote:
I generated the secondary structure profile of structure retrieved from 
the last frame of the simulation ... In that profile those amino acids 
that are shown as loops in VMD doesnot have any secondary structure 
assignment ... it means that during simulation the structure got changed 
some how ... and It's really surprising ?? ... Can u tell me where can 
the fault be as I am planning to do the simulation again and this time I 
will check the structure after every step .. but for that I want to know 
how can I save the structure after every step say for eg. after energy 
minimization ..




Secondary structure is dependent upon the chosen force field and the .mdp 
settings.  Since you've posted neither, there's no way to tell what might be to 
blame.


You can save more frequently by setting the proper output controls.  Read in the 
manual about the nst* options and set the accordingly.


-Justin

On Thu, Jan 27, 2011 at 8:35 PM, Justin A. Lemkul > wrote:




Mark Abraham wrote:



On 01/27/11, *bharat gupta * mailto:bharat.85.m...@gmail.com>> wrote:

I actually don't understand exactly what u are asking ..
since I am not an expert with gromacs..


Please leave the old context for the discussion in future
emails. Only you are paying so much attention to your work that
you can be sure of remembering things :-)

If your simulation started with these strands unfolded, then
your problem is somewhere else. However, you have to be able to
tell us what was the initial conformation, and when your "first
trajectory frame" (per last email) happened in the simulation.


I would also add that VMD does a fairly poor job sometimes of
guessing secondary structure.  So if no beta strand was present in
the very first frame, that doesn't necessarily mean the secondary
structure wasn't stable, it just means VMD didn't display it properly.

-Justin

Mark


I don't know when is was written .. Here are some lines from
the log files of simulation ...
Statistics over 151 steps using 31 frames

  Energies (kJ/mol)
 AngleProper Dih. Ryckaert-Bell.  LJ-14
Coulomb-14
   7.35090e+034.37413e+023.60104e+035.26705e+03
   2.58894e+04
   LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
 Potential
   1.05399e+05   -2.92853e+03   -6.79288e+05   -1.07015e+05
  -6.41286e+05
   Kinetic En.   Total EnergyTemperature Pres. DC (bar)
Pressure (bar)
   1.03484e+05   -5.37802e+053.3e+02   -2.37485e+02
   1.02890e+00
  Constr. rmsd
   0.0e+00

 Box-X  Box-Y  Box-Z
   7.42618e+007.42618e+007.42618e+00

  Total Virial (kJ/mol)
   3.44183e+043.40020e+01   -1.17357e+01
   3.42160e+013.45369e+04   -2.46337e+01
  -1.16644e+01   -2.48479e+013.44949e+04

  Pressure (bar)
   1.99809e+009.48448e-024.57909e-01
   7.74354e-024.97824e-011.84797e+00
   4.52125e-011.86535e+005.90776e-01

  Total Dipole (D)
  -1.86272e+024.46310e+012.08554e+02

 T-Protein  T-non-Protein
   2.99904e+023.00013e+02


M E G A - F L O P S   A C C O U N T I N G


There were in total 1502 frames (as shown in VMD )...
I don't know about how it compared with the coordinates of
the structure that I gave to grompp



Pls guide




-- 
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 
>


-- 



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


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


http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
 

Re: [gmx-users] Re: change in the secondary structure after simulation

[bharat gupta]

I used the same .mdp files that are given in the lysozyme tutorial .. Since
I was knowing what all parameters to change .. but after energy minimization
and equilibration steps , the graphs that I got were fine ... even the rmsd
graph of the final structure is also fine .. I have attached the final rmsd
graph of the structure ..




On Thu, Jan 27, 2011 at 3:44 AM, Justin A. Lemkul  wrote:

>
>
> bharat gupta wrote:
>
>> I generated the secondary structure profile of structure retrieved from
>> the last frame of the simulation ... In that profile those amino acids that
>> are shown as loops in VMD doesnot have any secondary structure assignment
>> ... it means that during simulation the structure got changed some how ...
>> and It's really surprising ?? ... Can u tell me where can the fault be as I
>> am planning to do the simulation again and this time I will check the
>> structure after every step .. but for that I want to know how can I save the
>> structure after every step say for eg. after energy minimization ..
>>
>>
> Secondary structure is dependent upon the chosen force field and the .mdp
> settings.  Since you've posted neither, there's no way to tell what might be
> to blame.
>
> You can save more frequently by setting the proper output controls.  Read
> in the manual about the nst* options and set the accordingly.
>
> -Justin
>
>  On Thu, Jan 27, 2011 at 8:35 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Mark Abraham wrote:
>>
>>
>>
>>On 01/27/11, *bharat gupta * > > wrote:
>>
>>I actually don't understand exactly what u are asking ..
>>since I am not an expert with gromacs..
>>
>>
>>Please leave the old context for the discussion in future
>>emails. Only you are paying so much attention to your work that
>>you can be sure of remembering things :-)
>>
>>If your simulation started with these strands unfolded, then
>>your problem is somewhere else. However, you have to be able to
>>tell us what was the initial conformation, and when your "first
>>trajectory frame" (per last email) happened in the simulation.
>>
>>
>>I would also add that VMD does a fairly poor job sometimes of
>>guessing secondary structure.  So if no beta strand was present in
>>the very first frame, that doesn't necessarily mean the secondary
>>structure wasn't stable, it just means VMD didn't display it properly.
>>
>>-Justin
>>
>>Mark
>>
>>
>>I don't know when is was written .. Here are some lines from
>>the log files of simulation ...
>>Statistics over 151 steps using 31 frames
>>
>>  Energies (kJ/mol)
>> AngleProper Dih. Ryckaert-Bell.  LJ-14
>>Coulomb-14
>>   7.35090e+034.37413e+023.60104e+035.26705e+03
>>   2.58894e+04
>>   LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>> Potential
>>   1.05399e+05   -2.92853e+03   -6.79288e+05   -1.07015e+05
>>  -6.41286e+05
>>   Kinetic En.   Total EnergyTemperature Pres. DC (bar)
>>Pressure (bar)
>>   1.03484e+05   -5.37802e+053.3e+02   -2.37485e+02
>>   1.02890e+00
>>  Constr. rmsd
>>   0.0e+00
>>
>> Box-X  Box-Y  Box-Z
>>   7.42618e+007.42618e+007.42618e+00
>>
>>  Total Virial (kJ/mol)
>>   3.44183e+043.40020e+01   -1.17357e+01
>>   3.42160e+013.45369e+04   -2.46337e+01
>>  -1.16644e+01   -2.48479e+013.44949e+04
>>
>>  Pressure (bar)
>>   1.99809e+009.48448e-024.57909e-01
>>   7.74354e-024.97824e-011.84797e+00
>>   4.52125e-011.86535e+005.90776e-01
>>
>>  Total Dipole (D)
>>  -1.86272e+024.46310e+012.08554e+02
>>
>> T-Protein  T-non-Protein
>>   2.99904e+023.00013e+02
>>
>>
>>M E G A - F L O P S   A C C O U N T I N G
>>
>>
>>There were in total 1502 frames (as shown in VMD )...
>>I don't know about how it compared with the coordinates of
>>the structure that I gave to grompp
>>
>>
>>
>>Pls guide
>>
>>
>>
>>
>>-- 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 
>>  

Re: [gmx-users] Re: change in the secondary structure after simulation

[Mark Abraham]

On 27/01/2011 11:11 PM, bharat gupta wrote:
I used the same .mdp files that are given in the lysozyme tutorial .. 
Since I was knowing what all parameters to change .. but after energy 
minimization and equilibration steps , the graphs that I got were fine 
... even the rmsd graph of the final structure is also fine .. I have 
attached the final rmsd graph of the structure ..


That suggests the problem was in the structure you started the 
simulation from, like I've suggested a few times now :-)


Mark
On Thu, Jan 27, 2011 at 3:44 AM, Justin A. Lemkul > wrote:




bharat gupta wrote:

I generated the secondary structure profile of structure
retrieved from the last frame of the simulation ... In that
profile those amino acids that are shown as loops in VMD
doesnot have any secondary structure assignment ... it means
that during simulation the structure got changed some how ...
and It's really surprising ?? ... Can u tell me where can the
fault be as I am planning to do the simulation again and this
time I will check the structure after every step .. but for
that I want to know how can I save the structure after every
step say for eg. after energy minimization ..


Secondary structure is dependent upon the chosen force field and
the .mdp settings.  Since you've posted neither, there's no way to
tell what might be to blame.

You can save more frequently by setting the proper output
controls.  Read in the manual about the nst* options and set the
accordingly.

-Justin

On Thu, Jan 27, 2011 at 8:35 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   Mark Abraham wrote:



   On 01/27/11, *bharat gupta * mailto:bharat.85.m...@gmail.com>
>> wrote:

   I actually don't understand exactly what u are
asking ..
   since I am not an expert with gromacs..


   Please leave the old context for the discussion in future
   emails. Only you are paying so much attention to your
work that
   you can be sure of remembering things :-)

   If your simulation started with these strands unfolded,
then
   your problem is somewhere else. However, you have to be
able to
   tell us what was the initial conformation, and when
your "first
   trajectory frame" (per last email) happened in the
simulation.


   I would also add that VMD does a fairly poor job sometimes of
   guessing secondary structure.  So if no beta strand was
present in
   the very first frame, that doesn't necessarily mean the
secondary
   structure wasn't stable, it just means VMD didn't display
it properly.

   -Justin

   Mark


   I don't know when is was written .. Here are some
lines from
   the log files of simulation ...
   Statistics over 151 steps using 31 frames

 Energies (kJ/mol)
AngleProper Dih. Ryckaert-Bell.  
   LJ-14

   Coulomb-14
  7.35090e+034.37413e+023.60104e+03  
 5.26705e+03

  2.58894e+04
  LJ (SR)  Disper. corr.   Coulomb (SR)  
Coul. recip.

Potential
  1.05399e+05   -2.92853e+03   -6.79288e+05  
-1.07015e+05

 -6.41286e+05
  Kinetic En.   Total EnergyTemperature Pres.
DC (bar)
   Pressure (bar)
  1.03484e+05   -5.37802e+053.3e+02  
-2.37485e+02

  1.02890e+00
 Constr. rmsd
  0.0e+00

Box-X  Box-Y  Box-Z
  7.42618e+007.42618e+007.42618e+00

 Total Virial (kJ/mol)
  3.44183e+043.40020e+01   -1.17357e+01
  3.42160e+013.45369e+04   -2.46337e+01
 -1.16644e+01   -2.48479e+013.44949e+04

 Pressure (bar)
  1.99809e+009.48448e-024.57909e-01
  7.74354e-024.97824e-011.84797e+00
  4.52125e-011.86535e+005.90776e-01

 Total Dipole (D)
 -1.86272e+024.46310e+012.08554e+02

T-Protein  T-non-Protein
  2.99904e+023.00013e+02


   M E G A - F L O P S   A C C O U N T I N G


  

Re: [gmx-users] proton proton exchange and constant pH simulations.

[Olga Ivchenko]

Just I heard that molecular mechanics proton proton transfer should be soon
implemented in gromacs. That's why I am, asking it.

2011/1/27 Mark Abraham 

> On 27/01/2011 9:44 PM, Olga Ivchenko wrote:
>
>> Dear gromacs users,
>>
>> I want to ask if is it possible to amke proton proton exchange simulations
>> by now and constant pH simulations in new versions of Gromacs.
>>
>
> Not sure what you mean, but probably not. See recent publications from
> Lindahl group for what is possible.
>
> Mark
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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Re: [gmx-users] proton proton exchange and constant pH simulations.

[Justin A. Lemkul]

Olga Ivchenko wrote:
Just I heard that molecular mechanics proton proton transfer should be 
soon implemented in gromacs. That's why I am, asking it.




When a new version is released, the new features will be announced.  As of right 
now, these algorithms are under development and have not yet been merged into 
the main development branch.


-Justin

2011/1/27 Mark Abraham >


On 27/01/2011 9:44 PM, Olga Ivchenko wrote:

Dear gromacs users,

I want to ask if is it possible to amke proton proton exchange
simulations by now and constant pH simulations in new versions
of Gromacs.


Not sure what you mean, but probably not. See recent publications
from Lindahl group for what is possible.

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


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.
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--


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] proton proton exchange and constant pH simulations.

[Miguel Machuqueiro]

On 27-01-2011 11:29, Mark Abraham wrote:

On 27/01/2011 9:44 PM, Olga Ivchenko wrote:

Dear gromacs users,

I want to ask if is it possible to amke proton proton exchange
simulations by now and constant pH simulations in new versions of Gromacs.

Not sure what you mean, but probably not. See recent publications from
Lindahl group for what is possible.

Mark


Hi all,

Constant-pH MD simulations using an older version of gromacs (v. 3.2.1) 
is possible:


http://dx.doi.org/10.1021/jp056456q
http://dx.doi.org/10.1529/biophysj.106.092445
http://dx.doi.org/10.1002/prot.21923
http://dx.doi.org/10.1021/ja808463e
http://dx.doi.org/10.1021/jp104753t

Unfortunately, newer versions (v. 4.x.x) do not allow the use of Freeze 
Groups in NPT simulations, which is essential for the method to work. In 
case this is "solved" in future releases, we will port the method to new 
and faster gromacs versions.


