[gmx-users] simulation in the high temperature

[shiva birgani]

Dear Justin
I want to simulate a protein in the high temperature (338 K).
I wan to know changing of ref_t in mdp file is enough and there is not any
other parameter to be changed in this regard?
and how much the results of this type of simulation (in high temperature) is
reliable?
thanks in advance

with regards
Shiva
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Re: [gmx-users] g_covar & g_anaeig problems

[Sebastian Breuers]

Hey,

taking fewer atoms by ignoring the hydrogens is a good advice. Thanks a 
lot.


I was wondering if a more appropriate error message could be generated 
before the program messes around in the memory. The program acts as if 
it could handle the system size and then crashes with a Segmentation 
fault meaning it does not properly handle its memory.


Nonetheless thanks again for the hydrogen advice. Had'nt really thought 
about it before.


Kind regards

Sebastian


Am 07.09.2010 03:44, schrieb Mark Abraham:



- Original Message -
From: Sebastian Breuers 
Date: Tuesday, September 7, 2010 0:42
Subject: Re: [gmx-users] g_covar & g_anaeig problems
To: gmx-users@gromacs.org

> Hey everyone,
>
> searching the list for the answer to a g_covar problem I've
> found this post of Arne who describes the very same problem that
> I encounter.
>
> I'm observing this problem on a linux cluster with 32GB memory
> on each node. The g_covar_d application was compiled in double
> precision with an intel compiler and works fine up to a number
> of atoms of around 15408. In tests I could find out that above
> this number +/- 48 atoms I receive the following error output:
>
>
> Calculating the average structure ...
> Last frame 50
> time 5000.000
>
> Constructing covariance matrix (46368x46368) ...
> Reading frame   0
> time0.000   Segmentation fault
>
> Meaning a matrix over around 46224x46224 elements starts to
> generate this problem.
>
> Did anyone encounter the same problem or does anyone has a hint
> to solve this issue?

Get more memory or use fewer atoms :-) The memory needs and run time 
will scale at least as high as the square of the number of atoms. 
Probably you can ignore at least your hydrogen atoms...


Mark 



--
_

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EMail: breue...@uni-koeln.de

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Department für Chemie   Department of Chemistry
Organische Chemie   Organic Chemistry

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_

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[gmx-users] Generalized Born segfaults with v4.5.1

[Silvio a Beccara]

Dear friends,

when trying to run a double precision vanilla MD, version 4.5.1, with a small 
hairpin molecule (248 atoms) in implicit solvent (generalized Born 
approximation) this is what I get:

-
Getting Loaded...
Reading file hairpin-md-gb-1.tpr, VERSION 4.5.1 (double precision)
Loaded with Money

starting mdrun 'Protein'
5 steps, 50.0 ps.
Segmentation fault
-

In some trials, I also get a message about the distance in an 1-4 interaction 
being beyond the table size, but this is not the case.

Strangely enough, the MD runs fine with a development version (4.0.99, 
downloaded from the GIT repository).

I am attaching my mdp and pdb files.


Regards


Silvio a Beccara


Dip. di Fisica - Universita` di Trento
14 Via Sommarive
38123 Povo - TN
tel: 0461-881631
;
;   Molecular dynamics thermostatted @ 1600.0 K 
;
cpp =  /usr/bin/cpp
define  =  -DFLEX_SPC
constraints =  none
integrator  =  md
comm_mode   =  angular
nsteps  =  5 
dt  =  0.001
pbc =  no
periodic_molecules  =  no
nstcomm =  10
nstxout =  10
; nstfout =  1
ns_type =  simple
rlist   =  2.0
rcoulomb=  2.0
rvdw=  2.0
coulombtype =  cut-off
vdwtype =  cut-off
; Extension of the potential lookup tables beyond the cut-off
table-extension  = 1
; Nose-Hoover temperature coupling is on in one group
Tcoupl  = nose-hoover
tau_t   = 0.3   
tc-grps = protein
; Generate velocites is on at 1600.0 K.
gen_vel = yes
ref_t   = 1600.0
gen_seed= 312500933 
; no barostat
Pcoupl  = no

; IMPLICIT SOLVENT ALGORITHM
implicit_solvent = gbsa

; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm = obc
; Frequency of calculating the Born radii inside rlist
nstgbradii   = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii = 2.0
; Dielectric coefficient of the implicit solvent
gb_epsilon_solvent   = 78.3
; Salt concentration in M for Generalized Born models
gb_saltconc  = 0
; Scaling factors used in the OBC GB model. Default values are OBC(II)
gb_obc_alpha = 1
gb_obc_beta  = 0.8
gb_obc_gamma = 4.85
gb_dielectric_offset = 0.009
sa_algorithm = still
; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
; The default value (2.092) corresponds to 0.005 kcal/mol/Angstrom^2.
sa_surface_tension   = 2.092


ratch-frame63.pdb
Description: application/vnd.palm
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Re: [gmx-users] Generalized Born segfaults with v4.5.1

[Per Larsson]

Hi!

I am currently working on another issue with the GB-double precision loops. 
I'll include this as well. 
But your pdb-file only contains 1 residue with the name UNK (by openBabel).
Could you please send me another pdb-file that reproduces this error off-list, 
and I'll get to it.

Cheers
/Per


7 sep 2010 kl. 09.59 skrev Silvio a Beccara:

> Dear friends,
> 
> when trying to run a double precision vanilla MD, version 4.5.1, with a small 
> hairpin molecule (248 atoms) in implicit solvent (generalized Born 
> approximation) this is what I get:
> 
> -
> Getting Loaded...
> Reading file hairpin-md-gb-1.tpr, VERSION 4.5.1 (double precision)
> Loaded with Money
> 
> starting mdrun 'Protein'
> 5 steps, 50.0 ps.
> Segmentation fault
> -
> 
> In some trials, I also get a message about the distance in an 1-4 interaction 
> being beyond the table size, but this is not the case.
> 
> Strangely enough, the MD runs fine with a development version (4.0.99, 
> downloaded from the GIT repository).
> 
> I am attaching my mdp and pdb files.
> 
> 
> Regards
> 
> 
> Silvio a Beccara
> 
> 
> Dip. di Fisica - Universita` di Trento
> 14 Via Sommarive
> 38123 Povo - TN
> tel: 0461-881631
> -- 
> gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] Generalized Born segfaults with v4.5.1

[Silvio a Beccara]

Hi, 

I had sent a wrong PDB file, right one sent offlist.

Cheers

Silvio


Il Tuesday 07 September 2010 10:06:15 Per Larsson ha scritto:
> Hi!
>
> I am currently working on another issue with the GB-double precision loops.
> I'll include this as well.
> But your pdb-file only contains 1 residue with the name UNK (by openBabel).
> Could you please send me another pdb-file that reproduces this error
> off-list, and I'll get to it.
>
> Cheers
> /Per
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Re: [gmx-users] pdb2gmx -chainsep vs -merge

[Tsjerk Wassenaar]

Hi,

> One work-around for the -chainsep situation you've observed is to remove or 
> rename the terminal oxygen atoms (OXT) that pdb2gmx is complaining about when 
> it tries to merge the chains. It should be taking care of that itself, but 
> handling it yourself might help. pdb2gmx can probably rebuild the carboxyl 
> oxygen. Keeping (one of the) OXT atoms and renaming it to "O" (keeping the 
> fixed-column format correct) might be needed.

There should be only one OXT per chain. Removing those seems like a good idea:

sed -i '/^ATOM.*OXT/d' file.pdb
(Remove all lines starting with ATOM and containing OXT, in the file)

Hope it helps,

Tsjerk


--
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology /
University of Groningen
The Netherlands
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[gmx-users] restraining atoms to the plane at the bilayer center: pull code ?

[maria goranovic]

I want to restrain certain atoms of my simulation to the plane perpendicular
to the bilayer normal, and at the bilayer center. Can someone please provide
a quick guide on how to do this? I read the pull-code options, but
restraining to a plane did not seem possible?



-- 
Maria G.
Technical University of Denmark
Copenhagen
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[gmx-users] git gromacs

[Alan]

Hi there,

Now that gromacs 4.5.1 is released I was wondering which branch should I
checkout if I want to test the bleeding edge gromacs development.

Thanks,

Alan

-- 
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Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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Re: [gmx-users] pdb2gmx -chainsep vs -merge

[nahren manuel]

Dear Gromacs Users,

thanks for all your suggestions. 

Tsjerk, I did try your idea, but unfortunately doesn't seem to work.

the pdb file is shared here : 
http://www.4shared.com/account/file/ijofD83b/DIMER.html

newpdb2gmx -f DIMER.pdb -chainsep interactive -ignh 

Fatal error:
Atom OXT in residue CYS 283 was not found in rtp entry CYS with 11 atoms
while sorting atoms.
.