Regards,

--

Miguel Machuqueiro
Department of Chemistry and Biochemistry
Faculty of Sciences, University of Lisbon
Campo Grande, Edifício C8 (sala 8.5.47)
1749-016 Lisboa, Portugal
Tel.  : +351 217500112 (int.ext.28547)
Mobile: +351 967562285
E-mail: machuque at fc.ul.pt
www1: http://webpages.fc.ul.pt/~mamachuqueiro
www2: http://intheochem.fc.ul.pt
__


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Re: [gmx-users] Re: change in the secondary structure after simulation

[bharat gupta]

I don't think that there is any problem in the structure .. since I am
simulating the crystal structure taken from PDB ... and I have checked the
structure generated after pdb2gmx and solvation..

Since I am reapeating the simulation again I want to know and I am on energy
minimzation step I want to know .. how can I retrieve the structure after
minimization ..

On Thu, Jan 27, 2011 at 4:16 AM, Mark Abraham wrote:

>  On 27/01/2011 11:11 PM, bharat gupta wrote:
>
> I used the same .mdp files that are given in the lysozyme tutorial .. Since
> I was knowing what all parameters to change .. but after energy minimization
> and equilibration steps , the graphs that I got were fine ... even the rmsd
> graph of the final structure is also fine .. I have attached the final rmsd
> graph of the structure ..
>
>
> That suggests the problem was in the structure you started the simulation
> from, like I've suggested a few times now :-)
>
> Mark
>
>
>
> On Thu, Jan 27, 2011 at 3:44 AM, Justin A. Lemkul  wrote:
>
>>
>>
>> bharat gupta wrote:
>>
>>> I generated the secondary structure profile of structure retrieved from
>>> the last frame of the simulation ... In that profile those amino acids that
>>> are shown as loops in VMD doesnot have any secondary structure assignment
>>> ... it means that during simulation the structure got changed some how ...
>>> and It's really surprising ?? ... Can u tell me where can the fault be as I
>>> am planning to do the simulation again and this time I will check the
>>> structure after every step .. but for that I want to know how can I save the
>>> structure after every step say for eg. after energy minimization ..
>>>
>>>
>> Secondary structure is dependent upon the chosen force field and the .mdp
>> settings.  Since you've posted neither, there's no way to tell what might be
>> to blame.
>>
>> You can save more frequently by setting the proper output controls.  Read
>> in the manual about the nst* options and set the accordingly.
>>
>> -Justin
>>
>>  On Thu, Jan 27, 2011 at 8:35 PM, Justin A. Lemkul >> jalem...@vt.edu>> wrote:
>>>
>>>
>>>
>>>Mark Abraham wrote:
>>>
>>>
>>>
>>>On 01/27/11, *bharat gupta * >> > wrote:
>>>
>>>I actually don't understand exactly what u are asking ..
>>>since I am not an expert with gromacs..
>>>
>>>
>>>Please leave the old context for the discussion in future
>>>emails. Only you are paying so much attention to your work that
>>>you can be sure of remembering things :-)
>>>
>>>If your simulation started with these strands unfolded, then
>>>your problem is somewhere else. However, you have to be able to
>>>tell us what was the initial conformation, and when your "first
>>>trajectory frame" (per last email) happened in the simulation.
>>>
>>>
>>>I would also add that VMD does a fairly poor job sometimes of
>>>guessing secondary structure.  So if no beta strand was present in
>>>the very first frame, that doesn't necessarily mean the secondary
>>>structure wasn't stable, it just means VMD didn't display it properly.
>>>
>>>-Justin
>>>
>>>Mark
>>>
>>>
>>>I don't know when is was written .. Here are some lines from
>>>the log files of simulation ...
>>>Statistics over 151 steps using 31 frames
>>>
>>>  Energies (kJ/mol)
>>> AngleProper Dih. Ryckaert-Bell.  LJ-14
>>>Coulomb-14
>>>   7.35090e+034.37413e+023.60104e+035.26705e+03
>>>   2.58894e+04
>>>   LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>>> Potential
>>>   1.05399e+05   -2.92853e+03   -6.79288e+05   -1.07015e+05
>>>  -6.41286e+05
>>>   Kinetic En.   Total EnergyTemperature Pres. DC (bar)
>>>Pressure (bar)
>>>   1.03484e+05   -5.37802e+053.3e+02   -2.37485e+02
>>>   1.02890e+00
>>>  Constr. rmsd
>>>   0.0e+00
>>>
>>> Box-X  Box-Y  Box-Z
>>>   7.42618e+007.42618e+007.42618e+00
>>>
>>>  Total Virial (kJ/mol)
>>>   3.44183e+043.40020e+01   -1.17357e+01
>>>   3.42160e+013.45369e+04   -2.46337e+01
>>>  -1.16644e+01   -2.48479e+013.44949e+04
>>>
>>>  Pressure (bar)
>>>   1.99809e+009.48448e-024.57909e-01
>>>   7.74354e-024.97824e-011.84797e+00
>>>   4.52125e-011.86535e+005.90776e-01
>>>
>>>  Total Dipole (D)
>>>  -1.86272e+024.46310e+012.08554e+02
>>>
>>> T-Protein  T-non-Protein
>>>   2.99904e+023.00013e+02
>>>
>>>
>>>M E G A - F L O P S   A C C O U N T I N G
>>>
>>>
>>>There were in total 15

Re: [gmx-users] Re: change in the secondary structure after simulation

[Justin A. Lemkul]

bharat gupta wrote:
I don't think that there is any problem in the structure .. since I am 
simulating the crystal structure taken from PDB ... and I have checked 
the structure generated after pdb2gmx and solvation..
 
Since I am reapeating the simulation again I want to know and I am on 
energy minimzation step I want to know .. how can I retrieve the 
structure after minimization ..




The structure after minimization (or any process done by mdrun) is contained in 
whatever filename you passed to the -c flag.  If you haven't specified any name, 
it is confout.gro.


-Justin

On Thu, Jan 27, 2011 at 4:16 AM, Mark Abraham > wrote:


On 27/01/2011 11:11 PM, bharat gupta wrote:

I used the same .mdp files that are given in the lysozyme tutorial
.. Since I was knowing what all parameters to change .. but after
energy minimization and equilibration steps , the graphs that I
got were fine ... even the rmsd graph of the final structure is
also fine .. I have attached the final rmsd graph of the structure ..


That suggests the problem was in the structure you started the
simulation from, like I've suggested a few times now :-)

Mark

 

On Thu, Jan 27, 2011 at 3:44 AM, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote:



bharat gupta wrote:

I generated the secondary structure profile of structure
retrieved from the last frame of the simulation ... In
that profile those amino acids that are shown as loops in
VMD doesnot have any secondary structure assignment ... it
means that during simulation the structure got changed
some how ... and It's really surprising ?? ... Can u tell
me where can the fault be as I am planning to do the
simulation again and this time I will check the structure
after every step .. but for that I want to know how can I
save the structure after every step say for eg. after
energy minimization ..


Secondary structure is dependent upon the chosen force field
and the .mdp settings.  Since you've posted neither, there's
no way to tell what might be to blame.

You can save more frequently by setting the proper output
controls.  Read in the manual about the nst* options and set
the accordingly.

-Justin

On Thu, Jan 27, 2011 at 8:35 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   Mark Abraham wrote:



   On 01/27/11, *bharat gupta *
mailto:bharat.85.m...@gmail.com>
   >> wrote:

   I actually don't understand exactly what u are
asking ..
   since I am not an expert with gromacs..


   Please leave the old context for the discussion in
future
   emails. Only you are paying so much attention to
your work that
   you can be sure of remembering things :-)

   If your simulation started with these strands
unfolded, then
   your problem is somewhere else. However, you have
to be able to
   tell us what was the initial conformation, and when
your "first
   trajectory frame" (per last email) happened in the
simulation.


   I would also add that VMD does a fairly poor job
sometimes of
   guessing secondary structure.  So if no beta strand was
present in
   the very first frame, that doesn't necessarily mean the
secondary
   structure wasn't stable, it just means VMD didn't
display it properly.

   -Justin

   Mark


   I don't know when is was written .. Here are
some lines from
   the log files of simulation ...
   Statistics over 151 steps using 31 frames

 Energies (kJ/mol)
AngleProper Dih. Ryckaert-Bell.  
   LJ-14

   Coulomb-14
  7.35090e+034.37413e+023.60104e+03  
 5.26705e+03

  2.58894e+04
  LJ (SR)  Disper. corr.   Coulomb (SR)  
Coul. recip.

Potential
  1.05399e+05   -2.92853e+03   -6.79288e+05  
-1.07015e+05

 -6.41286e+05
  Kinetic En.   Total EnergyTemperature
Pres. DC (bar)
   Pressure (bar)

[gmx-users] remove all waters from the pdb file

[ahmet yıldırım]

Dear users,

I want to remove all waters from the xxx.pdb file. Then, I want to save the
pdb file (new pdb) without waters because I will use the methanol as a
solvent. I looked at mail list but I could not find the answer I wanted.

What should I do?

Thanks in advance

-- 
Ahmet YILDIRIM
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Re: [gmx-users] remove all waters from the pdb file

[Justin A. Lemkul]

ahmet yıldırım wrote:

Dear users,

I want to remove all waters from the xxx.pdb file. Then, I want to save 
the pdb file (new pdb) without waters because I will use the methanol as 
a solvent. I looked at mail list but I could not find the answer I wanted.


What should I do?



Please read trjconv -h, with special attention to point #2 in the opening list.

-Justin


Thanks in advance

--
Ahmet YILDIRIM



--


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] Re: change in the secondary structure after simulation

[bharat gupta]

>  I didn't gave any -c flag while md run .. and there is no confout.gro in
> my folder .. I have attached the graph obtained after energy minimzation ..
> I want to ask why the graph is not coming like the one shown in the tutorial
> .. I guess I asked that same question earlier also ?? ..  Here is the
> details of energy minimization result
>
> Steepest Descents converged to Fmax < 1000 in 720 steps
> Potential Energy  = -6.7970475e+05
> Maximum force =  9.5201904e+02 on atom 78
> Norm of force =  1.9553707e+01
> On Thu, Jan 27, 2011 at 5:12 AM, Justin A. Lemkul  wrote:
>
>>
>>
>> bharat gupta wrote:
>>
>>> I don't think that there is any problem in the structure .. since I am
>>> simulating the crystal structure taken from PDB ... and I have checked the
>>> structure generated after pdb2gmx and solvation..
>>>  Since I am reapeating the simulation again I want to know and I am on
>>> energy minimzation step I want to know .. how can I retrieve the structure
>>> after minimization ..
>>>
>>>
>> The structure after minimization (or any process done by mdrun) is
>> contained in whatever filename you passed to the -c flag.  If you haven't
>> specified any name, it is confout.gro.
>>
>> -Justin
>>
>>  On Thu, Jan 27, 2011 at 4:16 AM, Mark Abraham 
>> >> mark.abra...@anu.edu.au>> wrote:
>>>
>>>On 27/01/2011 11:11 PM, bharat gupta wrote:
>>>
I used the same .mdp files that are given in the lysozyme tutorial
.. Since I was knowing what all parameters to change .. but after
energy minimization and equilibration steps , the graphs that I
got were fine ... even the rmsd graph of the final structure is
also fine .. I have attached the final rmsd graph of the structure ..

>>>
>>>That suggests the problem was in the structure you started the
>>>simulation from, like I've suggested a few times now :-)
>>>
>>>Mark
>>>
>>>
>>>
On Thu, Jan 27, 2011 at 3:44 AM, Justin A. Lemkul >>>> wrote:



bharat gupta wrote:

I generated the secondary structure profile of structure
retrieved from the last frame of the simulation ... In
that profile those amino acids that are shown as loops in
VMD doesnot have any secondary structure assignment ... it
means that during simulation the structure got changed
some how ... and It's really surprising ?? ... Can u tell
me where can the fault be as I am planning to do the
simulation again and this time I will check the structure
after every step .. but for that I want to know how can I
save the structure after every step say for eg. after
energy minimization ..


Secondary structure is dependent upon the chosen force field
and the .mdp settings.  Since you've posted neither, there's
no way to tell what might be to blame.

You can save more frequently by setting the proper output
controls.  Read in the manual about the nst* options and set
the accordingly.

-Justin

On Thu, Jan 27, 2011 at 8:35 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
 >> wrote:



   Mark Abraham wrote:



   On 01/27/11, *bharat gupta *
mailto:bharat.85.m...@gmail.com>
   >> wrote:

   I actually don't understand exactly what u are
asking ..
   since I am not an expert with gromacs..


   Please leave the old context for the discussion in
future
   emails. Only you are paying so much attention to
your work that
   you can be sure of remembering things :-)

   If your simulation started with these strands
unfolded, then
   your problem is somewhere else. However, you have
to be able to
   tell us what was the initial conformation, and when
your "first
   trajectory frame" (per last email) happened in the
simulation.


   I would also add that VMD does a fairly poor job
sometimes of
   guessing secondary structure.  So if no beta strand was
present in
   the very first frame, that doesn't necessarily mean the
secondary
   structure wasn't stable, it just means VMD didn't
display it properly.

  

Re: [gmx-users] Re: change in the secondary structure after simulation

[Justin A. Lemkul]

bharat gupta wrote:
I didn't gave any -c flag while md run .. and there is no confout.gro in 
my folder .. I have attached the graph obtained after energy minimzation 


I've never heard of such a thing.  mdrun produces several files automatically: 
traj.trr, ener.edr, md.log, and confout.gro.  The output configuration is always 
written.  If it wasn't, then something is preventing mdrun from writing this 
file (full disk, read/write permissions, etc).