Part of the file is pasted below:

ATOM   2836  N   CYS R 283 -27.431  91.636  -6.099  1.00  0.00   N
ATOM   2837  H   CYS R 283 -27.855  90.779  -6.392  1.00  0.00   H
ATOM   2838  CA  CYS R 283 -26.033  91.780  -6.514  1.00  0.00   C
ATOM   2839  CB  CYS R 283 -25.500  90.433  -7.060  1.00  0.00   C
ATOM   2840  SG  CYS R 283 -25.121  89.114  -5.829  1.00  0.00   S
ATOM   2841  HG  CYS R 283 -24.270  89.566  -4.957  1.00  0.00   H
ATOM   2842  C   CYS R 283 -25.867  92.922  -7.562  1.00  0.00   C
ATOM   2843  OXT CYS R 283 -26.993  93.593  -7.927  1.00  0.00   O
ATOM   2845  N   LYS B 284 -23.431 108.789  63.478  1.00  0.00   N
ATOM   2846  H1  LYS B 284 -23.779 109.339  64.238  1.00  0.00   H
ATOM   2847  H2  LYS B 284 -23.156 109.392  62.730  1.00  0.00   H


Best,
nahren

--- On Tue, 9/7/10, Tsjerk Wassenaar  wrote:

From: Tsjerk Wassenaar 
Subject: Re: [gmx-users] pdb2gmx -chainsep vs -merge
To: "Discussion list for GROMACS users" 
Date: Tuesday, September 7, 2010, 11:14 AM

Hi,

> One work-around for the -chainsep situation you've observed is to remove or 
> rename the terminal oxygen atoms (OXT) that pdb2gmx is complaining about when 
> it tries to merge the chains. It should be taking care of that itself, but 
> handling it yourself might help. pdb2gmx can probably rebuild the carboxyl 
> oxygen. Keeping (one of the) OXT atoms and renaming it to "O" (keeping the 
> fixed-column format correct) might be needed.

There should be only one OXT per chain. Removing those seems like a good idea:

sed -i '/^ATOM.*OXT/d' file.pdb
(Remove all lines starting with ATOM and containing OXT, in the file)

Hope it helps,

Tsjerk


--
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology /
University of Groningen
The Netherlands
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Re: [gmx-users] pdb2gmx -chainsep vs -merge

[Tsjerk Wassenaar]

Hi Nahren,

Can you paste your actual command line where you used sed?

Cheers,

Tsjerk

On Tue, Sep 7, 2010 at 12:11 PM, nahren manuel  wrote:

> Dear Gromacs Users,
>
> thanks for all your suggestions.
>
> Tsjerk, I did try your idea, but unfortunately doesn't seem to work.
>
> the pdb file is shared here :
> http://www.4shared.com/account/file/ijofD83b/DIMER.html
>
> newpdb2gmx -f DIMER.pdb -chainsep interactive -ignh
>
> Fatal error:
> Atom OXT in residue CYS 283 was not found in rtp entry CYS with 11 atoms
> while sorting atoms.
> .
>
>
> Part of the file is pasted below:
>
> ATOM   2836  N   CYS R 283 -27.431  91.636  -6.099  1.00
> 0.00   N
> ATOM   2837  H   CYS R 283 -27.855  90.779  -6.392  1.00
> 0.00   H
> ATOM   2838  CA  CYS R 283 -26.033  91.780  -6.514  1.00
> 0.00   C
> ATOM   2839  CB  CYS R 283 -25.500  90.433  -7.060  1.00
> 0.00   C
> ATOM   2840  SG  CYS R 283 -25.121  89.114  -5.829  1.00
> 0.00   S
> ATOM   2841  HG  CYS R 283 -24.270  89.566  -4.957  1.00
> 0.00   H
> ATOM   2842  C   CYS R 283 -25.867  92.922  -7.562  1.00
> 0.00   C
> ATOM   2843  OXT CYS R 283 -26.993  93.593  -7.927  1.00
> 0.00   O
> ATOM   2845  N   LYS B 284 -23.431 108.789  63.478  1.00
> 0.00   N
> ATOM   2846  H1  LYS B 284 -23.779 109.339  64.238  1.00
> 0.00   H
> ATOM   2847  H2  LYS B 284 -23.156 109.392  62.730  1.00
> 0.00   H
>
>
> Best,
> nahren
>
> --- On *Tue, 9/7/10, Tsjerk Wassenaar * wrote:
>
>
> From: Tsjerk Wassenaar 
> Subject: Re: [gmx-users] pdb2gmx -chainsep vs -merge
> To: "Discussion list for GROMACS users" 
> Date: Tuesday, September 7, 2010, 11:14 AM
>
> Hi,
>
> > One work-around for the -chainsep situation you've observed is to remove
> or rename the terminal oxygen atoms (OXT) that pdb2gmx is complaining about
> when it tries to merge the chains. It should be taking care of that itself,
> but handling it yourself might help. pdb2gmx can probably rebuild the
> carboxyl oxygen. Keeping (one of the) OXT atoms and renaming it to "O"
> (keeping the fixed-column format correct) might be needed.
>
> There should be only one OXT per chain. Removing those seems like a good
> idea:
>
> sed -i '/^ATOM.*OXT/d' file.pdb
> (Remove all lines starting with ATOM and containing OXT, in the file)
>
> Hope it helps,
>
> Tsjerk
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> Groningen Institute for Biomolecular Research and Biotechnology /
> University of Groningen
> The Netherlands
> --
>
> gmx-users mailing list
> gmx-users@gromacs.org
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> gmx-users-requ...@gromacs.org
> .
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>
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology /
University of Groningen
The Netherlands
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Re: [gmx-users] pdb2gmx -chainsep vs -merge

[nahren manuel]

Dear Gromacs Users,

Tsjerk, 

the original file did not contain OXT, as you can see, it has O1 &
O2, so I removed the O2 from the PDB and renamed O1 to OXT.

ATOM   2841  HG  CYS R 283 -24.270  89.566  -4.957  1.00  0.00   H
ATOM   2842  C   CYS R 283 -25.867  92.922  -7.562  1.00  0.00   C
ATOM   2843  O1  CYS R 283 -26.993  93.593  -7.927  1.00  0.00   O
ATOM   2844  O2  CYS R 283 -24.611  93.156  -8.027  1.00  0.00   O
ATOM   2845  N   LYS B 284 -23.431 108.789  63.478  1.00  0.00   N
ATOM   2846  H1  LYS B 284 -23.779 109.339  64.238  1.00  0.00   H



sed -i '/^ATOM.*O2/d' DIMER.pdb

Am i going wrong here?

the original PDB file is here : 

http://www.4shared.com/account/file/bTulGDPs/DIMER_FINAL.html

Best,
nahren

--- On Tue, 9/7/10, Tsjerk Wassenaar  wrote:

From: Tsjerk Wassenaar 
Subject: Re: [gmx-users] pdb2gmx -chainsep vs -merge
To: "Discussion list for GROMACS users" 
Date: Tuesday, September 7, 2010, 12:22 PM

Hi Nahren,

Can you paste your actual command line where you used sed?

Cheers,

Tsjerk

On Tue, Sep 7, 2010 at 12:11 PM, nahren manuel  wrote:


Dear Gromacs Users,

thanks for all your suggestions. 

Tsjerk, I did try your idea, but unfortunately doesn't seem to work.

the pdb file is shared here : 
http://www.4shared.com/account/file/ijofD83b/DIMER.html


newpdb2gmx -f DIMER.pdb -chainsep interactive -ignh 

Fatal error:
Atom OXT in residue CYS 283 was not found in rtp entry CYS with 11 atoms
while sorting atoms.
.


Part of the file is pasted below:


ATOM   2836  N   CYS R 283 -27.431  91.636  -6.099  1.00  0.00   N
ATOM   2837  H   CYS R 283 -27.855  90.779  -6.392  1.00  0.00  
 H
ATOM   2838  CA  CYS R 283 -26.033  91.780  -6.514  1.00  0.00   C
ATOM   2839  CB  CYS R 283 -25.500  90.433  -7.060  1.00  0.00   C
ATOM   2840  SG  CYS R 283 -25.121  89.114  -5.829  1.00  0.00   S

ATOM   2841  HG  CYS R 283 -24.270  89.566  -4.957  1.00  0.00   H
ATOM   2842  C   CYS R 283 -25.867  92.922  -7.562  1.00  0.00  
 C
ATOM   2843  OXT CYS R 283 -26.993  93.593  -7.927  1.00  0.00   O
ATOM   2845  N   LYS B 284 -23.431 108.789  63.478  1.00  0.00   N
ATOM   2846  H1  LYS B 284 -23.779 109.339  64.238  1.00  0.00   H

ATOM   2847  H2  LYS B 284 -23.156 109.392  62.730  1.00  0.00   H


Best,
nahren

--- On Tue, 9/7/10, Tsjerk Wassenaar  wrote:


From: Tsjerk Wassenaar 
Subject: Re: [gmx-users] pdb2gmx -chainsep vs -merge

To: "Discussion list for GROMACS users" 
Date: Tuesday, September 7, 2010, 11:14 AM


Hi,

> One work-around for the -chainsep situation you've observed is to remove or 
> rename the terminal oxygen atoms (OXT) that pdb2gmx is complaining about when 
> it tries to merge the chains. It should be taking care of that itself, but 
> handling it yourself might help. pdb2gmx can probably rebuild the carboxyl 
> oxygen. Keeping (one of the) OXT atoms and renaming it to "O" (keeping the 
> fixed-column format correct) might be needed.