.. I want to ask why the graph is not coming like the one shown in the 
tutorial .. I guess I asked that same question earlier also ?? ..  Here 
is the details of energy minimization result
 


The shape of the graph is nearly identical.  You converged to an acceptable 
energy and force, so what's the problem?


If you're following the tutorial's procedure with a different system, there is 
absolutely no reason to expect that one system will converge to the same 
potential energy as another.  They're fundamentally different.  Even if you are 
working with the same system, there can be differences in the final energy.  EM 
is just a procedure to optimize the orientation of the molecules in the system. 
 It may converge somewhat differently each time you do it.


-Justin


Steepest Descents converged to Fmax < 1000 in 720 steps
Potential Energy  = -6.7970475e+05
Maximum force =  9.5201904e+02 on atom 78
Norm of force =  1.9553707e+01
 



 
On Thu, Jan 27, 2011 at 5:12 AM, Justin A. Lemkul > wrote:




bharat gupta wrote:

I don't think that there is any problem in the structure ..
since I am simulating the crystal structure taken from PDB ...
and I have checked the structure generated after pdb2gmx and
solvation..
 Since I am reapeating the simulation again I want to know and I
am on energy minimzation step I want to know .. how can I
retrieve the structure after minimization ..


The structure after minimization (or any process done by mdrun) is
contained in whatever filename you passed to the -c flag.  If you
haven't specified any name, it is confout.gro.

-Justin

On Thu, Jan 27, 2011 at 4:16 AM, Mark Abraham
mailto:mark.abra...@anu.edu.au>
>> wrote:

   On 27/01/2011 11:11 PM, bharat gupta wrote:

   I used the same .mdp files that are given in the lysozyme
tutorial
   .. Since I was knowing what all parameters to change ..
but after
   energy minimization and equilibration steps , the graphs
that I
   got were fine ... even the rmsd graph of the final
structure is
   also fine .. I have attached the final rmsd graph of the
structure ..


   That suggests the problem was in the structure you started the
   simulation from, like I've suggested a few times now :-)

   Mark

   


   On Thu, Jan 27, 2011 at 3:44 AM, Justin A. Lemkul
mailto:jalem...@vt.edu>
   >> wrote:



   bharat gupta wrote:

   I generated the secondary structure profile of
structure
   retrieved from the last frame of the simulation
... In
   that profile those amino acids that are shown as
loops in
   VMD doesnot have any secondary structure
assignment ... it
   means that during simulation the structure got
changed
   some how ... and It's really surprising ?? ...
Can u tell
   me where can the fault be as I am planning to do the
   simulation again and this time I will check the
structure
   after every step .. but for that I want to know
how can I
   save the structure after every step say for eg. after
   energy minimization ..


   Secondary structure is dependent upon the chosen
force field
   and the .mdp settings.  Since you've posted neither,
there's
   no way to tell what might be to blame.

   You can save more frequently by setting the proper output
   controls.  Read in the manual about the nst* options
and set
   the accordingly.

   -Justin

   On Thu, Jan 27, 2011 at 8:35 PM, Justin A. Lemkul
   mailto:jalem...@vt.edu>
>
   

Re: [gmx-users] Re: change in the secondary structure after simulation

[Thomas Piggot]

Hi Bharat,

If you have used the -deffnm option then the output gro will be called 
whatever name you used for the -deffnm option and not the default 
confout.gro.


Tom

Justin A. Lemkul wrote:


bharat gupta wrote:

I didn't gave any -c flag while md run .. and there is no confout.gro in
my folder .. I have attached the graph obtained after energy minimzation


I've never heard of such a thing.  mdrun produces several files automatically:
traj.trr, ener.edr, md.log, and confout.gro.  The output configuration is always
written.  If it wasn't, then something is preventing mdrun from writing this
file (full disk, read/write permissions, etc).


.. I want to ask why the graph is not coming like the one shown in the
tutorial .. I guess I asked that same question earlier also ?? ..  Here
is the details of energy minimization result



The shape of the graph is nearly identical.  You converged to an acceptable
energy and force, so what's the problem?

If you're following the tutorial's procedure with a different system, there is
absolutely no reason to expect that one system will converge to the same
potential energy as another.  They're fundamentally different.  Even if you are
working with the same system, there can be differences in the final energy.  EM
is just a procedure to optimize the orientation of the molecules in the system.
  It may converge somewhat differently each time you do it.

-Justin


Steepest Descents converged to Fmax < 1000 in 720 steps
Potential Energy  = -6.7970475e+05
Maximum force =  9.5201904e+02 on atom 78
Norm of force =  1.9553707e+01




On Thu, Jan 27, 2011 at 5:12 AM, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote:



bharat gupta wrote:

I don't think that there is any problem in the structure ..
since I am simulating the crystal structure taken from PDB ...
and I have checked the structure generated after pdb2gmx and
solvation..
 Since I am reapeating the simulation again I want to know and I
am on energy minimzation step I want to know .. how can I
retrieve the structure after minimization ..


The structure after minimization (or any process done by mdrun) is
contained in whatever filename you passed to the -c flag.  If you
haven't specified any name, it is confout.gro.

-Justin

On Thu, Jan 27, 2011 at 4:16 AM, Mark Abraham
mailto:mark.abra...@anu.edu.au>
>> wrote:

   On 27/01/2011 11:11 PM, bharat gupta wrote:

   I used the same .mdp files that are given in the lysozyme
tutorial
   .. Since I was knowing what all parameters to change ..
but after
   energy minimization and equilibration steps , the graphs
that I
   got were fine ... even the rmsd graph of the final
structure is
   also fine .. I have attached the final rmsd graph of the
structure ..


   That suggests the problem was in the structure you started the
   simulation from, like I've suggested a few times now :-)

   Mark



   On Thu, Jan 27, 2011 at 3:44 AM, Justin A. Lemkul
mailto:jalem...@vt.edu>
   >> wrote:



   bharat gupta wrote:

   I generated the secondary structure profile of
structure
   retrieved from the last frame of the simulation
... In
   that profile those amino acids that are shown as
loops in
   VMD doesnot have any secondary structure
assignment ... it
   means that during simulation the structure got
changed
   some how ... and It's really surprising ?? ...
Can u tell
   me where can the fault be as I am planning to do the
   simulation again and this time I will check the
structure
   after every step .. but for that I want to know
how can I
   save the structure after every step say for eg. after
   energy minimization ..


   Secondary structure is dependent upon the chosen
force field
   and the .mdp settings.  Since you've posted neither,
there's
   no way to tell what might be to blame.

   You can save more frequently by setting the proper output
   controls.  Read in the manual about the nst* options
and set
   the accordingly.

   -Justin

   On Thu, Jan 27, 2011 at 8:35 PM, Justin A. Lemkul
   mailto:jalem...@vt.edu>

[gmx-users] solvation_box_preparation

[shahid nayeem]

Dear All

I am sending this mail again on user list because my reply to Mark’s
query was not uploaded on the list.

Original messge:

I am trying to prepare a solvation box of chaps. After generating .itp
and .gro at ProDrg and thorough check of charges, I started with a box
size of 6x6x6. Energy minimization, simulated annealing (Cooling under
high pressure and again heating at normal pressure) as well as final
equilibration ran smoothly. But finally I get a box where all water
molecules get accumulated in two three small region within the box and
all chaps molecules gets accumulated in another small regions.I wanted
near random uniform distribution of chaps in water. Any help from
user, where I am wrong and what should I do.

Reply to query.

I created a box of 6x6x6 inserting 7 molecule of chaps with (genbox
–ci 7 chaps.gro).Then I solvated the output box  with genbox using
-maxsol 500 and spc216.gro. On visualization, at this stage itself
uniform solvation did not occur (I got water in one region and chaps
molecule in other region) but I observed a similar situation while
preparing 10M urea salvation box. This was followed by 1ns simulated
annealing from temp 300K to 0K and pressure 100 bar, then 1ns
simulated annealing from temp. 0k to 300k and then ins equilibriation
at this temperature. In case of urea finally I got uniformly solvated
urea_water_box but in chaps I couldn’t get it.

Shahid Nayeem
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Re: [gmx-users] solvation_box_preparation

[Justin A. Lemkul]

shahid nayeem wrote:

Dear All

I am sending this mail again on user list because my reply to Mark’s
query was not uploaded on the list.

Original messge:

I am trying to prepare a solvation box of chaps. After generating .itp
and .gro at ProDrg and thorough check of charges, I started with a box
size of 6x6x6. Energy minimization, simulated annealing (Cooling under
high pressure and again heating at normal pressure) as well as final
equilibration ran smoothly. But finally I get a box where all water
molecules get accumulated in two three small region within the box and
all chaps molecules gets accumulated in another small regions.I wanted
near random uniform distribution of chaps in water. Any help from
user, where I am wrong and what should I do.

Reply to query.

I created a box of 6x6x6 inserting 7 molecule of chaps with (genbox
–ci 7 chaps.gro).Then I solvated the output box  with genbox using
-maxsol 500 and spc216.gro. On visualization, at this stage itself
uniform solvation did not occur (I got water in one region and chaps
molecule in other region) but I observed a similar situation while


If your box was not completely solvated, then don't use -maxsol.  A box of 6x6x6 
nm should require more than 500 molecules of water to fill.  If you're trying to 
achieve some specific mole fraction or concentration, then re-figure your box size.


-Justin


preparing 10M urea salvation box. This was followed by 1ns simulated
annealing from temp 300K to 0K and pressure 100 bar, then 1ns
simulated annealing from temp. 0k to 300k and then ins equilibriation
at this temperature. In case of urea finally I got uniformly solvated
urea_water_box but in chaps I couldn’t get it.

Shahid Nayeem


--


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] Using g_select to detect water pores in a bilayer

[Manuel Nuno Melo]

Hello,

I have a coarse-grain lipid bilayer system with a pore-forming peptide. I am
trying to use g_select to automate the detection of the opening of a water
pore.

My idea is to count the number of water molecules within a certain z
distance of the bilayer center, and flag a pore above a certain threshold.
The problem is that the position of this z-slab cannot be hardcoded because
my simulations are relatively long and there is sometimes a drift of the
bilayer.

I tried instead to define the z-distance of the waters relatively to the COM
of the acyl chains (my terminal acyl beads are named C4A and C4B, and the
water residues PW):

centerbilayer = com of name "C4[AB]"
resname PW and within 0.5 of centerbilayer

However, as expected, this defines a sphere around the COM, not a z-slab. Is
there anyway to achieve that using g_select?

Another approach to count pore waters like:
resname PW and within 0.8 of name "C4[AB]"

also fails because the pore is lined by peptide molecules and a relatively
large distance for the PW-C4 distance must be allowed. This means that
interfacial waters will be frequently counted in.


Any suggestions are welcome.

Manuel Melo
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Re: [gmx-users] QMMM with ORCA

[Christoph Riplinger]

Hi Xiaohu,

We are using gromacs/ORCA quite a lot. It works like any of the other 
interfaced programs and whether you should use it depends on your needs 
to the QM part of the QM/MM calculation.


I am using gromacs 4.0.7, but I downloaded the 4.5.3 version to test it.

I could not reproduce your problem with ONIOM. For the electrostatic 
embedding bug, I agree. This didn't work in my test calculation, but my 
gdb told me that the abort occured before the qm_orca.c was even called. 
I suspect the bug is in the general qmmm.c code. I do not have access to 
the other QM-programs and cannot test this, so if you have, could you 
please run the same job with a different QM-program.


Hope that helps

Christoph



On 01/26/2011 06:48 AM, Xiaohu Li wrote:

Hi, All,
 I'm trying to see if anybody has experience of using the 
interface of gromacs and ORCA(since it's free). I know that the 
following link gave information on how
http://wwwuser.gwdg.de/~ggroenh/qmmm.html#code 

 But.But, the gromacs in the above link is quite old(3.2). I 
download the latest 4.5.3 and followed the instructions in the above 
link and I was trying to optimize an simple cluster(no pbc) where part 
of it are treated using QM. here is the example mdp file

=
title   =  cpeptide
integrator  =  steep   ;integrator includes energy 
minimization algorithms

dt  =  0.002; ps !
nsteps  =   1
nstlist =  1
ns_type =  simple
rlist   =  3.0
rcoulomb=  3.0
coulombtype = cut-off
vdwtype = cut-off
rvdw= 3.0
pbc =  no
periodic_molecules  =  no
constraints = none
energygrps  = qm_part mm_part
; QM/MM calculation stuff
QMMM = yes
QMMM-grps = qm_part
QMmethod = rhf
QMbasis = 3-21G
QMMMscheme = oniom
QMcharge = 0
QMmult = 1
;
;   Energy minimizing stuff
;
emtol   =  60   ; minimization thresold (kj/mol.nm-1)1 
hartree/bohr= 49614.75241 kj/mol.nm-1  1 kj/mol.nm-1=2.01553e-5 
hartree/bohr

emstep  =  0.01  ; minimization step in nm
=
I set up the BASENAME and ORCA_PATH as told in the instruction.
first of all, the normal electronic embedding just simply gave 
segmentation fault error right after the it prints information on 
number of steps of optimization.