There should be only one OXT per chain. Removing those seems like a good idea:

sed -i '/^ATOM.*OXT/d' file.pdb
(Remove all lines starting with ATOM and containing OXT, in the file)

Hope it helps,


Tsjerk


--
Tsjerk A.
 Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology /
University of Groningen
The Netherlands
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Tsjerk A. Wassenaar, Ph.D.


post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology / 
University of Groningen
The Netherlands


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http://li

[gmx-users] membrane protein-free energy

[Poojari, Chetan]

Hi,

I have done MD simulations of membrane-protein. I want to calculate interaction 
energies between protein and headgroup, protein and hydrophobic core (in the 
bilayer).
Please can anyone suggest me the method that should be followed to carry out 
these analysis.


kind regards and best wishes,
chetan



Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt


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Re: [gmx-users] simulation in the high temperature

[Justin A. Lemkul]

shiva birgani wrote:

Dear Justin
I want to simulate a protein in the high temperature (338 K).
I wan to know changing of ref_t in mdp file is enough and there is not 
any other parameter to be changed in this regard?


If you need to generate velocities, then gen_temp should also be set to this 
value.

and how much the results of this type of simulation (in high 
temperature) is reliable?


Please search the literature for high-temperature MD papers.  They may provide 
you insight.


-Justin


thanks in advance
 
with regards
Shiva 



--


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] restraining atoms to the plane at the bilayer center: pull code ?

[Justin A. Lemkul]

maria goranovic wrote:
I want to restrain certain atoms of my simulation to the plane 
perpendicular to the bilayer normal, and at the bilayer center. Can 
someone please provide a quick guide on how to do this? I read the 
pull-code options, but restraining to a plane did not seem possible?




You can restrain atoms to a plane using position restraints.  See the manual for 
an example.


-Justin




--
Maria G.
Technical University of Denmark
Copenhagen



--


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] membrane protein-free energy

[Justin A. Lemkul]

Poojari, Chetan wrote:

Hi,

I have done MD simulations of membrane-protein. I want to calculate
interaction energies between protein and headgroup, protein and hydrophobic
core (in the bilayer). Please can anyone suggest me the method that should be
followed to carry out these analysis.



Please read in the manual (and list archive for that matter) about energygrps.

-Justin



kind regards and best wishes, chetan


 

 Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich 
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 
Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher 
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft

(stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M.
Schmidt 

 




--


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] git gromacs

[Carsten Kutzner]

Hi Alan,

'bleeding edge' gromacs development is as always in the 'master' branch.
The latest bugfixes for the 4.5.x versions you are going to find in the
'release-4-5-patches' branch.

Carsten


On Sep 7, 2010, at 12:09 PM, Alan wrote:

> Hi there,
> 
> Now that gromacs 4.5.1 is released I was wondering which branch should I 
> checkout if I want to test the bleeding edge gromacs development.
> 
> Thanks,
> 
> Alan
> 
> -- 
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge. 
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> >>http://www.bio.cam.ac.uk/~awd28<<
> -- 
> gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] git gromacs

[Alan]

Thanks Carsten.

I am trying release-4-5-patches and now I can see it's compiling and
installing. However, 'make install' puts the bins only in
/usr/local/gromacs/bin and I don't have (or don't find) how to 'make links'
or similar to have the gmx bins in /usr/local/bin.

I am using cmake.

Thanks,

Alan

On 7 September 2010 11:57, Carsten Kutzner  wrote:

> Hi Alan,
>
> 'bleeding edge' gromacs development is as always in the 'master' branch.
> The latest bugfixes for the 4.5.x versions you are going to find in the
> 'release-4-5-patches' branch.
>
> Carsten
>
>
> On Sep 7, 2010, at 12:09 PM, Alan wrote:
>
> Hi there,
>
> Now that gromacs 4.5.1 is released I was wondering which branch should I
> checkout if I want to test the bleeding edge gromacs development.
>
> Thanks,
>
> Alan
>
> --
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> >>http://www.bio.cam.ac.uk/~awd28<<
>  --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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>
>
>
>
> --
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>



-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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[gmx-users] Restarts: Truncation of file *.xtc failed

[David de Sancho]

Dear Gromacs users
I am experiencing a problem with restarts in a REMD simulation with explicit
solvent in Gromacs 4.0.5. I am trying to continue a set of simulations that
finished after the maximum time in our cluster queue had been reached.
Therefore I just directly (i.e. without modifying my input file with
tpbconv) try continuing my run using

mpiexec "bindir"/mdrun_openmpi_intel -multi 32 -replex 5000 -v -s
tprfile.tpr -x xtcfile.xtc -o trrfile.trr  -c grofile.gro -e enefile.ene -g
logfile.log -cpi cptfile.cpt -cpo cptfile.cpt -append

This has worked before in previous continuations of this REMD simulation, so
in principle the pbs script I am using should be fine. However, now I find
two types of error messages:

(1) Reading checkpoint file cptfile{i}.cpt generated: ***
#PME-nodes mismatch,
current program: -1
 checkpoint file: 0
Gromacs binary or parallel settings not identical to previous run.
Continuation is exact, but is not guaranteed to be binary identical.

(2) Fatal error:
Truncation of file xtcfile${i}.xtc failed.

I have been browsing the lists and apparently the first problem is not very
important. However the second error, reached after loading the tpr and cpt
files, is fatal. I have thus checked what the problem was with my xtc files
by running gmxcheck on them and obtained messages like

# Atoms  6950
Precision 0.001 (nm)
Reading frame   9 time 18.016

Item#frames Timestep (ps)
Step 908782
Time 908782
Lambda   0
Coords   908782
Velocities   0
Forces   0
Box  908782

Nothing here tells me much about what can be going wrong. Also, I have
looked at the last frame of the simulation using vmd in case there were
missing atoms in my protein but it definitely looks like there is nothing
wrong. I have tried with the cpt and prev.cpt files in case there was
something wrong with the cpt file but still I got the fatal error.
Any hints on what it is that I am doing wrong?
Thanks


David
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Re: [gmx-users] git gromacs

[Rossen Apostolov]

 On 9/7/10 1:19 PM, Alan wrote:
I am trying release-4-5-patches and now I can see it's compiling and 
installing. However, 'make install' puts the bins only in 
/usr/local/gromacs/bin and I don't have (or don't find) how to 'make 
links' or similar to have the gmx bins in /usr/local/bin.


I am using cmake.

CMake doesn't have a 'make links' target yet.

Are there a lot of people who actually use it?

Rossen
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Re: [gmx-users] restraining atoms to the plane at the bilayer center: pull code ?

[maria goranovic]

The manual does discuss restraining to a plane, but this must be the plane
in which the atom is already present.

[  position_restraints ]
; ai   functfc
...
3   1   1000   0   0

How about restraining the atom to some other plane? For example, how about
restraining a phosphate group initially at the lipid-water interface to the
bilayer center (for whatever fancy reasons) ? Won't this require pulling the
atom to that plane first?

If it can be achieved using the position restraints alone, it is not clear
to me how to do this?

-Maria



On Tue, Sep 7, 2010 at 12:53 PM, Justin A. Lemkul  wrote:

>
>
> maria goranovic wrote:
>
>> I want to restrain certain atoms of my simulation to the plane
>> perpendicular to the bilayer normal, and at the bilayer center. Can someone
>> please provide a quick guide on how to do this? I read the pull-code
>> options, but restraining to a plane did not seem possible?
>>
>>
> You can restrain atoms to a plane using position restraints.  See the
> manual for an example.
>
> -Justin
>
>
>
>>
>> --
>> Maria G.
>> Technical University of Denmark
>> Copenhagen
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>



-- 
Maria G.
Technical University of Denmark
Copenhagen
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Re: [gmx-users] git gromacs

[Alan]

If using links or simply copying in /usr/local/bin I don't mind, but it
would easier, at least for me, once installing gromacs from source to be
able to have the gmx bins in /usr/local/bin and, of course, be able to
uninstall all gromacs as well (and undoing links or removing copies from
/usr/local/bin).

Of course, I can just put another path in $PATH, although I do not prefer
this solution: one reason, I have all my scripts and testing sets looking at
/usr/local/bin. Yet, I can fix this... but oh boy. Anyway, I took this
former approach because somehow one of gmx 4.5 betas was installing gmx bin
in /usr/local/bin. I praise consistency.

Thanks,

Alan

On 7 September 2010 13:05, Rossen Apostolov wrote:

>  On 9/7/10 1:19 PM, Alan wrote:
>
>> I am trying release-4-5-patches and now I can see it's compiling and
>> installing. However, 'make install' puts the bins only in
>> /usr/local/gromacs/bin and I don't have (or don't find) how to 'make links'
>> or similar to have the gmx bins in /usr/local/bin.
>>
>> I am using cmake.
>>
> CMake doesn't have a 'make links' target yet.
>
> Are there a lot of people who actually use it?
>
> Rossen
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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>



-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
-- 
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[gmx-users] restraining atoms to the plane at the bilayer center: pull code ?

[chris . neale]

Maria, try this. There actually is a lot of this on the mailing list,  
so I suggest checking it a little deeper for your next querry, or at  
least outlining how you looked and what you found so that it is clear  
you have tried.


Also, read about pull_pbcatomN and think carefully about how you want  
to set that up. It is a *global* index.


; COM PULLING
pull = umbrella
pull_geometry= position
pull_dim = N N Y
pull_start   = no
pull_nstxout = 500
pull_nstfout = 500
pull_ngroups = 1
pull_group0  = <<>>
pull_pbcatom0= 0
pull_group1  = <<>>
pull_pbcatom1= 0
pull_init1   = 0 0 0.0
pull_rate1   = 0
pull_k1  = <<>>
pull_vec1= 0 0 0

-- original message --


The manual does discuss restraining to a plane, but this must be the plane
in which the atom is already present.