So I switch to ONIOM, this time, at least, orca is called and energy 
and gradient are both generated. However, when it comes to read the 
energy and gradient, it always crashes when tried to read gradient, 
this is at *line 346* source code src/mdlib/qm_orca.c


sscanf(buf,"%lf\n", &QMgrad[k][XX]);

a segmentation fault error is printed. If I replace the &QMgrad[k][XX] 
by an temporary variable temp

 sscanf(buf,"%lf\n", &temp);
temp gets the correct value and if I use,
QMgrad[k][XX]=temp
and tries to print QMgrad[k][XX], a bus error will be printed.
I did some research online, seems that usually this implies an memory 
bug in the code which is the most difficult bug one can ever encounter.

So has anyone successfully used gromacs and orca to do QMMM?
Generally, would anyone recommend using gromacs to do QMMM?

Cheers,
Xiaohu


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[gmx-users] protein movement in lipid bilayer during simulation

[ram bio]

Dear Gromacs Users,

I am performing an all-atom simulation of protein ligand complex in
lipid bilayer , but after around 100ns, I see that the protein started
moving in one dimension in the lipid bilayer that is it is not in the
centre, I want the position of the protein fixed through out the
simulation, so pl suggest regarding this..

and is it ok if I increase the position restraints for the protein by
changing the values of forces on x y and z dimensions in the posre.itp
file (below) of the protein, and if so how much can i increase the
force, so that i doesnot effect the simulation.

[ position_restraints ]
; atom  type  fx  fy  fz
 1 1  2000  2000  2000
 5 1  2000  2000  2000
 7 1  2000  2000  2000
10 1  2000  2000  2000
13 1  2000  2000  2000
14 1  2000  2000  2000
18 1  2000  2000  2000
19 1  2000  2000  2000
20 1  2000  2000  2000
21 1  2000  2000  2000
23 1  2000  2000  2000
26 1  2000  2000  2000
29 1  2000  2000  2000
32 1  2000  2000  2000
33 1  2000  2000  2000
34 1  2000  2000  2000
35 1  2000  2000  2000
37 1  2000  2000  2000
40 1  2000  2000  2000

Thanks in advance,

Ram
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Re: [gmx-users] Using g_select to detect water pores in a bilayer

[Teemu Murtola]

Hi

On Thu, Jan 27, 2011 at 16:18, Manuel Nuno Melo  wrote:
> My idea is to count the number of water molecules within a certain z
> distance of the bilayer center, and flag a pore above a certain threshold.
> The problem is that the position of this z-slab cannot be hardcoded because
> my simulations are relatively long and there is sometimes a drift of the
> bilayer.
>
> also fails because the pore is lined by peptide molecules and a relatively
> large distance for the PW-C4 distance must be allowed. This means that
> interfacial waters will be frequently counted in.

This is unfortunately not possible with the current version of
g_select, as the number of available keywords is quite limited.  If
you want to do some programming, it should be relatively
straightforward (although the learning curve for the selection engine
can be quite steep) to add new keywords.  There is some documentation
in the headers selmethod.h and selparam.h, and you should be able to
implement, e.g., a selection keyword like "zwithin 0.5 of com of name
..." by looking at the existing implementations in sm_distance.c
(contains, e.g., 'within' and 'dist') and sm_simple.c (contains, e.g.,
'z').

Best regards,
Teemu
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[gmx-users] Center of mass motion removal for partial filled PBC box

[WU Yanbin]

Dear GMXers,

I would like to reproduce the water droplet contact angle on graphite
surface, as in Werder, T.; Walther, J. H.; Halicioglu, T.; Koumoutsakos, P.
*J. Phys. Chem. B* *2003*, *107*, 1345-1352.

The box size is 20nm by 20nm by 30nm. Graphite is represented by a two-layer
carbon sheet. After equilibration, the water droplet is around 3.5nm in
radius. A large part of the box is vacuum. Periodic boundary condition (PBC)
is applied. Graphite is fixed throughout the simulation.

>From the manual, the "comm_mode=Linear" option should be applied, which
means the translational motion of the center of mass of the water droplet
should be removed. My first question is: If the time step is 2fs, what's the
recommended value for nstcomm? (nstlist is updated very 3 time step)

Also in the manual and this mail list, it's mentioned that for non-PBC,
isolated system, "comm_mode=Angular" should be applied. Does this also
applied to my partial filled PBC box?

Do let me know if the question is not clear.

Thank you.

Best,
Yanbin
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Re: [gmx-users] protein movement in lipid bilayer during simulation

[Justin A. Lemkul]

ram bio wrote:

Dear Gromacs Users,

I am performing an all-atom simulation of protein ligand complex in
lipid bilayer , but after around 100ns, I see that the protein started
moving in one dimension in the lipid bilayer that is it is not in the
centre, I want the position of the protein fixed through out the
simulation, so pl suggest regarding this..



This is a normal consequence of diffusion in a periodic system.  There is no 
such thing as a "center."  For visualization purposes, just post-process your 
trajectory with trjconv.



and is it ok if I increase the position restraints for the protein by
changing the values of forces on x y and z dimensions in the posre.itp
file (below) of the protein, and if so how much can i increase the
force, so that i doesnot effect the simulation.



If you're trying to get around the diffusion issue, don't.  If this is part of 
equilibration, all you're doing is setting up a higher energy barrier for the 
movement of these atoms.  The difference between 1000 and 2000 should be 
relatively minimal, as far as the end result is concerned.


-Justin


[ position_restraints ]
; atom  type  fx  fy  fz
 1 1  2000  2000  2000
 5 1  2000  2000  2000
 7 1  2000  2000  2000
10 1  2000  2000  2000
13 1  2000  2000  2000
14 1  2000  2000  2000
18 1  2000  2000  2000
19 1  2000  2000  2000
20 1  2000  2000  2000
21 1  2000  2000  2000
23 1  2000  2000  2000
26 1  2000  2000  2000
29 1  2000  2000  2000
32 1  2000  2000  2000
33 1  2000  2000  2000
34 1  2000  2000  2000
35 1  2000  2000  2000
37 1  2000  2000  2000
40 1  2000  2000  2000

Thanks in advance,

Ram


--


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] protein movement in lipid bilayer during simulation

[ram bio]

Dear Justin,

Thanks for the suggestion.

Best,

Ram

On Thu, Jan 27, 2011 at 6:46 PM, Justin A. Lemkul  wrote:
>
>
> ram bio wrote:
>>
>> Dear Gromacs Users,
>>
>> I am performing an all-atom simulation of protein ligand complex in
>> lipid bilayer , but after around 100ns, I see that the protein started
>> moving in one dimension in the lipid bilayer that is it is not in the
>> centre, I want the position of the protein fixed through out the
>> simulation, so pl suggest regarding this..
>>
>
> This is a normal consequence of diffusion in a periodic system.  There is no
> such thing as a "center."  For visualization purposes, just post-process
> your trajectory with trjconv.
>
>> and is it ok if I increase the position restraints for the protein by
>> changing the values of forces on x y and z dimensions in the posre.itp
>> file (below) of the protein, and if so how much can i increase the
>> force, so that i doesnot effect the simulation.
>>
>
> If you're trying to get around the diffusion issue, don't.  If this is part
> of equilibration, all you're doing is setting up a higher energy barrier for
> the movement of these atoms.  The difference between 1000 and 2000 should be
> relatively minimal, as far as the end result is concerned.
>
> -Justin
>
>> [ position_restraints ]
>> ; atom  type      fx      fy      fz
>>     1     1  2000  2000  2000
>>     5     1  2000  2000  2000
>>     7     1  2000  2000  2000
>>    10     1  2000  2000  2000
>>    13     1  2000  2000  2000
>>    14     1  2000  2000  2000
>>    18     1  2000  2000  2000
>>    19     1  2000  2000  2000
>>    20     1  2000  2000  2000
>>    21     1  2000  2000  2000
>>    23     1  2000  2000  2000
>>    26     1  2000  2000  2000
>>    29     1  2000  2000  2000
>>    32     1  2000  2000  2000
>>    33     1  2000  2000  2000
>>    34     1  2000  2000  2000
>>    35     1  2000  2000  2000
>>    37     1  2000  2000  2000
>>    40     1  2000  2000  2000
>>
>> Thanks in advance,
>>
>> Ram
>
> --
> 
>
> 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] remove all waters from the pdb file

[Tsjerk Wassenaar]

Hey,

Well, for those things it also doesn't hurt to know a few standard linux tools:

grep -v "SOL" xxx.pdb > nosol.pdb

And if there are also ions in play:

grep -v "\(SOL\|NA\|CL\)" xxx.pdb > nosol.pdb

Hope it helps,

Tsjerk

2011/1/27 Justin A. Lemkul :
>
>
> ahmet yıldırım wrote:
>>
>> Dear users,
>>
>> I want to remove all waters from the xxx.pdb file. Then, I want to save
>> the pdb file (new pdb) without waters because I will use the methanol as a
>> solvent. I looked at mail list but I could not find the answer I wanted.
>>
>> What should I do?
>>
>
> Please read trjconv -h, with special attention to point #2 in the opening
> list.
>
> -Justin
>
>> Thanks in advance
>>
>> --
>> Ahmet YILDIRIM
>>
>
> --
> 
>
> 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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[gmx-users] QMMM with ORCA

[Xiaohu Li]

Dear GMX code writters,
 Could anyone tell me why this comments in the code *mdlib/qmmm.c
appear*?(version 4.5.3)
at *line ~ 714*, in the beginning of subroutine* update_QMMMrec*
==
*/* updates the coordinates of both QM atoms and MM atoms and stores
   * them in the QMMMrec.
   *
   * NOTE: is NOT yet working if there are no PBC. Also in ns.c, simple
   * ns needs to be fixed!
*/*
==
First of all, I have a non-PBC job with electronic embedding and it
fails right in this routine. So I guess this is the reason, for non-PBC, it
crashes. But for oniom, it went through. Is there any simple fix to have the
non-PBC qmmm work? I'm also interested in doing non-PBC calculation(large
cluster).


Xiaohu

On Thu, Jan 27, 2011 at 9:11 AM, Christoph Riplinger
wrote:

>  Hi Xiaohu,
>
> We are using gromacs/ORCA quite a lot. It works like any of the other
> interfaced programs and whether you should use it depends on your needs to
> the QM part of the QM/MM calculation.
>
> I am using gromacs 4.0.7, but I downloaded the 4.5.3 version to test it.
>
> I could not reproduce your problem with ONIOM. For the electrostatic
> embedding bug, I agree. This didn't work in my test calculation, but my gdb
> told me that the abort occured before the qm_orca.c was even called. I
> suspect the bug is in the general qmmm.c code. I do not have access to the
> other QM-programs and cannot test this, so if you have, could you please run
> the same job with a different QM-program.
>
> Hope that helps
>
> Christoph
>
>
>
>
> On 01/26/2011 06:48 AM, Xiaohu Li wrote:
>
> Hi, All,
>  I'm trying to see if anybody has experience of using the interface of
> gromacs and ORCA(since it's free). I know that the following link gave
> information on how
> http://wwwuser.gwdg.de/~ggroenh/qmmm.html#code
>  But.But, the gromacs in the above link is quite old(3.2). I
> download the latest 4.5.3 and followed the instructions in the above link
> and I was trying to optimize an simple cluster(no pbc) where part of it are
> treated using QM. here is the example mdp file
>
> =
>  title   =  cpeptide
> integrator  =  steep   ;integrator includes energy minimization
> algorithms
> dt  =  0.002; ps !
> nsteps  =   1
> nstlist =  1
> ns_type =  simple
> rlist   =  3.0
> rcoulomb=  3.0
> coulombtype = cut-off
> vdwtype = cut-off
> rvdw= 3.0
> pbc =  no
> periodic_molecules  =  no
> constraints = none
> energygrps  = qm_part mm_part
> ; QM/MM calculation stuff
> QMMM = yes
> QMMM-grps = qm_part
> QMmethod = rhf
> QMbasis = 3-21G
> QMMMscheme = oniom
> QMcharge = 0
> QMmult = 1
> ;
> ;   Energy minimizing stuff
> ;
> emtol   =  60   ; minimization thresold (kj/mol.nm-1)1
> hartree/bohr= 49614.75241 kj/mol.nm-1  1 kj/mol.nm-1=2.01553e-5 hartree/bohr
> emstep  =  0.01  ; minimization step in nm
>
> =
>  I set up the BASENAME and ORCA_PATH as told in the instruction.
> first of all, the normal electronic embedding just simply gave segmentation
> fault error right after the it prints information on number of steps of
> optimization.
>
>  So I switch to ONIOM, this time, at least, orca is called and energy and
> gradient are both generated. However, when it comes to read the energy and
> gradient, it always crashes when tried to read gradient, this is at *line
> 346* source code src/mdlib/qm_orca.c
> 
> sscanf(buf,"%lf\n", &QMgrad[k][XX]);
> 
> a segmentation fault error is printed. If I replace the &QMgrad[k][XX] by
> an temporary variable temp
>  sscanf(buf,"%lf\n", &temp);
> temp gets the correct value and if I use,
> QMgrad[k][XX]=temp
> and tries to print QMgrad[k][XX], a bus error will be printed.
> I did some research online, seems that usually this implies an memory bug
> in the code which is the most difficult bug one can ever encounter.
> So has anyone successfully used gromacs and orca to do QMMM?
> Generally, would anyone recommend using gromacs to do QMMM?
>
>  Cheers,
> Xiaohu
>
>
>


-- 
=
Xiaohu Li
Post-doctoral Research Associate
Department of Chemistry
Northwestern University
2145 Sheridan Road
Evanston IL 60208
U.S.A
=
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Re: [gmx-users] remove all waters from the pdb file

[ahmet yıldırım]

Dear Tsjerk,

Thank you. Problem is solved.