[  position_restraints ]
; ai   functfc
...
3   1   1000   0   0

How about restraining the atom to some other plane? For example, how about
restraining a phosphate group initially at the lipid-water interface to the
bilayer center (for whatever fancy reasons) ? Won't this require pulling the
atom to that plane first?

If it can be achieved using the position restraints alone, it is not clear
to me how to do this?

-Maria



On Tue, Sep 7, 2010 at 12:53 PM, Justin A. Lemkul  wrote:




maria goranovic wrote:


I want to restrain certain atoms of my simulation to the plane
perpendicular to the bilayer normal, and at the bilayer center. Can someone
please provide a quick guide on how to do this? I read the pull-code
options, but restraining to a plane did not seem possible?



You can restrain atoms to a plane using position restraints.  See the
manual for an example.

-Justin





--
Maria G.
Technical University of Denmark
Copenhagen





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Re: [gmx-users] grompp_d and mdrun_d issues with GBSA and normal mode analysis

[Per Larsson]

This has been fixed with Berk's commit c06ee471...
The error was not related to GB, but rather a combination of domain 
decomp.+nm+cut-offs.

Cheers
/Per


6 sep 2010 kl. 11.38 skrev Ehud Schreiber:

> Dear GROMACS users,
>  
> I am encountering a couple of issues when trying to perform normal mode 
> analysis in an implicit solvent (GBSA) setting.
> I am using version 4.5.1 with double precision; unfortunately I do not have 
> the single precision version installed for comparison.
>  
> The starting point is a small protein which was energy minimized in two 
> stages, also in double precision and with GBSA, producing “em2” files. The 
> mdp file used for the normal mode analysis is the following:
>  
> - nm.mdp -
> integrator   = nm
> nsteps   = 1
> implicit_solvent = GBSA
> gb_algorithm = Still ; the default
> rgbradii = 1.0 ; must be equal to rlist
> rlist= 1.0
> coulombtype  = cut-off
> rcoulomb = 1.0
> vdwtype  = cut-off
> rvdw = 1.0
> ---  
>  
> The command used is
>  
> grompp_d -f nm.mdp -p topol.top -c em2.gro -t em2.trr -o nm.tpr
>  
> which ran fine except for the following note:
>  
> NOTE 1 [file nm.mdp]:
>   You are using a plain Coulomb cut-off, which might produce artifacts.
>   You might want to consider using PME electrostatics.
>  
> Then, I tried to run
>  
> mdrun_d -v -nice 0 -deffnm nm
>  
> However, the command seems to be stuck, and the following serious warning is 
> produced:
>  
> Warning: 1-4 interaction between 64 and 71 at distance 3.114 which is larger 
> than the 1-4 table size 2.000 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size
> Maximum force: 3.48709e+06
> Maximum force probably not small enough to ensure that you are in an
> energy well. Be aware that negative eigenvalues may occur when the
> resulting matrix is diagonalized.
>  
> The em2.gro is definitely not having such a large distance between atoms 64 
> and 71:
>  
> 6GLN CB   64   1.879   1.895   2.423
> .
> .
> 6GLNOE1   71   2.047   1.715   2.642
>  
> which are only about 0.346 nm apart. Also, the energy minimization, which 
> used the same options, mutatis mutandis,
>  
> -- em2.mdp --
> integrator   = cg
> nsteps   = 1000
> nstcgsteep   = 40
> implicit_solvent = GBSA
> gb_algorithm = Still ; the default
> rgbradii = 1.0 ; must be equal to rlist
> nstlist  = 10
> rlist= 1.0
> coulombtype  = cut-off
> rcoulomb = 1.0
> vdwtype  = cut-off
> rvdw = 1.0
> nstenergy= 10
> -
>  
> converged to machine precision having a much smaller maximum force:
>  
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 10
>  
> Polak-Ribiere Conjugate Gradients converged to machine precision in 0 steps,
> but did not reach the requested Fmax < 10.
> Potential Energy  = -2.71868395521758e+04
> Maximum force =  4.63436548427712e+02 on atom 584
> Norm of force =  1.25296847735530e+02
>  
> The other problem arises when I try to follow the grompp_d note above and 
> change in nm.mdp to
>  
> coulombtype  = pme
>  
> I then have a fatal error:
>  
> ERROR 1 [file nm.mdp]:
>   With GBSA, coulombtype must be equal to Cut-off
>  
> Am I doing something wrong or are there still some problems in the new GBSA 
> option of version 4.5.1?
>  
> Thanks,
> Ehud Schreiber.
>   
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RE: [gmx-users] grompp_d and mdrun_d issues with GBSA and normal mode analysis

[Berk Hess]

Hi,

For the moment you can add the option -nt 1 to mdrun, which will make it run 
without problems.

Berk

From: per.lars...@sbc.su.se
Subject: Re: [gmx-users] grompp_d and mdrun_d issues with GBSA and normal mode  
analysis
Date: Tue, 7 Sep 2010 16:12:28 +0200
To: gmx-users@gromacs.org



This has been fixed with Berk's commit c06ee471...The error was not related to 
GB, but rather a combination of domain decomp.+nm+cut-offs.
Cheers/Per

6 sep 2010 kl. 11.38 skrev Ehud Schreiber:Dear GROMACS users, I am encountering 
a couple of issues when trying to perform normal mode analysis in an implicit 
solvent (GBSA) setting.I am using version 4.5.1 with double precision; 
unfortunately I do not have the single precision version installed for 
comparison. The starting point is a small protein which was energy minimized in 
two stages, also in double precision and with GBSA, producing “em2” files. The 
mdp file used for the normal mode analysis is the following: - 
nm.mdp -integrator   = nmnsteps   = 
1implicit_solvent = GBSAgb_algorithm = Still ; the defaultrgbradii 
= 1.0 ; must be equal to rlistrlist= 1.0coulombtype  = 
cut-offrcoulomb = 1.0vdwtype  = cut-offrvdw = 
1.0---   The command used 
is grompp_d -f nm.mdp -p topol.top -c em2.gro -t em2.trr -o nm.tpr which ran 
fine except for the following note: NOTE 1 [file nm.mdp]:  You are using a 
plain Coulomb cut-off, which might produce artifacts.  You might want to 
consider using PME electrostatics. Then, I tried to run mdrun_d -v -nice 0 
-deffnm nm However, the command seems to be stuck, and the following serious 
warning is produced: Warning: 1-4 interaction between 64 and 71 at distance 
3.114 which is larger than the 1-4 table size 2.000 nmThese are ignored for the 
rest of the simulationThis usually means your system is exploding,if not, you 
should increase table-extension in your mdp fileor with user tables increase 
the table sizeMaximum force: 3.48709e+06Maximum force probably not small enough 
to ensure that you are in anenergy well. Be aware that negative eigenvalues may 
occur when theresulting matrix is diagonalized. The em2.gro is definitely not 
having such a large distance between atoms 64 and 71: 6GLN CB   64   
1.879   1.895   2.423..6GLNOE1   71   2.047   1.715   2.642 which are 
only about 0.346 nm apart. Also, the energy minimization, which used the same 
options, mutatis mutandis, -- em2.mdp 
--integrator   = cgnsteps   = 
1000nstcgsteep   = 40implicit_solvent = GBSAgb_algorithm = Still ; the 
defaultrgbradii = 1.0 ; must be equal to rlistnstlist  = 
10rlist= 1.0coulombtype  = cut-offrcoulomb = 1.0vdwtype 
 = cut-offrvdw = 1.0nstenergy= 
10- 
converged to machine precision having a much smaller maximum force: Stepsize 
too small, or no change in energy.Converged to machine precision,but not to the 
requested precision Fmax < 10 Polak-Ribiere Conjugate Gradients converged to 
machine precision in 0 steps,but did not reach the requested Fmax < 
10.Potential Energy  = -2.71868395521758e+04Maximum force =  
4.63436548427712e+02 on atom 584Norm of force =  1.25296847735530e+02 The 
other problem arises when I try to follow the grompp_d note above and change in 
nm.mdp to coulombtype  = pme I then have a fatal error: ERROR 1 [file 
nm.mdp]:  With GBSA, coulombtype must be equal to Cut-off Am I doing something 
wrong or are there still some problems in the new GBSA option of version 4.5.1? 
Thanks,Ehud Schreiber.  -- 
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[gmx-users] Re: gmx-users Digest, Vol 77, Issue 33

[Moeed]

Hello Justin,

1- Actually since I was focusing on rdf for C-C I didnt explain my
understanding from that post well. Anyway, I have only C and H in the system
and no protein. You mean I have to make separate groups of C and H for all
polymer chains by hand? I trying to find a more smart way of doing this..
for big polymers doing this by hand is really awful.

2- I dont see much information about structure factor in the manual or in
the archive. When I  use -sq option of g_rdf  it asks for index groups. Does
it make sense to define structure factor for a single chain?
 (It takes much time and I wanted to know how it is calculated in gromacs).

Thank you for your help,


***

>
> > Now I am trying to do the same thing to get rdf for C-C or C-H for
> > polymer chains. I looked into default index groups and I guess
> > Protein-H, BAckbone and Mainchain groups for my system should give only
> > carbon atoms (I have only polyethylene chains), and Non-Protein should
> > give only H. but I do not know how I can use them since System is the
> > only default group I see.
> >
>
> Do you have protein molecules?  If not, then you won't have default groups
> like
> Protein, Protein-H...
>
> > 2- What doesy axis show? the average number density? ( I am calculating
>
> Please use Google to answer this question.
>
> > rdf between chains 1 and 2 for instance. y-axis is in the range of 0-300
> > ?! and x-axis varies between 0-15 nm?!. normally g(r) is in the range of
> > 1 to 5 ..). and also I noticed it takes much time for the program to
>
> Normally?  Based on what assessment?  Unless you have exceptionally good
> sampling, your RDF plot probably won't converge very well for large
> molecules,
> especially if you are analyzing all possible atomic pairs.
>
> > read all frames when I issue the command below even for only 2 chains
> > having 60 ethylene units. Am I doing something wrong?
> >
>
> No, but g_rdf is doing something on the order of 362*362 calculations, so
> you
> can count on that taking a lot of time (and memory).
>
> -Justin
>
>
>
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Re: [gmx-users] about rdf

[Justin A. Lemkul]

Moeed wrote:


Hello Justin,

1- Actually since I was focusing on rdf for C-C I didnt explain my 
understanding from that post well. Anyway, I have only C and H in the 
system and no protein. You mean I have to make separate groups of C and 
H for all polymer chains by hand? I trying to find a more smart way of 
doing this.. for big polymers doing this by hand is really awful.




Simply defining "C" and "H" is relatively meaningless, isn't it?  You have a C60 
chain, so you have 30 "different" types of C based on the symmetry of the 
molecules.  Perhaps you need to refine what it is you're looking to analyze. 
For large molecules, you will likely need exceptional sampling to get a nicely 
converged RDF plot.  I don't know how long that might take, but tens (if not 
hundreds) of ns might be necessary.


2- I dont see much information about structure factor in the manual or 
in the archive. When I  use -sq option of g_rdf  it asks for index 
groups. Does it make sense to define structure factor for a single chain?

 (It takes much time and I wanted to know how it is calculated in gromacs).


I've never used this option, but if you want to know what it's doing, that's why 
the source code is publicly available.


-Justin



Thank you for your help,


***


 > Now I am trying to do the same thing to get rdf for C-C or C-H for
 > polymer chains. I looked into default index groups and I guess
 > Protein-H, BAckbone and Mainchain groups for my system should
give only
 > carbon atoms (I have only polyethylene chains), and Non-Protein
should
 > give only H. but I do not know how I can use them since System is the
 > only default group I see.
 >

Do you have protein molecules?  If not, then you won't have default
groups like
Protein, Protein-H...

 > 2- What doesy axis show? the average number density? ( I am
calculating

Please use Google to answer this question.

 > rdf between chains 1 and 2 for instance. y-axis is in the range
of 0-300
 > ?! and x-axis varies between 0-15 nm?!. normally g(r) is in the
range of
 > 1 to 5 ..). and also I noticed it takes much time for the program to

Normally?  Based on what assessment?  Unless you have exceptionally good
sampling, your RDF plot probably won't converge very well for large
molecules,
especially if you are analyzing all possible atomic pairs.

 > read all frames when I issue the command below even for only 2 chains
 > having 60 ethylene units. Am I doing something wrong?
 >

No, but g_rdf is doing something on the order of 362*362
calculations, so you
can count on that taking a lot of time (and memory).

-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] gmx 4.5.1 and opemm not compiling on Mac SL

[Alan]

Hi there,

I am trying:

~/Downloads/gromacs-4.5.1/build% cmake -DGMX_OPENMM=ON ..

~/Downloads/gromacs-4.5.1/build% make mdrun
[  1%] Building NVCC (Device) object
src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_memtestG80_core.cu.o
[  1%] Building NVCC (Device) object
src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
Scanning dependencies of target gmx_gpu_utils
Linking CXX shared library libgmx_gpu_utils.dylib
Undefined symbols:
  "_gmx_strncasecmp", referenced from:
  is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  "_debug", referenced from:
  is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  do_timed_memtest(int, int)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  do_full_memtest(int)  in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  do_quick_memtest(int)  in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  "_trim", referenced from:
  is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
ld: symbol(s) not found
collect2: ld returned 1 exit status
make[3]: *** [src/kernel/gmx_gpu_utils/libgmx_gpu_utils.dylib] Error 1
make[2]: *** [src/kernel/gmx_gpu_utils/CMakeFiles/gmx_gpu_utils.dir/all]
Error 2
make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/rule] Error 2
make: *** [mdrun] Error 2

Same thing with gmx from git. Any idea? Thanks.

Alan
-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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Re: [gmx-users] Restarts: Truncation of file *.xtc failed

[Yongchul Chung]

Hi,

How big is your file? I assume since you are running 18ps simulation, it
might be big. I remember there's a problem with gromacs not being able to
truncate file size >4Gb.

Greg

On Tue, Sep 7, 2010 at 8:04 AM, David de Sancho wrote:

> Dear Gromacs users
> I am experiencing a problem with restarts in a REMD simulation with
> explicit solvent in Gromacs 4.0.5. I am trying to continue a set of
> simulations that finished after the maximum time in our cluster queue had
> been reached. Therefore I just directly (i.e. without modifying my input
> file with tpbconv) try continuing my run using
>
> mpiexec "bindir"/mdrun_openmpi_intel -multi 32 -replex 5000 -v -s
> tprfile.tpr -x xtcfile.xtc -o trrfile.trr  -c grofile.gro -e enefile.ene -g
> logfile.log -cpi cptfile.cpt -cpo cptfile.cpt -append
>
> This has worked before in previous continuations of this REMD simulation,
> so in principle the pbs script I am using should be fine. However, now I
> find two types of error messages:
>
> (1) Reading checkpoint file cptfile{i}.cpt generated: ***
> #PME-nodes mismatch,
> current program: -1
>  checkpoint file: 0
> Gromacs binary or parallel settings not identical to previous run.
> Continuation is exact, but is not guaranteed to be binary identical.
>
> (2) Fatal error:
> Truncation of file xtcfile${i}.xtc failed.
>
> I have been browsing the lists and apparently the first problem is not very
> important. However the second error, reached after loading the tpr and cpt
> files, is fatal. I have thus checked what the problem was with my xtc files
> by running gmxcheck on them and obtained messages like
>
> # Atoms  6950
> Precision 0.001 (nm)
> Reading frame   9 time 18.016
>
> Item#frames Timestep (ps)
> Step 908782
> Time 908782
> Lambda   0
> Coords   908782
> Velocities   0
> Forces   0
> Box  908782
>
> Nothing here tells me much about what can be going wrong. Also, I have
> looked at the last frame of the simulation using vmd in case there were
> missing atoms in my protein but it definitely looks like there is nothing
> wrong. I have tried with the cpt and prev.cpt files in case there was
> something wrong with the cpt file but still I got the fatal error.
> Any hints on what it is that I am doing wrong?
> Thanks
>
>
> David
>
>
>
>
> --
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Re: [gmx-users] pdb2gmx -chainsep vs -merge

[Tsjerk Wassenaar]

Hey Nahren,

>
> sed -i '/^ATOM.*O2/d' DIMER.pdb
>
> Am i going wrong here?

You should try :) But it looks quite okay to me ;)

Cheers,

Tsjerk

--
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post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology /
University of Groningen
The Netherlands
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[gmx-users] hessian.mtx----> readable format

[Vishal Agarwal]

Dear Gromacs Users,
Is there a way to convert the hessian.mtx file into a readable format using
any of the gromacs utilities?
Any help on this would be highly apprecaited..
Thanks,
Vishal
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Re: [gmx-users] hessian.mtx----> readable format

[Justin A. Lemkul]

Vishal Agarwal wrote:

Dear Gromacs Users,
Is there a way to convert the hessian.mtx file into a readable format 
using any of the gromacs utilities?


gmxdump -mtx
g_nmeig

-Justin


Any help on this would be highly apprecaited..
Thanks,
Vishal





--


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] gromacs (4.5) installation

[Moeed]

Dear experts,

I have installed newest version of gromacs (4.5) on our cluster. When I
issue the command below to test installation I get an error about atom type
CU+2. I am not using such atom type at all! Could you please help me what
wrong is. Thanks.


grompp -f *.mdp -c *.gro -p *.top -o out >& output.grompp_md


NOTE 1 [file md-NVT-revised.mdp]:
  nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
  nstcomm to nstcalcenergy

Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations

---
Program grompp, VERSION 4.5
Source code file: toppush.c, line: 1166

Fatal error:
Atomtype CU2+ not found
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
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Re: [gmx-users] gromacs (4.5) installation

[Justin A. Lemkul]

Moeed wrote:

Dear experts,

I have installed newest version of gromacs (4.5) on our cluster. When I 
issue the command below to test installation I get an error about atom 
type CU+2. I am not using such atom type at all! Could you please help 
me what wrong is. Thanks.




No one can tell unless you describe what should be in the system, what is in the 
topology, what force field you're using, etc.