Removing waters from the pdb file:

grep -v "HOH" xxx.pdb > nosol.pdb


27 Ocak 2011 21:37 tarihinde Tsjerk Wassenaar  yazdı:

> Hey,
>
> Well, for those things it also doesn't hurt to know a few standard linux
> tools:
>
> grep -v "SOL" xxx.pdb > nosol.pdb
>
> And if there are also ions in play:
>
> grep -v "\(SOL\|NA\|CL\)" xxx.pdb > nosol.pdb
>
> Hope it helps,
>
> Tsjerk
>
> 2011/1/27 Justin A. Lemkul :
> >
> >
> > ahmet yıldırım wrote:
> >>
> >> Dear users,
> >>
> >> I want to remove all waters from the xxx.pdb file. Then, I want to save
> >> the pdb file (new pdb) without waters because I will use the methanol as
> a
> >> solvent. I looked at mail list but I could not find the answer I wanted.
> >>
> >> What should I do?
> >>
> >
> > Please read trjconv -h, with special attention to point #2 in the opening
> > list.
> >
> > -Justin
> >
> >> Thanks in advance
> >>
> >> --
> >> Ahmet YILDIRIM
> >>
> >
> > --
> > 
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > MILES-IGERT Trainee
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > 
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > Please don't post (un)subscribe requests to the list. Use the www
> interface
> > or send it to gmx-users-requ...@gromacs.org.
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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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
>



-- 
Ahmet YILDIRIM
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[gmx-users] Eigenvectors

[Yao Yao]

Hi Gmxers,

I am just wondering if the eigenvectors in gromacs are normalized or not, and 
how to check that after the normal mode analysis/

thanks,

Yao


  
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[gmx-users] Eigenvectors

[Yao Yao]

Hi Gmxers,

I am just wondering if the eigenvectors in gromacs are normalized or not, and 
how to check that after the normal mode analysis/

thanks,

Yao


  
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[gmx-users] Slow Runs

[Denny Frost]

I am taking over a project for a graduate student who did MD using Gromacs
3.3.3.  I now run similar simulations with Gromacs 4.5.1 and find that they
run only about 1/2 to 1/3 as fast as the previous runs done in Gromacs
3.3.3.  The runs have about the same number of atoms and both use opls force
fields.  The mdp files is virtually the same (I copied them).  The only
major difference is that my runs have difference species and thus have
different (although smaller) itp files.  The runs are stable and give
reasonable thermodynamic properties - they're just slow.  Has anyone had any
experience with something like this?
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RE: [gmx-users] Slow Runs

[Dallas Warren]

You will need to provide more details on the system.  How many atoms,
what sort of computer system is it being run on, how many nodes, copy of
the mdp file etc.

 

Catch ya,

Dr. Dallas Warren

Medicinal Chemistry and Drug Action

Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu

+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble
a nail. 

 

From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Denny Frost
Sent: Friday, 28 January 2011 9:34 AM
To: Discussion list for GROMACS users
Subject: [gmx-users] Slow Runs

 

I am taking over a project for a graduate student who did MD using
Gromacs 3.3.3.  I now run similar simulations with Gromacs 4.5.1 and
find that they run only about 1/2 to 1/3 as fast as the previous runs
done in Gromacs 3.3.3.  The runs have about the same number of atoms and
both use opls force fields.  The mdp files is virtually the same (I
copied them).  The only major difference is that my runs have difference
species and thus have different (although smaller) itp files.  The runs
are stable and give reasonable thermodynamic properties - they're just
slow.  Has anyone had any experience with something like this? 

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Re: [gmx-users] Slow Runs

[Denny Frost]

about 12000 atoms, 8 nodes, CentOS 5.3/Linux, infiniband.  Below is a copy
of my mdp file.

title   =  BMIM+PF6
cpp =  /lib/cpp
constraints =  all_bonds
integrator  =  md
dt  =  0.004   ; ps !
nsteps  =  2000   ; total 4ns.
nstcomm =  1
nstxout =  5
nstvout =  5
nstfout =  0
nstlog  =  5000
nstenergy   =  5000
nstxtcout   =  25000
nstlist =  10
ns_type =  grid
pbc =  xyz
coulombtype =  PME
vdwtype =  Shift
rlist   =  1.0
rcoulomb=  1.0
rvdw=  1.0
fourierspacing  =  0.6
;pme_order   =  4
ewald_rtol  =  1e-5
; Berendsen temperature coupling is on in two groups
Tcoupl  =  berendsen
tc_grps =  BMI  PF6
tau_t   =  0.1  0.1
ref_t   =  300  300
nsttcouple  =  1
; Energy monitoring
energygrps  =  BMI  PF6
; Isotropic pressure coupling is now on
Pcoupl  =  berendsen
pcoupltype  =  isotropic
;pc-grps =  BMI  PFF
tau_p   =  1.0
ref_p   =  1.0
compressibility =  4.5e-5

; Generate velocites is off at 300 K.
gen_vel =  yes
gen_temp=  300.0
gen_seed=  10


On Thu, Jan 27, 2011 at 4:12 PM, Dallas Warren wrote:

> You will need to provide more details on the system.  How many atoms, what
> sort of computer system is it being run on, how many nodes, copy of the mdp
> file etc.
>
>
>
> Catch ya,
>
> Dr. Dallas Warren
>
> Medicinal Chemistry and Drug Action
>
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.war...@monash.edu
>
> +61 3 9903 9304
> -
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
>
> *From:* gmx-users-boun...@gromacs.org [mailto:
> gmx-users-boun...@gromacs.org] *On Behalf Of *Denny Frost
> *Sent:* Friday, 28 January 2011 9:34 AM
> *To:* Discussion list for GROMACS users
> *Subject:* [gmx-users] Slow Runs
>
>
>
> I am taking over a project for a graduate student who did MD using Gromacs
> 3.3.3.  I now run similar simulations with Gromacs 4.5.1 and find that they
> run only about 1/2 to 1/3 as fast as the previous runs done in Gromacs
> 3.3.3.  The runs have about the same number of atoms and both use opls force
> fields.  The mdp files is virtually the same (I copied them).  The only
> major difference is that my runs have difference species and thus have
> different (although smaller) itp files.  The runs are stable and give
> reasonable thermodynamic properties - they're just slow.  Has anyone had any
> experience with something like this?
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
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Re: [gmx-users] Slow Runs

[Justin A. Lemkul]

Denny Frost wrote:
about 12000 atoms, 8 nodes, CentOS 5.3/Linux, infiniband.  Below is a 
copy of my mdp file.


title   =  BMIM+PF6
cpp =  /lib/cpp
constraints =  all_bonds
integrator  =  md
dt  =  0.004   ; ps !
nsteps  =  2000   ; total 4ns.
nstcomm =  1
nstxout =  5
nstvout =  5
nstfout =  0
nstlog  =  5000
nstenergy   =  5000
nstxtcout   =  25000
nstlist =  10
ns_type =  grid
pbc =  xyz
coulombtype =  PME
vdwtype =  Shift
rlist   =  1.0
rcoulomb=  1.0
rvdw=  1.0
fourierspacing  =  0.6


This fourierspacing is 5-6 times larger than what is normally accepted as 
sufficiently accurate.  A sparse grid will make the PME algorithm faster, 
actually, but at the expense of accuracy.


Can you post the domain decomposition statistics from the .log file?  They 
appear just above the energies from time 0.  What did grompp tell you about the 
relative PME:PP load?


-Justin


;pme_order   =  4
ewald_rtol  =  1e-5
; Berendsen temperature coupling is on in two groups
Tcoupl  =  berendsen
tc_grps =  BMI  PF6  
tau_t   =  0.1  0.1

ref_t   =  300  300
nsttcouple  =  1
; Energy monitoring
energygrps  =  BMI  PF6
; Isotropic pressure coupling is now on
Pcoupl  =  berendsen
pcoupltype  =  isotropic
;pc-grps =  BMI  PFF
tau_p   =  1.0
ref_p   =  1.0
compressibility =  4.5e-5

; Generate velocites is off at 300 K.
gen_vel =  yes
gen_temp=  300.0
gen_seed=  10


On Thu, Jan 27, 2011 at 4:12 PM, Dallas Warren > wrote:


You will need to provide more details on the system.  How many
atoms, what sort of computer system is it being run on, how many
nodes, copy of the mdp file etc.

 


Catch ya,

Dr. Dallas Warren

Medicinal Chemistry and Drug Action

Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu 

+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to
resemble a nail.

 


*From:* gmx-users-boun...@gromacs.org

[mailto:gmx-users-boun...@gromacs.org
] *On Behalf Of *Denny Frost
*Sent:* Friday, 28 January 2011 9:34 AM
*To:* Discussion list for GROMACS users
*Subject:* [gmx-users] Slow Runs

 


I am taking over a project for a graduate student who did MD using
Gromacs 3.3.3.  I now run similar simulations with Gromacs 4.5.1 and
find that they run only about 1/2 to 1/3 as fast as the previous
runs done in Gromacs 3.3.3.  The runs have about the same number of
atoms and both use opls force fields.  The mdp files is virtually
the same (I copied them).  The only major difference is that my runs
have difference species and thus have different (although smaller)
itp files.  The runs are stable and give reasonable thermodynamic
properties - they're just slow.  Has anyone had any experience with
something like this?


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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] Center of mass motion removal for partial filled PBC box

[Mark Abraham]

On 28/01/2011 4:25 AM, WU Yanbin wrote:

Dear GMXers,

I would like to reproduce the water droplet contact angle on graphite 
surface, as in Werder, T.; Walther, J. H.; Halicioglu, T.; 
Koumoutsakos, P. /J. Phys. Chem. B/ *2003*, /107/, 1345-1352.


The box size is 20nm by 20nm by 30nm. Graphite is represented by a 
two-layer carbon sheet. After equilibration, the water droplet is 
around 3.5nm in radius. A large part of the box is vacuum. Periodic 
boundary condition (PBC) is applied. Graphite is fixed throughout the 
simulation.


I'm not sure what PBC is gaining for you. I think you want vacuum 
boundary conditions, which may as well be non-periodic.




From the manual, the "comm_mode=Linear" option should be applied, 
which means the translational motion of the center of mass of the 
water droplet should be removed. My first question is: If the time 
step is 2fs, what's the recommended value for nstcomm? (nstlist is 
updated very 3 time step)


10 is probably fine.



Also in the manual and this mail list, it's mentioned that for 
non-PBC, isolated system, "comm_mode=Angular" should be applied. Does 
this also applied to my partial filled PBC box?


No, this is referring to simulations like a protein in vacuum.

Mark


Do let me know if the question is not clear.

Thank you.

Best,
Yanbin


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Re: [gmx-users] truncated LJ potential

[Mark Abraham]

On 27/01/2011 12:11 PM, Makoto Yoneya wrote:

Dear Berk and all:

I'd tried to rewrite the routine


src/gmxlib/nonbonded/nb_generic.c

to modify the LJ potential to the shifted and truncated one.

First, I'd add the new switch(ivdw) as case 4, but when I'd tried;
[ defaults ]
; nbfunc comb-rule   gen-pairs   fudgeLJ  fudgeQQ
   4  1 no1.0   1.0,
I'd got,
ERROR 1 [file topol.top, line 8]:
   Invalid nonbond function selector '4' using LJ.


So you have to update the machinery that parses the .top to recognise 
that the value of 4 is now legal.



Then, I'd rewrite the standard switch(ivdw) case 1 as follows
(with real tc12c5 and int factor).

#ifdef TRUNCATED_LJ
tc12c6 = 2.0*c12/c6;
factor = ceil(floor(tc12c6*rinvsix)/(tc12c6*rinvsix));
fscal += factor*(12.0*Vvdw_rep-6.0*Vvdw_disp)*rinvsq;
Vvdwtot = Vvdwtot+factor*(Vvdw_rep-Vvdw_disp+0.5*c6/tc12c6);
#else
fscal += (12.0*Vvdw_rep-6.0*Vvdw_disp)*rinvsq;
Vvdwtot = Vvdwtot+Vvdw_rep-Vvdw_disp;
#endif

However with this modification (recompile with #define TRUNCATED_LJ),
the simulation result was exactly the same.

I'd appreciate to tell me what kind of mistake I'd done?


Did you set the environment variable to actually call the generic 
nonbonded lists?


Mark


Makoto Yoneya, Dr.
AIST
http://staff.aist.go.jp/makoto-yoneya/


Yes.

The pow function is expensive though. The code will run much faster
if you can use rinvsix, such as check for  2*rinvsix>  c6/c12.
(I forgot the factor 2 in my previous mail).

Berk

From: makoto-yoneya at aist.go.jp
To: gmx-users at gromacs.org
Date: Tue, 11 Jan 2011 10:10:56 +0900
Subject: [gmx-users] truncated LJ potential

Dear Berk:

Thanks again for the further reply.


The LJ potential and force code in the above looks like in the c6-c12

form

not in epsilon-sigma one.
The LJ potential modification I'd like to try is based on the epsilon-
sigma form and the mixing rule is the Lorents-Bertelot's one.
Could you kindly tell me the LJ potential and force routine in the

epsilon-

Sigma form.

There is no such code.