-Justin



grompp -f *.mdp -c *.gro -p *.top -o out >& output.grompp_md


NOTE 1 [file md-NVT-revised.mdp]:
  nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
  nstcomm to nstcalcenergy

Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations

---
Program grompp, VERSION 4.5
Source code file: toppush.c, line: 1166

Fatal error:
Atomtype CU2+ not found
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---



--


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


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[gmx-users] Re: Restarts: Truncation of file *.xtc failed

[David de Sancho]

Hi
Thanks Greg for your answer.
Yes, my simulation is in fact pretty long and its files are considerably
large. The size of the xtc files is approximately ~2 GB when I am trying to
do the restart.
I thought on the contrary that my problem was related to another post in
today's list (
http://lists.gromacs.org/pipermail/gmx-users/2010-September/053701.html). My
xtc files were not synchronized (by very little). The answer to that other
message was that in case the xtc files were not synchronized one would have
to create new and synchronized tpr files using tpbconv and the trr files
with positions and velocities.
Can anyone confirm this?
Thanks


David
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RE: [gmx-users] about rdf

[Dallas Warren]

> > 1- Actually since I was focusing on rdf for C-C I didnt explain my
> > understanding from that post well. Anyway, I have only C and H in
the
> > system and no protein. You mean I have to make separate groups of C
> and
> > H for all polymer chains by hand? I trying to find a more smart way
> of
> > doing this.. for big polymers doing this by hand is really awful.

No need to do anything by hand there, use make_ndx

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 9909 9304
-
When the only tool you own is a hammer, every problem begins to resemble
a nail.
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Re: [gmx-users] Restarts: Truncation of file *.xtc failed

[Mark Abraham]

- Original Message -
From: Yongchul Chung 
Date: Wednesday, September 8, 2010 4:10
Subject: Re: [gmx-users] Restarts: Truncation of file *.xtc failed
To: Discussion list for GROMACS users 

> Hi,
> 
> How big is your file? I assume since you are running 18ps simulation, it 
> might be big. I remember there's a problem with gromacs not being able to 
> truncate file size >4Gb. 

Strictly speaking, *GROMACS* doesn't have an intrinsic file-size limit, but the 
underlying file system can have a limitation, and GROMACS doesn't work around 
this. The best solution is to use a better file system.

Mark

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Re: [gmx-users] Re: Restarts: Truncation of file *.xtc failed

[Mark Abraham]

- Original Message -
From: David de Sancho 
Date: Wednesday, September 8, 2010 8:04
Subject: [gmx-users] Re: Restarts: Truncation of file *.xtc failed
To: gmx-users@gromacs.org

> Hi
> Thanks Greg for your answer.
> Yes, my simulation is in fact pretty long and its files are considerably 
> large. The size of the xtc files is approximately ~2 GB when I am trying to 
> do the restart.
> I thought on the contrary that my problem was related to another post in 
> today's list 
> (http://lists.gromacs.org/pipermail/gmx-users/2010-September/053701.html). My 
> xtc files were not synchronized (by very little). The answer to that other 
> message was that in case the xtc files were not synchronized one would have 
> to create new and synchronized tpr files using tpbconv and the trr files with 
> positions and velocities.

4.0.x would write checkpoint files for REMD out of sync under some 
circumstances. One approach is to truncate all the files to a time when you 
have a checkpoint available for all replicas. Another would be to take the .tpr 
and .cpt for each replica on its own, adjust the final timestep with tpbconv so 
that you can synchronise each replica in a single-replica simulation, simulate, 
and once everything's in sync, restart REMD.

Mark

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Re: [gmx-users] pdb2gmx -chainsep vs -merge

[Mark Abraham]

- Original Message -
From: nahren manuel 
Date: Tuesday, September 7, 2010 20:33
Subject: Re: [gmx-users] pdb2gmx -chainsep vs -merge
To: Discussion list for GROMACS users 

---
| > Dear Gromacs Users,
> 
> Tsjerk, 
> 
> the original file did not contain OXT, as you can see, it has O1 & O2, so I 
> removed the O2 from the PDB and renamed O1 to OXT.

OK, so now that OXT is causing a problem, go back to the original version and 
don't introduce OXT. 

It does look like you're going to have a serious problem merging these 
chains... the termini are nowhere near each other!

If I recall your original problem correctly, you're trying to use pdb2gmx to 
generate a [moleculetype] that has multiple molecules in it so that you can use 
"inter-molecular" distance restraints in a GROMACS-legal intra-moleculetype 
way. If pdb2gmx is sensitive to chain ID, and the -chainsep/TER combination is 
suitable, then it's conceivable this would work in the way you hope, however it 
is not clear to me that pdb2gmx will have this functionality. -chainsep 
comments in pdb2gmx -h imply that a new chain and a new moleculetype go 
together.

There's no ready way to merge [moleculetype] .itp files after the fact. All the 
atom numbers after the first molecule would have to be renumbered, and their 
interactions likewise. That would be a job for Perl - read the first .itp file, 
count the atoms and break the file into chunks for each directive, then read 
each subsequent .itp file, break the file into chunks, add the appropriate 
integer to each atom number, and append the chunks. Finally, write out all the 
chunks. Regular expressions will probably be good friends there.

I seem to recall intent at some point to implement inter-molecular distance 
restraints in GROMACS to avoid this issue. I don't know if this was ever done, 
though. Check the manual and search the mailing list and wiki.

Mark
 |
---

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Re: [gmx-users] g_covar & g_anaeig problems

[Mark Abraham]

- Original Message -
From: Sebastian Breuers 
Date: Tuesday, September 7, 2010 17:47
Subject: Re: [gmx-users] g_covar & g_anaeig problems
To: gmx-users@gromacs.org

> Hey,
> 
> taking fewer atoms by ignoring the hydrogens is a good advice. 
> Thanks a lot.

That's just the tip of the iceberg, of course. Even as little as your C-alpha 
atoms might be sufficient for the purpose.

 
> I was wondering if a more appropriate error message could be 
> generated before the program messes around in the memory. The 
> program acts as if it could handle the system size and then 
> crashes with a Segmentation fault meaning it does not properly 
> handle its memory.

Sure, that would be nice behaviour. Unfortunately the algorithms used for 
diagonalization are called from another library, and GROMACS can't 
realistically anticipate its memory usage. Moreover, finding out from the 
system how much virtual memory is available and from the user whether virtual 
memory use is acceptable is all more work than it's worth. I have added a note 
in the g_covar documentation to clue the user in to how best to manage the 
situation.

Mark

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Re: [gmx-users] Tables and forcefield parameters

[Mark Abraham]

- Original Message -
From: Sai Pooja 
Date: Sunday, September 5, 2010 8:19
Subject: [gmx-users] Tables and forcefield parameters
To: Discussion list for GROMACS users 

> Hi,
> 
> ques1:
> I have 3 energy groups.
> I am interested in using tables for LJ and coulomb  interactions for 
> Group1-group2 interactions. 
> For all other interactions:
> 1) Group1-group1 -all interactions-bonded and non-bonded
>   2) Group2-group2 -all interactions -bonded and non-bonded
> 3) All possible combinations for group3
> I want to use gromacs defined standard energy functions.
> 
> For all other types of interactions, e.g. 1-4 pair interactions and bonded 
> interactions I would like to use gromacs defined interactions. 
  > 
> And for all these cases, I am still looking to use parameters defined by the 
> forcefield. I would like to specify that I am will be using a functional form 
> in the tables differing from coulomb and 6-12 LJ interactions by a numeric 
> constant.
  > 
> Is it possible? If not entirely, which is possible? Any suggestions on which 
> part might be easier to program?

You just take the normal table and multiply the values in it by the constant. 
Then use that table for the energygrp_table entry for the appropriate groups. 
No coding required. Manual 6.7.2 points you at some starting points for tables 
to modify.

Mark

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[gmx-users] GFP Simulation

[Rama G]

Dear Gmxers,

I am working on a new project and I plan to do some molecular dynamic 
simulation on an engineered GFP molecule. I have been searching for the 
parameters for the GFP chromophore without success. Could some one help me? Any 
reference or parameters will be appreciated.

Thanks,

Juju


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Re: [gmx-users] Tables and forcefield parameters

[Sai Pooja]

Thanks Mark :).

On Tue, Sep 7, 2010 at 10:06 PM, Mark Abraham wrote:

>
>
> - Original Message -
> From: Sai Pooja 
> Date: Sunday, September 5, 2010 8:19
> Subject: [gmx-users] Tables and forcefield parameters
> To: Discussion list for GROMACS users 
>
> > Hi,
> >
> > ques1:
> > I have 3 energy groups.
> > I am interested in using tables for LJ and coulomb  interactions for
> Group1-group2 interactions.
> > For all other interactions:
> > 1) Group1-group1 -all interactions-bonded and non-bonded
> > 2) Group2-group2 -all interactions -bonded and non-bonded
> > 3) All possible combinations for group3
> > I want to use gromacs defined standard energy functions.
> >
> > For all other types of interactions, e.g. 1-4 pair interactions and
> bonded interactions I would like to use gromacs defined interactions.
> >
> > And for all these cases, I am still looking to use parameters defined by
> the forcefield. I would like to specify that I am will be using a functional
> form in the tables differing from coulomb and 6-12 LJ interactions by a
> numeric constant.
> >
> > Is it possible? If not entirely, which is possible? Any suggestions on
> which part might be easier to program?
>
> You just take the normal table and multiply the values in it by the
> constant. Then use that table for the energygrp_table entry for the
> appropriate groups. No coding required. Manual 6.7.2 points you at some
> starting points for tables to modify.
>
> Mark
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>



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[gmx-users] Alanine dipeptide simulations

[Sai Pooja]

Hi,

I am running an npt simulation on alanine dipeptide in explicit solvent
using charmm forcefield and tip3p.

The pressure is set to 1bar and the barostat is Parrinello-Rahman. The
simulation has been running for 45 ns and has not achieved the target
average pressure of 1 bar.