You can simply check for rinvsix>  c6/c12

Is it means that the LJ potential in epsion-sigma form (with the
Lorents-Bertelot
mixing rule) is evaluated after the coversion into c6-c12 form in GROMACS?
Then, may I evaluate the modified LJ potential:


V(r)
= 4*epsilon*{ (sigma/r)^(12) - (sigma/r)^6 + (1/4) } for r<=
2^(1/6)*sigma
= 0 for r>   2^(1/6)*sigma

with translated into the equivalent c6-c12 form:

V(r)
= (c12/r)^(12) - (c6/r)^6 + (c6/2)*(c6/2*c12) for r<= (2*c12/c6)^(1/6)
= 0 for r>  (2*c12/c6)^(1/6)

in the following routines.

You can also set the environment variable nb_generic.c and modify
src/gmxlib/nonbonded/nb_generic.c, but might lead to somewhat
slower simulations.

If my understanding in the above would correct, I'll try that.


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[gmx-users] Slow Runs

[Chris Neale]

In addition, you're only updating your neighbourlist every 40 ps. If 
you're going to use a 4 fs timestep, I suggest that you use nstlist=5. 
Also, you appear to not be using any constraints while you are using a 4 
fs timestep.


I suggest that you stop worrying about why the run is slower and do some 
tutorials and read the manual and ensure that you understand the 
consequences of your .mdp options.


Chris.

-- original message --

Denny Frost wrote:

/  about 12000 atoms, 8 nodes, CentOS 5.3/Linux, infiniband.  Below is a

/>/  copy of my mdp file.
/>/
/>/  title   =  BMIM+PF6
/>/  cpp =  /lib/cpp
/>/  constraints =  all_bonds
/>/  integrator  =  md
/>/  dt  =  0.004   ; ps !
/>/  nsteps  =  2000   ; total 4ns.
/>/  nstcomm =  1
/>/  nstxout =  5
/>/  nstvout =  5
/>/  nstfout =  0
/>/  nstlog  =  5000
/>/  nstenergy   =  5000
/>/  nstxtcout   =  25000
/>/  nstlist =  10
/>/  ns_type =  grid
/>/  pbc =  xyz
/>/  coulombtype =  PME
/>/  vdwtype =  Shift
/>/  rlist   =  1.0
/>/  rcoulomb=  1.0
/>/  rvdw=  1.0
/>/  fourierspacing  =  0.6
/
This fourierspacing is 5-6 times larger than what is normally accepted as
sufficiently accurate.  A sparse grid will make the PME algorithm faster,
actually, but at the expense of accuracy.

Can you post the domain decomposition statistics from the .log file?  They
appear just above the energies from time 0.  What did grompp tell you about the
relative PME:PP load?

-Justin


/  ;pme_order   =  4

/>/  ewald_rtol  =  1e-5
/>/  ; Berendsen temperature coupling is on in two groups
/>/  Tcoupl  =  berendsen
/>/  tc_grps =  BMI  PF6
/>/  tau_t   =  0.1  0.1
/>/  ref_t   =  300  300
/>/  nsttcouple  =  1
/>/  ; Energy monitoring
/>/  energygrps  =  BMI  PF6
/>/  ; Isotropic pressure coupling is now on
/>/  Pcoupl  =  berendsen
/>/  pcoupltype  =  isotropic
/>/  ;pc-grps =  BMI  PFF
/>/  tau_p   =  1.0
/>/  ref_p   =  1.0
/>/  compressibility =  4.5e-5
/>/
/>/  ; Generate velocites is off at 300 K.
/>/  gen_vel =  yes
/>/  gen_temp=  300.0
/>/  gen_seed=  10
/>/
/>/
/>/  On Thu, Jan 27, 2011 at 4:12 PM, Dallas Warrenhttp://lists.gromacs.org/mailman/listinfo/gmx-users>
/>/  >>  wrote:
/>/
/>/  You will need to provide more details on the system.  How many
/>/  atoms, what sort of computer system is it being run on, how many
/>/  nodes, copy of the mdp file etc.
/>/
/>/
/>/
/>/  Catch ya,
/>/
/>/  Dr. Dallas Warren
/>/
/>/  Medicinal Chemistry and Drug Action
/>/
/>/  Monash Institute of Pharmaceutical Sciences, Monash University
/>/  381 Royal Parade, Parkville VIC 3010
/>/  dallas.warren at monash.edu   
 >
/>/
/>/  +61 3 9903 9304
/>/  -
/>/  When the only tool you own is a hammer, every problem begins to
/>/  resemble a nail.
/>/
/>/
/>/
/>/  *From:*gmx-users-bounces at gromacs.org  

/>/  >
/>/  [mailto:gmx-users-bounces at gromacs.org  

/>/  >] *On Behalf Of *Denny Frost
/>/  *Sent:* Friday, 28 January 2011 9:34 AM
/>/  *To:* Discussion list for GROMACS users
/>/  *Subject:* [gmx-users] Slow Runs
/>/
/>/
/>/
/>/  I am taking over a project for a graduate student who did MD using
/>/  Gromacs 3.3.3.  I now run similar simulations with Gromacs 4.5.1 and
/>/  find that they run only about 1/2 to 1/3 as fast as the previous
/>/  runs done in Gromacs 3.3.3.  The runs have about the same number of
/>/  atoms and both use opls force fields.  The mdp files is virtually
/>/  the same (I copied them).  The only major difference is that my runs
/>/  have difference species and thus have different (although smaller)
/>/  itp files.  The runs are stable and give reasonable thermodynamic
/>/  properties - they're just slow.  Has anyone had any experience with
/>/  something like this?
/>/
/>/
/>/  --
/>/  gmx-users mailing listgmx-users at gromacs.org  

/>/  

Re: [gmx-users] Slow Runs

[Jussi Lehtola]

On Thu, 27 Jan 2011 19:17:18 -0500
Chris Neale  wrote:

> In addition, you're only updating your neighbourlist every 40 ps.

Surely, this should be *femto*seconds.

> If you're going to use a 4 fs timestep, I suggest that you use
> nstlist=5. Also, you appear to not be using any constraints while you
> are using a 4 fs timestep.
> 
> I suggest that you stop worrying about why the run is slower and do
> some tutorials and read the manual and ensure that you understand the 
> consequences of your .mdp options.

I agree. Remember - garbage in, garbage out. Even if you get a number
out it doesn't mean that it's the right one...
-- 
--
Mr. Jussi Lehtola, M. Sc., Doctoral Student
Department of Physics, University of Helsinki, Finland
jussi.leht...@helsinki.fi
--
Jussi Lehtola, FM, Tohtorikoulutettava
Fysiikan laitos, Helsingin Yliopisto
jussi.leht...@helsinki.fi, p. 191 50632
--
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[gmx-users] Eigenvectors

[Yao Yao]

> Hi Gmxers,
> 
> I am just wondering if the eigenvectors in gromacs are
> normalized or not. 
> 

thanks,
> 
> Yao



  
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[gmx-users] Output error mpirun/mdrun_mpi

[Justin Kat]

Dear gmx-users,

My colleague seems to be experiencing an output containing errors after
issuing the command below:

mpirun -np 8 mdrun_mpi  -s  *.tpr -o *.tpr -c out -v >& outt.mdrun_md

The output reads as follows:

NNODES=8, MYRANK=0, HOSTNAME=node3.reyclus.loc
NODEID=0 argc=8
 :-)  G  R  O  M  A  C  S  (-:

NNODES=8, MYRANK=7, HOSTNAME=node3.reyclus.loc
NNODES=8, MYRANK=5, HOSTNAME=node3.reyclus.loc
   GRoups of Organic Molecules in ACtion for Science

:-)  VERSION 4.0.7  (-:


  Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
   Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.

 This program is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License
 as published by the Free Software Foundation; either version 2
 of the License, or (at your option) any later version.

  :-)  mdrun_mpi  (-:

NNODES=8, MYRANK=4, HOSTNAME=node3.reyclus.loc
NODEID=4 argc=8
NNODES=8, MYRANK=1, HOSTNAME=node3.reyclus.loc
NODEID=1 argc=8
NODEID=5 argc=8

NNODES=8, MYRANK=2, HOSTNAME=node3.reyclus.loc
NODEID=2 argc=8
NNODES=8, MYRANK=6, HOSTNAME=node3.reyclus.loc
NODEID=6 argc=8

100 steps,   1000.0 ps.
step 0
imb F  3% step 100, will finish Sat Jan 29 14:50:02 2011
imb F 394% step 200, will finish Sat Jan 29 17:50:38 2011
imb F  3% step 300, will finish Sat Jan 29 17:00:30 2011
imb F  3% step 400, will finish Sat Jan 29 15:12:15 2011
imb F  3% step 500, will finish Sat Jan 29 14:40:28 2011
imb F  4% step 600, will finish Sat Jan 29 13:51:32 2011
imb F  5% step 700, will finish Sat Jan 29 13:16:34 2011


It would be much appreciated if some light could be shed on what is going
wrong perhaps.

Thank you,
Justin
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Re: [gmx-users] Output error mpirun/mdrun_mpi

[Justin A. Lemkul]

Justin Kat wrote:

Dear gmx-users,

My colleague seems to be experiencing an output containing errors after 
issuing the command below:


mpirun -np 8 mdrun_mpi  -s  *.tpr -o *.tpr -c out -v >& outt.mdrun_md

The output reads as follows:

NNODES=8, MYRANK=0, HOSTNAME=node3.reyclus.loc
NODEID=0 argc=8
 :-)  G  R  O  M  A  C  S  (-:

NNODES=8, MYRANK=7, HOSTNAME=node3.reyclus.loc
NNODES=8, MYRANK=5, HOSTNAME=node3.reyclus.loc
   GRoups of Organic Molecules in ACtion for Science

:-)  VERSION 4.0.7  (-:


  Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
   Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org  
for more information.


 This program is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License
 as published by the Free Software Foundation; either version 2
 of the License, or (at your option) any later version.

  :-)  mdrun_mpi  (-:

NNODES=8, MYRANK=4, HOSTNAME=node3.reyclus.loc
NODEID=4 argc=8
NNODES=8, MYRANK=1, HOSTNAME=node3.reyclus.loc
NODEID=1 argc=8
NODEID=5 argc=8

NNODES=8, MYRANK=2, HOSTNAME=node3.reyclus.loc
NODEID=2 argc=8
NNODES=8, MYRANK=6, HOSTNAME=node3.reyclus.loc
NODEID=6 argc=8

100 steps,   1000.0 ps.  
step 0
imb F  3% step 100, will finish Sat Jan 29 14:50:02 2011
imb F 394% step 200, will finish Sat Jan 29 17:50:38 2011  
imb F  3% step 300, will finish Sat Jan 29 17:00:30 2011  
imb F  3% step 400, will finish Sat Jan 29 15:12:15 2011 
imb F  3% step 500, will finish Sat Jan 29 14:40:28 2011
imb F  4% step 600, will finish Sat Jan 29 13:51:32 2011  
imb F  5% step 700, will finish Sat Jan 29 13:16:34 2011



It would be much appreciated if some light could be shed on what is 
going wrong perhaps.




There is no error here.  The -v flag causes this information to be printed, and 
it is entirely normal.


-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] nstcomm set to 10

[NG HUI WEN]

Dear gmxusers,

 

I have a question here concerning nstcomm.

 

I got the note below after doing grompp, I'd like to do something about
it.

NOTE 1 [file HW_NPT.mdp]:

  nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting

  nstcomm to nstcalcenergy

 

Currently, my nstcomm is set at 1 while nstlist at 10 (default
nstcalcenergy, nsttcouple, nstpcouple = -1). I would like to know, if I
set nstcomm to 10, therefore removing the center of mass motion every 10
steps instead of every step, will it adversely affect my simulation
(because the center of mass is allowed to move in between the 10-step
interval)?

 

I notice the default value for nstcomm is actually 10, so I gather
setting it to 10 should be OK?  Thank you.

 

HW

 

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[gmx-users] g_mindist clarification

[Chandan Choudhury]

Hi all !!

Can some one clarify me what the g_mindist does. As far as I understood, it
takes two inputs from the index file. If I have more than one entry in both
of the indexes than how would g_mindist function?
eg; echo "7 8" |  g_mindist  -s ../md30-60.tpr -n index.ndx -f
../30-60.part0004.trr  -od mindist.xvg -nice 0 -b 35000 -e 4 -xvgr
My 7th and 8th indexes are :
[ N ]
1   11   20   29   38   47   56   65   74   83   92  101  110  119  128
137  146  155
  164  173  183  193  202  211  220  229  238  247  256  265  274  283  292
301  310  319
  328  337  346  355  365  375  384  393  402  411  420  429  438  447  456
465  474  483
  492  501  510  519  528  537  547  557  566  575  584  593  602  611  620
629  638  647
  656  665  674  683  692  701  710  719  729  739  748  757  766  775  784
793  802  811
  820  829  838  847  856  865  874  883  892  901  911  921  930  939  948
957  966  975
  984  993 1002 1011 1020 1029 1038 1047 1056 1065 1074 1083 1093 1103 1112
1121 1130 1139
 1148 1157 1166 1175 1184 1193 1202 1211 1220 1229 1238 1247 1256 1265 1275
1285 1294 1303
 1312 1321 1330 1339 1348 1357 1366 1375 1384 1393 1402 1411 1420 1429 1438
1447 1457 1467
 1476 1485 1494 1503 1512 1521 1530 1539 1548 1557 1566 1575 1584 1593 1602
1611 1620 1629
 1639 1649 1658 1667 1676 1685 1694 1703 1712 1721 1730 1739 1748 1757 1766
1775 1784 1793
 1802 1811

[ O ]
 1858 1960 2062 2164 2266 2368 2470 2572 2674 2776 2878 2980 3082 3184 3286
3388 3490 3592
 3694 3796 3898 4000 4102 4204 4306 4408 4510 4612 4714 4816 4918 5020 5122
5224 5326 5428
 5530 5632 5734 5836 5938 6040 6142 6244 6346 6448 6550 6652 6754 1865 1967
2069 2171 2273
 2375 2477 2579 2681 2783 2885 2987 3089 3191 3293 3395 3497 3599 3701 3803
3905 4007 4109
 4211 4313 4415 4517 4619 4721 4823 4925 5027 5129 5231 5333 5435 5537 5639
5741 5843 5945
 6047 6149 6251 6353 6455 6557 6659 6761 1872 1974 2076 2178 2280 2382 2484
2586 2688 2790
 2892 2994 3096 3198 3300 3402 3504 3606 3708 3810 3912 4014 4116 4218 4320
4422 4524 4626
 4728 4830 4932 5034 5136 5238 5340 5442 5544 5646 5748 5850 5952 6054 6156
6258 6360 6462
 6564  6768 1879 1981 2083 2185 2287 2389 2491 2593 2695 2797 2899 3001
3103 3205 3307
 3409 3511 3613 3715 3817 3919 4021 4123 4225 4327 4429 4531 4633 4735 4837
4939 5041 5143
 5245 5347 5449 5551 5653 5755 5857 5959 6061 6163 6265 6367 6469 6571 6673
6775 1886 1988
 2090 2192 2294 2396 2498 2600 2702 2804 2906 3008 3110 3212 3314 3416 3518
3620 3722 3824
 3926 4028 4130 4232 4334 4436 4538 4640 4742 4844 4946 5048 5150 5252 5354
5456 5558 5660
 5762 5864 5966 6068 6170 6272 6374 6476 6578 6680 6782 1893 1995 2097 2199
2301 2403 2505
 2607 2709 2811 2913 3015 3117 3219 3321 3423 3525 3627 3729 3831 3933 4035
4137 4239 4341
 4443 4545 4647 4749 4851 4953 5055 5157 5259 5361 5463 5565 5667 5769 5871
5973 6075 6177
 6279 6381 6483 6585 6687 6789 1900 2002 2104 2206 2308 2410 2512 2614 2716
2818 2920 3022
 3124 3226 3328 3430 3532 3634 3736 3838 3940 4042 4144 4246 4348 4450 4552
4654 4756 4858
 4960 5062 5164 5266 5368 5470 5572 5674 5776 5878 5980 6082 6184 6286 6388
6490 6592 6694
 6796 1907 2009 2111 2213 2315 2417 2519 2621 2723 2825 2927 3029 3131 3233
3335 3437 3539
 3641 3743 3845 3947 4049 4151 4253 4355 4457 4559 4661 4763 4865 4967 5069
5171 5273 5375
 5477 5579 5681 5783 5885 5987 6089 6191 6293 6395 6497 6599 6701 6803 1914
2016 2118 2220
 2322 2424 2526 2628 2730 2832 2934 3036 3138 3240 3342 3444 3546 3648 3750
3852 3954 4056
 4158 4260 4362 4464 4566 4668 4770 4872 4974 5076 5178 5280 5382 5484 5586
5688 5790 5892
 5994 6096 6198 6300 6402 6504 6606 6708 6810 1921 2023 2125 2227 2329 2431
2533 2635 2737
 2839 2941 3043 3145 3247 3349 3451 3553 3655 3757 3859 3961 4063 4165 4267
4369 4471 4573
 4675 4777 4879 4981 5083 5185 5287 5389 5491 5593 5695 5797 5899 6001 6103
6205 6307 6409
 6511 6613 6715 6817

With one entry in the g_mindist (-od) and g_dist produces the same graph.


--
Chandan kumar Choudhury
NCL, Pune
INDIA
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[gmx-users] truncated LJ potential

[Makoto Yoneya]

Dear Mark and all:

Dr. Mark Abraham wrote:
> So you have to update the machinery that parses the .top to recognise 
> that the value of 4 is now legal.
and also
> Did you set the environment variable to actually call the generic 
> nonbonded lists?

Thanks a lot for your comments.
I did not care these at all.
Which part of the manual contain the info?
(I'd tried a search in the GROMACS web page, but I could not find that.)
How can I do the recognision and set the environment variable?

Regards

Makoto Yoneya, Dr.
http://staff.aist.go.jp/makoto-yoneya/


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Re: [gmx-users] solvation_box_preparation

[shahid nayeem]

Thanks Justin
I tried with new box size of 2.8x2.8x2.8 . During energy minimization
with steepest descent to force of 2000 and constraint=none, the system
converged in 754 steps with positive potential energy. In subsequent
simulated annealing with constraint all bonds it starts giving link
warning in 0 step with rms 7407.805164, max 66989.116545 (between atom
94 and 117) and a list of bond thar rotated more than 30 degree almost
atom number belonging to chaps molecule.
Please help.
shahid Nayeem

On Thu, Jan 27, 2011 at 7:06 PM, Justin A. Lemkul  wrote:
>
>
> shahid nayeem wrote:
>>
>> Dear All
>>
>> I am sending this mail again on user list because my reply to Mark’s
>> query was not uploaded on the list.
>>
>> Original messge:
>>
>> I am trying to prepare a solvation box of chaps. After generating .itp
>> and .gro at ProDrg and thorough check of charges, I started with a box
>> size of 6x6x6. Energy minimization, simulated annealing (Cooling under
>> high pressure and again heating at normal pressure) as well as final
>> equilibration ran smoothly. But finally I get a box where all water
>> molecules get accumulated in two three small region within the box and
>> all chaps molecules gets accumulated in another small regions.I wanted
>> near random uniform distribution of chaps in water. Any help from
>> user, where I am wrong and what should I do.
>>
>> Reply to query.
>>
>> I created a box of 6x6x6 inserting 7 molecule of chaps with (genbox
>> –ci 7 chaps.gro).Then I solvated the output box  with genbox using
>> -maxsol 500 and spc216.gro. On visualization, at this stage itself
>> uniform solvation did not occur (I got water in one region and chaps
>> molecule in other region) but I observed a similar situation while
>
> If your box was not completely solvated, then don't use -maxsol.  A box of
> 6x6x6 nm should require more than 500 molecules of water to fill.  If you're
> trying to achieve some specific mole fraction or concentration, then
> re-figure your box size.
>
> -Justin
>
>> preparing 10M urea salvation box. This was followed by 1ns simulated
>> annealing from temp 300K to 0K and pressure 100 bar, then 1ns
>> simulated annealing from temp. 0k to 300k and then ins equilibriation
>> at this temperature. In case of urea finally I got uniformly solvated
>> urea_water_box but in chaps I couldn’t get it.
>>
>> Shahid Nayeem
>
> --
> 
>
> 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] Eigenvectors

[Tsjerk Wassenaar]

Hi Yao,

They are. But if you really want to check, convert the eigenvectors to
a human readable format (.gro/.g96) and calculate inner products :)

Cheers,

Tsjerk

On Fri, Jan 28, 2011 at 2:43 AM, Yao Yao  wrote:
>
>
>
>> Hi Gmxers,
>>
>> I am just wondering if the eigenvectors in gromacs are
>> normalized or not.
>>
>
> thanks,
>>
>> Yao
>
>
>
>
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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] truncated LJ potential

[Mark Abraham]

On 28/01/2011 3:44 PM, Makoto Yoneya wrote:

Dear Mark and all:

Dr. Mark Abraham wrote:

So you have to update the machinery that parses the .top to recognise
that the value of 4 is now legal.

and also

Did you set the environment variable to actually call the generic
nonbonded lists?

Thanks a lot for your comments.
I did not care these at all.
Which part of the manual contain the info?


None. Unfortunately, not everything that every developer might want to 
know for every project can be documented.



(I'd tried a search in the GROMACS web page, but I could not find that.)
How can I do the recognision


Find the part of the code that triggers that error message, examine what 
circumstances and data structures trigger it and modify suitably. Then 
look where else that data structure is used and adapt as necessary.



and set the environment variable?


You'd only have learned to do this if you'd used a debugger to step 
through the flow of the code. I highly recommend that procedure. 
init_forcerec() checks an environment variable and triggers the use of 
generic kernels accordingly. Various other environment variables have 
various other effects there and deeper in the code.


Mark
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Re: [gmx-users] solvation_box_preparation

[Mark Abraham]

On 28/01/2011 3:51 PM, shahid nayeem wrote:

Thanks Justin
I tried with new box size of 2.8x2.8x2.8 . During energy minimization
with steepest descent to force of 2000 and constraint=none, the system
converged in 754 steps with positive potential energy. In subsequent
simulated annealing with constraint all bonds it starts giving link
warning in 0 step with rms 7407.805164, max 66989.116545 (between atom
94 and 117) and a list of bond thar rotated more than 30 degree almost
atom number belonging to chaps molecule.


You've set up a system that isn't stable, but we don't have enough 
information to have any idea why. "I tried with new box size" doesn't go 
close to describing your method in enough detail for anyone to know 
where you went wrong.


See http://www.gromacs.org/Documentation/Terminology/Blowing_Up for 
generic tips


Mark


Please help.
shahid Nayeem

On Thu, Jan 27, 2011 at 7:06 PM, Justin A. Lemkul  wrote:


shahid nayeem wrote:

Dear All

I am sending this mail again on user list because my reply to Mark’s
query was not uploaded on the list.

Original messge:

I am trying to prepare a solvation box of chaps. After generating .itp
and .gro at ProDrg and thorough check of charges, I started with a box
size of 6x6x6. Energy minimization, simulated annealing (Cooling under
high pressure and again heating at normal pressure) as well as final
equilibration ran smoothly. But finally I get a box where all water
molecules get accumulated in two three small region within the box and
all chaps molecules gets accumulated in another small regions.I wanted
near random uniform distribution of chaps in water. Any help from
user, where I am wrong and what should I do.

Reply to query.

I created a box of 6x6x6 inserting 7 molecule of chaps with (genbox
–ci 7 chaps.gro).Then I solvated the output box  with genbox using
-maxsol 500 and spc216.gro. On visualization, at this stage itself
uniform solvation did not occur (I got water in one region and chaps
molecule in other region) but I observed a similar situation while

If your box was not completely solvated, then don't use -maxsol.  A box of
6x6x6 nm should require more than 500 molecules of water to fill.  If you're
trying to achieve some specific mole fraction or concentration, then
re-figure your box size.

-Justin


preparing 10M urea salvation box. This was followed by 1ns simulated
annealing from temp 300K to 0K and pressure 100 bar, then 1ns
simulated annealing from temp. 0k to 300k and then ins equilibriation
at this temperature. In case of urea finally I got uniformly solvated
urea_water_box but in chaps I couldn’t get it.

Shahid Nayeem

--


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] Simulation time losses with REMD

[Mark Abraham]

Hi,

I compared the .log file time accounting for same .tpr file run alone in 
serial or as part of an REMD simulation (with each replica on a single 
proessor). It ran about 5-10% slower in the latter. The effect was a bit 
larger when comparing the same .tpr on 8 processors with REMD with 8 
processers per replica. The effect seems fairly independent of whether I 
compare the lowest or highest replica.


The system is 1ns of Ace-(Ala)_10-NME in CHARMM27 with GROMACS 4.5.3 
using NVT, PME, virtual sites, 4fs timesteps, rlist=rvdw=rcoulomb=1.0nm 
with REMD ranging over 20 replicas distributed exponentially from 298K 
to 431.57K using v-rescale T-coupling. The machine has two quad-core 
processors per node with Inifiniband connection. The Infiniband switch 
is shared with other users' calculations, so some load-based variability 
can and does occur, but this should have shown up in a named part of the 
time accounting.


My first thought was that REMD exchange latency was to blame, so I 
quickly hacked in a change to report the length of time spent in the 
REMD initialization routine, and then each call to the REMD 
exchange-attempt routine.


Comparing the performance between REMD and serial of the lowest replica 
on a single processor, I saw with diff:

   Computing: Nodes Number G-CyclesSeconds %
7394,7403c6910,6918
<  Vsite constr.  1 250001   40.271   13.8 0.7
<  Neighbor search1  25011  434.982  148.7 7.1
<  Force  1 250001 3607.375 1232.859.1
<  PME mesh   1 250001 1270.407  434.120.8
<  Vsite spread   1 52   41.671   14.2 0.7
<  Write traj.1  37.8732.7 0.1
<  Update 1 250001   82.822   28.3 1.4
<  Constraints1 250001  154.231   52.7 2.5
<  REMD   1100   59.070   20.2 1.0
<  Rest   1 409.862  140.1 6.7
---
>  Vsite constr.  1 250001   40.526   13.8 0.7
>  Neighbor search1  25001  434.871  148.6 7.5
>  Force  1 250001 3601.463 1230.862.2
>  PME mesh   1 250001 1292.675  441.822.3
>  Vsite spread   1 52   41.479   14.2 0.7
>  Write traj.1  3   17.1535.9 0.3
>  Update 1 250001   82.114   28.1 1.4
>  Constraints1 250001  154.426   52.8 2.7
>  Rest   1 122.023   41.7 2.1
7405c6920
<  Total  16108.562 2087.5   100.0
---
>  Total  15786.731 1977.5   100.0

So "Rest" goes up from 122 s to 409 s under REMD, even after factoring 
out the 59 s actually spent in REMD. With the highest replica:


   Computing: Nodes Number G-CyclesSeconds %
7394,7403c6910,6918
<  Vsite constr.  1 250001   40.261   13.8 0.7
<  Neighbor search1  25016  434.878  148.6 7.1
<  Force  1 250001 3606.913 1232.659.0
<  PME mesh   1 250001 1264.716  432.220.7
<  Vsite spread   1 52   41.268   14.1 0.7
<  Write traj.1  37.1132.4 0.1
<  Update 1 250001   82.491   28.2 1.4
<  Constraints1 250001  153.207   52.4 2.5
<  REMD   1100   60.272   20.6 1.0
<  Rest   1 417.399  142.6 6.8
---
>  Vsite constr.  1 250001   40.518   13.8 0.7
>  Neighbor search1  25001  435.069  148.7 7.6
>  Force  1 250001 3609.196 1233.462.6
>  PME mesh   1 250001 1283.082  438.522.3
>  Vsite spread   1 52   41.825   14.3 0.7
>  Write traj.1  3   13.0634.5 0.2
>  Update 1 250001   82.011   28.0 1.4
>  Constraints1 250001  154.350   52.7 2.7
>  Rest   1 102.249   34.9 1.8
7405c6920
<  Total  16108.520 2087.5   100.0
---
>  Total  15761.363 1968.8   100.0

Here 102 s becomes 417 s despite factoring out 60 s for REMD. So the 
time spent doing the exchange is just noticeable, but quite a bit less 
than the observed increase in total time.


For the lowest replica in parallel:

8481,8496c7971,7985
<  Domain decomp. 8  25010  152.338   52.1 1.8
<  DD comm. load  8  242261.0850.4 0.0
<  

[gmx-users] truncated LJ potential

[Makoto Yoneya]

Dear Mark and all:

Dr. Mark Abraham wrote:
> > and set the environment variable?
>
> You'd only have learned to do this if you'd used a debugger to step 
> through the flow of the code. I highly recommend that procedure. 
> init_forcerec() checks an environment variable and triggers the use of 
> generic kernels accordingly. Various other environment variables have 
> various other effects there and deeper in the code.
Thanks a lot of the great info.
I'd found the environment variable is GMX_NB_GENERIC.
By setting this, my modification code was activated and the LJ potential
outputs were turned from negative to positive values (since the LJ was
truncated till its repulsive part).

> > How can I do the recognision
>
> Find the part of the code that triggers that error message, examine what 
> circumstances and data structures trigger it and modify suitably. Then 
> look where else that data structure is used and adapt as necessary.
For this, I still could not figured out.
The variable eNBF_NR limits the case number in the routin topio.c, but
I could not find how the variable was defined.
I'll try more.

Thanks a lot again.

Makoto Yoneya, Dr.
http://staff.aist.go.jp/makoto-yoneya/

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[gmx-users] Re: QMMM with ORCA

[Gerrit Groenhof]

Dear Xiaohu,

Thanks for bringing this up. The comment has been there for ever. Since I could 
not think of an application where one would not be using pbc at the time. 
However, your clusters prove me wrong.

In any case, as a work-around, you may want to use a bigger box, with long 
enough cut-offs, no PME.

Hope this gets you started,

Gerrit

On 27 Jan 2011, at 21:02, Xiaohu Li wrote:

> Dear GMX code writters,
>  Could anyone tell me why this comments in the code mdlib/qmmm.c 
> appear?(version 4.5.3)
> at line ~ 714, in the beginning of subroutine update_QMMMrec
> ==
> /* updates the coordinates of both QM atoms and MM atoms and stores
>* them in the QMMMrec.  
>*
>* NOTE: is NOT yet working if there are no PBC. Also in ns.c, simple
>* ns needs to be fixed!  
> */
> ==
> First of all, I have a non-PBC job with electronic embedding and it 
> fails right in this routine. So I guess this is the reason, for non-PBC, it 
> crashes. But for oniom, it went through. Is there any simple fix to have the 
> non-PBC qmmm work? I'm also interested in doing non-PBC calculation(large 
> cluster).
> 
> 
> Xiaohu
> 
> On Thu, Jan 27, 2011 at 9:11 AM, Christoph Riplinger  
> wrote:
> Hi Xiaohu,
> 
> We are using gromacs/ORCA quite a lot. It works like any of the other 
> interfaced programs and whether you should use it depends on your needs to 
> the QM part of the QM/MM calculation.
> 
> I am using gromacs 4.0.7, but I downloaded the 4.5.3 version to test it.
> 
> I could not reproduce your problem with ONIOM. For the electrostatic 
> embedding bug, I agree. This didn't work in my test calculation, but my gdb 
> told me that the abort occured before the qm_orca.c was even called. I 
> suspect the bug is in the general qmmm.c code. I do not have access to the 
> other QM-programs and cannot test this, so if you have, could you please run 
> the same job with a different QM-program. 
> 
> Hope that helps
> 
> Christoph
> 
> 
> 
> 
> On 01/26/2011 06:48 AM, Xiaohu Li wrote:
>> 
>> Hi, All,
>>  I'm trying to see if anybody has experience of using the interface of 
>> gromacs and ORCA(since it's free). I know that the following link gave 
>> information on how
>> http://wwwuser.gwdg.de/~ggroenh/qmmm.html#code
>>  But.But, the gromacs in the above link is quite old(3.2). I 
>> download the latest 4.5.3 and followed the instructions in the above link 
>> and I was trying to optimize an simple cluster(no pbc) where part of it are 
>> treated using QM. here is the example mdp file
>> =
>> title   =  cpeptide
>> integrator  =  steep   ;integrator includes energy minimization 
>> algorithms
>> dt  =  0.002; ps !
>> nsteps  =   1
>> nstlist =  1
>> ns_type =  simple
>> rlist   =  3.0
>> rcoulomb=  3.0
>> coulombtype = cut-off
>> vdwtype = cut-off
>> rvdw= 3.0
>> pbc =  no
>> periodic_molecules  =  no
>> constraints = none
>> energygrps  = qm_part mm_part
>> ; QM/MM calculation stuff
>> QMMM = yes
>> QMMM-grps = qm_part
>> QMmethod = rhf
>> QMbasis = 3-21G
>> QMMMscheme = oniom
>> QMcharge = 0
>> QMmult = 1
>> ;
>> ;   Energy minimizing stuff
>> ;
>> emtol   =  60   ; minimization thresold (kj/mol.nm-1)1 
>> hartree/bohr= 49614.75241 kj/mol.nm-1  1 kj/mol.nm-1=2.01553e-5 hartree/bohr
>> emstep  =  0.01  ; minimization step in nm
>> =
>> I set up the BASENAME and ORCA_PATH as told in the instruction.
>> first of all, the normal electronic embedding just simply gave segmentation 
>> fault error right after the it prints information on number of steps of 
>> optimization.
>> 
>> So I switch to ONIOM, this time, at least, orca is called and energy and 
>> gradient are both generated. However, when it comes to read the energy and 
>> gradient, it always crashes when tried to read gradient, this is at line 346 
>> source code src/mdlib/qm_orca.c
>> 
>> sscanf(buf,"%lf\n", &QMgrad[k][XX]);
>> 
>> a segmentation fault error is printed. If I replace the &QMgrad[k][XX] by an 
>> temporary variable temp 
>>  sscanf(buf,"%lf\n", &temp);
>> temp gets the correct value and if I use,
>> QMgrad[k][XX]=temp 
>> and tries to print QMgrad[k][XX], a bus error will be printed.
>> I did some research online, seems that usually this implies an memory bug in 
>> the code which is the most difficult bug one can ever encounter.
>> So has anyone successfully used gromacs and orca to do QM

[gmx-users] Re: QMMM with ORCA

[Xiaohu Li]

Dear Gerrit,
Thanks for your comments. Strange enough, once I set up the
neighbour search from simple to grid, even the electronic embedding went
through. But I'm not sure if the calculation is right.
Generally, what happens if one is running a calculation without PBC
but the calculation actually goes through. Is there anything dramatic
happening?
Thank you again.


Xiaohu

On Fri, Jan 28, 2011 at 12:47 AM, Gerrit Groenhof  wrote:

> Dear Xiaohu,
>
> Thanks for bringing this up. The comment has been there for ever. Since I
> could not think of an application where one would not be using pbc at the
> time. However, your clusters prove me wrong.
>
> In any case, as a work-around, you may want to use a bigger box, with long
> enough cut-offs, no PME.
>
> Hope this gets you started,
>
> Gerrit
>
> On 27 Jan 2011, at 21:02, Xiaohu Li wrote:
>
> Dear GMX code writters,
>  Could anyone tell me why this comments in the code *mdlib/qmmm.c
> appear*?(version 4.5.3)
> at *line ~ 714*, in the beginning of subroutine* update_QMMMrec*
> ==
> */* updates the coordinates of both QM atoms and MM atoms and stores
>* them in the QMMMrec.
>*
>* NOTE: is NOT yet working if there are no PBC. Also in ns.c, simple
>* ns needs to be fixed!
> */*
> ==
> First of all, I have a non-PBC job with electronic embedding and it
> fails right in this routine. So I guess this is the reason, for non-PBC, it
> crashes. But for oniom, it went through. Is there any simple fix to have the
> non-PBC qmmm work? I'm also interested in doing non-PBC calculation(large
> cluster).
>
>
> Xiaohu
>
> On Thu, Jan 27, 2011 at 9:11 AM, Christoph Riplinger  > wrote:
>
>>  Hi Xiaohu,
>>
>> We are using gromacs/ORCA quite a lot. It works like any of the other
>> interfaced programs and whether you should use it depends on your needs to
>> the QM part of the QM/MM calculation.
>>
>> I am using gromacs 4.0.7, but I downloaded the 4.5.3 version to test it.
>>
>> I could not reproduce your problem with ONIOM. For the electrostatic
>> embedding bug, I agree. This didn't work in my test calculation, but my gdb
>> told me that the abort occured before the qm_orca.c was even called. I
>> suspect the bug is in the general qmmm.c code. I do not have access to the
>> other QM-programs and cannot test this, so if you have, could you please run
>> the same job with a different QM-program.
>>
>> Hope that helps
>>
>> Christoph
>>
>>
>>
>>
>> On 01/26/2011 06:48 AM, Xiaohu Li wrote:
>>
>> Hi, All,
>>  I'm trying to see if anybody has experience of using the interface of
>> gromacs and ORCA(since it's free). I know that the following link gave
>> information on how
>> http://wwwuser.gwdg.de/~ggroenh/qmmm.html#code
>>  But.But, the gromacs in the above link is quite old(3.2). I
>> download the latest 4.5.3 and followed the instructions in the above link
>> and I was trying to optimize an simple cluster(no pbc) where part of it are
>> treated using QM. here is the example mdp file
>>
>> =
>>  title   =  cpeptide
>> integrator  =  steep   ;integrator includes energy minimization
>> algorithms
>> dt  =  0.002; ps !
>> nsteps  =   1
>> nstlist =  1
>> ns_type =  simple
>> rlist   =  3.0
>> rcoulomb=  3.0
>> coulombtype = cut-off
>> vdwtype = cut-off
>> rvdw= 3.0
>> pbc =  no
>> periodic_molecules  =  no
>> constraints = none
>> energygrps  = qm_part mm_part
>> ; QM/MM calculation stuff
>> QMMM = yes
>> QMMM-grps = qm_part
>> QMmethod = rhf
>> QMbasis = 3-21G
>> QMMMscheme = oniom
>> QMcharge = 0
>> QMmult = 1
>> ;
>> ;   Energy minimizing stuff
>> ;
>> emtol   =  60   ; minimization thresold (kj/mol.nm-1)1
>> hartree/bohr= 49614.75241 kj/mol.nm-1  1 kj/mol.nm-1=2.01553e-5 hartree/bohr
>> emstep  =  0.01  ; minimization step in nm
>>
>> =
>>  I set up the BASENAME and ORCA_PATH as told in the instruction.
>> first of all, the normal electronic embedding just simply gave
>> segmentation fault error right after the it prints information on number of
>> steps of optimization.
>>
>>  So I switch to ONIOM, this time, at least, orca is called and energy and
>> gradient are both generated. However, when it comes to read the energy and
>> gradient, it always crashes when tried to read gradient, this is at *line
>> 346* source code src/mdlib/qm_orca.c
>> 
>> sscanf(buf,"%lf\n", &QMgrad[k][XX]);

[gmx-users] local pressure calcuation for Gromacs-4.5

[Jianguo Li]

Hi All,

I found there is a customised version "gromacs-4.0.2_localpressure" for 
calculating the local pressure from the Gromacs website. I am wondering is 
there 
a higher version? The reason is that I am using CHARMM  FF and have done 
membrane simulations using Gromacs-4.5.  If I understand correctly, I need to 
rerun the simulation using the customized version of Gromacs to calculate the 
local pressure. However, I cannot use the -rerun option of 
"gromacs-4.0.2_localpressure" as my trajectory is from a higher version. 


Or is there any other tools that can calculate the local pressure of the 
membrane?

Thanks very much!

best regards,
Jianguo

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