I don;t understand why is this the case.

My mdp file:

; RUN CONTROL PARAMETERS
integrator   = md
dt   = 0.002
nsteps   = 50

; OUTPUT CONTROL OPTIONS
nstxout  = 0; No output, except for last
frame (coordinates)
nstvout  = 0; No output, except for last
frame (velocities)
nstfout  = 0; No output, except for last
frame (forces)
nstlog   = 5000; Write every step to the log
nstenergy= 5000; Write energies at every
step
xtc_grps = Protein SOL
nstxtcout= 5000; Do not write a
compressed trajectory
energygrps   = Protein SOL  ; Write energy information
separately for these groups

; NEIGHBORSEARCHING PARAMETERS
nstlist  = 5
ns-type  = Grid
pbc  = xyz
rlist= 0.9

; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype  = PME
fourierspacing   = 0.15
rcoulomb = 0.9
vdw-type = Cut-off
rvdw = 1.0

; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters =
pme_order= 4
ewald_rtol   = 1e-05
epsilon_surface  = 0
optimize_fft = no
; Temperature coupling
tcoupl   = nose-hoover
tc-grps  = Protein  Non-Protein
tau_t= 0.2  0.2
ref_t= 300  300

; Pressure coupling
Pcoupl   = Parrinello-Rahman
Pcoupltype   = Isotropic
tau_p= 1.0
compressibility  = 4.5e-5
ref_p= 1.0

; OPTIONS FOR BONDS
constraints  = all-bonds


Pooja




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RE: [gmx-users] Alanine dipeptide simulations

[Dallas Warren]

What pressure has it reached?

 

Probably best graph the pressure versus time plot for the run and show
that.


I suspect what you are concerned about is the fact that with pressure
coupling, the pressure can fluctuation from step to step, very widely,
100s atm is not out of the question.

 

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 9909 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 Sai Pooja
Sent: Wednesday, 8 September 2010 3:18 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] Alanine dipeptide simulations

 

Hi,

I am running an npt simulation on alanine dipeptide in explicit solvent
using charmm forcefield and tip3p.

The pressure is set to 1bar and the barostat is Parrinello-Rahman. The
simulation has been running for 45 ns and has not achieved the target
average pressure of 1 bar.

I don;t understand why is this the case.

My mdp file:

; RUN CONTROL PARAMETERS
integrator   = md
dt   = 0.002
nsteps   = 50

; OUTPUT CONTROL OPTIONS
nstxout  = 0; No output, except for
last frame (coordinates)
nstvout  = 0; No output, except for
last frame (velocities)
nstfout  = 0; No output, except for
last frame (forces)
nstlog   = 5000; Write every step to the
log
nstenergy= 5000; Write energies at
every step
xtc_grps = Protein SOL
nstxtcout= 5000; Do not write a
compressed trajectory
energygrps   = Protein SOL  ; Write energy information
separately for these groups

; NEIGHBORSEARCHING PARAMETERS
nstlist  = 5
ns-type  = Grid
pbc  = xyz
rlist= 0.9

; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype  = PME
fourierspacing   = 0.15
rcoulomb = 0.9
vdw-type = Cut-off
rvdw = 1.0

; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters =
pme_order= 4
ewald_rtol   = 1e-05
epsilon_surface  = 0
optimize_fft = no
; Temperature coupling
tcoupl   = nose-hoover
tc-grps  = Protein  Non-Protein
tau_t= 0.2  0.2
ref_t= 300  300

; Pressure coupling
Pcoupl   = Parrinello-Rahman
Pcoupltype   = Isotropic
tau_p= 1.0
compressibility  = 4.5e-5
ref_p= 1.0

; OPTIONS FOR BONDS
constraints  = all-bonds


Pooja




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[gmx-users] reg compilation problem in Mopac gromacs

[vidhya sankar]

Dear sir, 
thanks in advance
  When i type the following command in gromacs directory
./configure --with-qmmm-mopac --disable-float
it configure successfully
but when i compile by make command i got the following error at the end of my 
compilation
　
libs/libgmxpreprocess_d.a ../mdlib/.libs/libmd_d.a 
/root/gromacs-4.0.5/src/gmxlib/.libs/libgmx_d.a ../gmxlib/.libs/libgmx_d.a 
-lnsl -lfftw3 -lm -lmopac -ltest 
../mdlib/.libs/libmd_d.a(qm_mopac.o): In function `call_mopac_SH':
qm_mopac.c:(.text+0x2a7): undefined reference to `domop_'
../mdlib/.libs/libmd_d.a(qm_mopac.o): In function `call_mopac':
qm_mopac.c:(.text+0x70b): undefined reference to `domop_'
../mdlib/.libs/libmd_d.a(qm_mopac.o): In function `init_mopac':
qm_mopac.c:(.text+0x964): undefined reference to `domldt_'
collect2: ld returned 1 exit status
make[3]: *** [grompp] Error 1
make[3]: Leaving directory `/root/gromacs-4.0.5/src/kernel'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/root/gromacs-4.0.5/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/root/gromacs-4.0.5/src'
make: *** [all-recursive] Error 1
What should i do to avoid this error? i am expecting your reply
also when i use ./configure --without-qmmm-mopac --disable-float it compiles 
successfully

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RE: [gmx-users] Alanine dipeptide simulations

[Dallas Warren]

See http://www.gromacs.org/Documentation/Terminology/Pressure for
further details

 

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 9909 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 Dallas Warren
Sent: Wednesday, 8 September 2010 3:21 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] Alanine dipeptide simulations

 

What pressure has it reached?

 

Probably best graph the pressure versus time plot for the run and show
that.


I suspect what you are concerned about is the fact that with pressure
coupling, the pressure can fluctuation from step to step, very widely,
100s atm is not out of the question.

 

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 9909 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 Sai Pooja
Sent: Wednesday, 8 September 2010 3:18 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] Alanine dipeptide simulations

 

Hi,

I am running an npt simulation on alanine dipeptide in explicit solvent
using charmm forcefield and tip3p.

The pressure is set to 1bar and the barostat is Parrinello-Rahman. The
simulation has been running for 45 ns and has not achieved the target
average pressure of 1 bar.

I don;t understand why is this the case.

My mdp file:

; RUN CONTROL PARAMETERS
integrator   = md
dt   = 0.002
nsteps   = 50

; OUTPUT CONTROL OPTIONS
nstxout  = 0; No output, except for
last frame (coordinates)
nstvout  = 0; No output, except for
last frame (velocities)
nstfout  = 0; No output, except for
last frame (forces)
nstlog   = 5000; Write every step to the
log
nstenergy= 5000; Write energies at
every step
xtc_grps = Protein SOL
nstxtcout= 5000; Do not write a
compressed trajectory
energygrps   = Protein SOL  ; Write energy information
separately for these groups

; NEIGHBORSEARCHING PARAMETERS
nstlist  = 5
ns-type  = Grid
pbc  = xyz
rlist= 0.9

; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype  = PME
fourierspacing   = 0.15
rcoulomb = 0.9
vdw-type = Cut-off
rvdw = 1.0

; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters =
pme_order= 4
ewald_rtol   = 1e-05
epsilon_surface  = 0
optimize_fft = no
; Temperature coupling
tcoupl   = nose-hoover
tc-grps  = Protein  Non-Protein
tau_t= 0.2  0.2
ref_t= 300  300

; Pressure coupling
Pcoupl   = Parrinello-Rahman
Pcoupltype   = Isotropic
tau_p= 1.0
compressibility  = 4.5e-5
ref_p= 1.0

; OPTIONS FOR BONDS
constraints  = all-bonds


Pooja




-- 
Quaerendo Invenietis-Seek and you shall discover.

-- 
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Re: [gmx-users] Alanine dipeptide simulations

[Sai Pooja]

Hi

Yes, the fluctuations are large but even the average pressure hasn't
converged. Its close 2.5 bar. RMSD ~600 bar.

Pooja

On Wed, Sep 8, 2010 at 1:27 AM, Dallas Warren wrote:

>  See http://www.gromacs.org/Documentation/Terminology/Pressure for further
> details
>
>
>
> 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 9909 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 *Dallas Warren
> *Sent:* Wednesday, 8 September 2010 3:21 PM
>
> *To:* Discussion list for GROMACS users
> *Subject:* RE: [gmx-users] Alanine dipeptide simulations
>
>
>
> What pressure has it reached?
>
>
>
> Probably best graph the pressure versus time plot for the run and show
> that.
>
>
> I suspect what you are concerned about is the fact that with pressure
> coupling, the pressure can fluctuation from step to step, very widely, 100s
> atm is not out of the question.
>
>
>
> 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 9909 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 *Sai Pooja
> *Sent:* Wednesday, 8 September 2010 3:18 PM
> *To:* Discussion list for GROMACS users
> *Subject:* [gmx-users] Alanine dipeptide simulations
>
>
>
> Hi,
>
>
> I am running an npt simulation on alanine dipeptide in explicit solvent
> using charmm forcefield and tip3p.
>
> The pressure is set to 1bar and the barostat is Parrinello-Rahman. The
> simulation has been running for 45 ns and has not achieved the target
> average pressure of 1 bar.
>
> I don;t understand why is this the case.
>
> My mdp file:
>
> ; RUN CONTROL PARAMETERS
> integrator   = md
> dt   = 0.002
> nsteps   = 50
>
> ; OUTPUT CONTROL OPTIONS
> nstxout  = 0; No output, except for
> last frame (coordinates)
> nstvout  = 0; No output, except for
> last frame (velocities)
> nstfout  = 0; No output, except for
> last frame (forces)
> nstlog   = 5000; Write every step to the
> log
> nstenergy= 5000; Write energies at
> every step
> xtc_grps = Protein SOL
> nstxtcout= 5000; Do not write a
> compressed trajectory
> energygrps   = Protein SOL  ; Write energy information
> separately for these groups
>
> ; NEIGHBORSEARCHING PARAMETERS
> nstlist  = 5
> ns-type  = Grid
> pbc  = xyz
> rlist= 0.9
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> coulombtype  = PME
> fourierspacing   = 0.15
> rcoulomb = 0.9
> vdw-type = Cut-off
> rvdw = 1.0
>
> ; FFT grid size, when a value is 0 fourierspacing will be used =
> fourier_nx   = 0
> fourier_ny   = 0
> fourier_nz   = 0
> ; EWALD/PME/PPPM parameters =
> pme_order= 4
> ewald_rtol   = 1e-05
> epsilon_surface  = 0
> optimize_fft = no
> ; Temperature coupling
> tcoupl   = nose-hoover
> tc-grps  = Protein  Non-Protein
> tau_t= 0.2  0.2
> ref_t= 300  300
>
> ; Pressure coupling
> Pcoupl   = Parrinello-Rahman
> Pcoupltype   = Isotropic
> tau_p= 1.0
> compressibility  = 4.5e-5
> ref_p= 1.0
>
> ; OPTIONS FOR BONDS
> constraints  = all-bonds
>
>
> Pooja
>
>
>
>
> --
> Quaerendo Invenietis-Seek and you shall discover.
>
> --
> 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
>



-- 
Quaerendo Invenietis-Seek and you shall discover.
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
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RE: [gmx-users] Alanine dipeptide simulations

[Dallas Warren]

Is that really that surprising? 

 

You have variations of the order of 100s of bar and are looking for an
average that is 1.0

 

What you are observing is nothing out of the ordinary, from my
experience and what others have discussed here on the emailing list.

 

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 9909 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 Sai Pooja
Sent: Wednesday, 8 September 2010 3:38 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Alanine dipeptide simulations

 

Hi

Yes, the fluctuations are large but even the average pressure hasn't
converged. Its close 2.5 bar. RMSD ~600 bar.

Pooja

On Wed, Sep 8, 2010 at 1:27 AM, Dallas Warren 
wrote:

See http://www.gromacs.org/Documentation/Terminology/Pressure for
further details

 

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 9909 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 Dallas Warren
Sent: Wednesday, 8 September 2010 3:21 PM


To: Discussion list for GROMACS users

Subject: RE: [gmx-users] Alanine dipeptide simulations

 

What pressure has it reached?

 

Probably best graph the pressure versus time plot for the run and show
that.


I suspect what you are concerned about is the fact that with pressure
coupling, the pressure can fluctuation from step to step, very widely,
100s atm is not out of the question.

 

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 9909 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 Sai Pooja
Sent: Wednesday, 8 September 2010 3:18 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] Alanine dipeptide simulations

 

Hi,



I am running an npt simulation on alanine dipeptide in explicit solvent
using charmm forcefield and tip3p.

The pressure is set to 1bar and the barostat is Parrinello-Rahman. The
simulation has been running for 45 ns and has not achieved the target
average pressure of 1 bar.

I don;t understand why is this the case.

My mdp file:

; RUN CONTROL PARAMETERS
integrator   = md
dt   = 0.002
nsteps   = 50

; OUTPUT CONTROL OPTIONS
nstxout  = 0; No output, except for
last frame (coordinates)
nstvout  = 0; No output, except for
last frame (velocities)
nstfout  = 0; No output, except for
last frame (forces)
nstlog   = 5000; Write every step to the
log
nstenergy= 5000; Write energies at
every step
xtc_grps = Protein SOL
nstxtcout= 5000; Do not write a
compressed trajectory
energygrps   = Protein SOL  ; Write energy information
separately for these groups

; NEIGHBORSEARCHING PARAMETERS
nstlist  = 5
ns-type  = Grid
pbc  = xyz
rlist= 0.9

; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype  = PME
fourierspacing   = 0.15
rcoulomb = 0.9
vdw-type = Cut-off
rvdw = 1.0

; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters =
pme_order= 4
ewald_rtol   = 1e-05
epsilon_surface  = 0
optimize_fft = no
; Temperature coupling
tcoupl   = nose-hoover
tc-grps  = Protein  Non-Protein
tau_t= 0.2  0.2
ref_t= 300  300

; Pressure coupling
Pcoupl   = Parrinello-Rahman
Pcoupltype   = Isotropic
tau_p= 1.0
compressibility  = 4.5e-5
ref_p= 1.0

; OPTIONS FOR BONDS
constraints  = all-bonds


Pooja




-- 
Quaerendo Invenietis-Seek and you shall discover.


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

RE: [gmx-users] Gibbs Energy Calculation, Water/Octanol Partioning

[Dallas Warren]

Justin,

> Have you tried using the sd integrator?  That's what the authors of this paper
> used.  I don't know if there are stability issues with md vs. sd, but it's a
> starting point.

That does appear to be the issue.  We have repeated the pentane in octanol 
lambda runs and it completed without any errors.  Going back now to repeat a 
few other things, and will report back once have checked everything out.

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 9909 9304
-
When the only tool you own is a hammer, every problem begins to resemble a nail.
-- 
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

Re: [gmx-users] Alanine dipeptide simulations

[Sai Pooja]

So, what should I aim for when running an NPT simulation?

Pooja

On Wed, Sep 8, 2010 at 1:42 AM, Dallas Warren wrote:

>  Is that really that surprising?
>
>
>
> You have variations of the order of 100s of bar and are looking for an
> average that is 1.0
>
>
>
> What you are observing is nothing out of the ordinary, from my experience
> and what others have discussed here on the emailing list.
>
>
>
> 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 9909 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 *Sai Pooja
> *Sent:* Wednesday, 8 September 2010 3:38 PM
>
> *To:* Discussion list for GROMACS users
> *Subject:* Re: [gmx-users] Alanine dipeptide simulations
>
>
>
> Hi
>
> Yes, the fluctuations are large but even the average pressure hasn't
> converged. Its close 2.5 bar. RMSD ~600 bar.
>
> Pooja
>
> On Wed, Sep 8, 2010 at 1:27 AM, Dallas Warren 
> wrote:
>
> See http://www.gromacs.org/Documentation/Terminology/Pressure for further
> details
>
>
>
> 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 9909 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 *Dallas Warren
> *Sent:* Wednesday, 8 September 2010 3:21 PM
>
>
> *To:* Discussion list for GROMACS users
>
> *Subject:* RE: [gmx-users] Alanine dipeptide simulations
>
>
>
> What pressure has it reached?
>
>
>
> Probably best graph the pressure versus time plot for the run and show
> that.
>
>
> I suspect what you are concerned about is the fact that with pressure
> coupling, the pressure can fluctuation from step to step, very widely, 100s
> atm is not out of the question.
>
>
>
> 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 9909 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 *Sai Pooja
> *Sent:* Wednesday, 8 September 2010 3:18 PM
> *To:* Discussion list for GROMACS users
> *Subject:* [gmx-users] Alanine dipeptide simulations
>
>
>
> Hi,
>
>
>
> I am running an npt simulation on alanine dipeptide in explicit solvent
> using charmm forcefield and tip3p.
>
> The pressure is set to 1bar and the barostat is Parrinello-Rahman. The
> simulation has been running for 45 ns and has not achieved the target
> average pressure of 1 bar.
>
> I don;t understand why is this the case.
>
> My mdp file:
>
> ; RUN CONTROL PARAMETERS
> integrator   = md
> dt   = 0.002
> nsteps   = 50
>
> ; OUTPUT CONTROL OPTIONS
> nstxout  = 0; No output, except for
> last frame (coordinates)
> nstvout  = 0; No output, except for
> last frame (velocities)
> nstfout  = 0; No output, except for
> last frame (forces)
> nstlog   = 5000; Write every step to the
> log
> nstenergy= 5000; Write energies at
> every step
> xtc_grps = Protein SOL
> nstxtcout= 5000; Do not write a
> compressed trajectory
> energygrps   = Protein SOL  ; Write energy information
> separately for these groups
>
> ; NEIGHBORSEARCHING PARAMETERS
> nstlist  = 5
> ns-type  = Grid
> pbc  = xyz
> rlist= 0.9
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> coulombtype  = PME
> fourierspacing   = 0.15
> rcoulomb = 0.9
> vdw-type = Cut-off
> rvdw = 1.0
>
> ; FFT grid size, when a value is 0 fourierspacing will be used =
> fourier_nx   = 0
> fourier_ny   = 0
> fourier_nz   = 0
> ; EWALD/PME/PPPM parameters =
> pme_order= 4
> ewald_rtol   = 1e-05
> epsilon_surface  = 0
> optimize_fft = no
> ; Temperature coupling
> tcoupl   = nose-hoover
> tc-grps  = Protein  Non-Protein
> tau_t= 0.2  0.2
> ref_t= 300  300
>
> ; Pressure coupling

Re: [gmx-users] reg compilation problem in Mopac gromacs

[Mark Abraham]

Hi,

Please do not cross-post your mailing list questions to individuals unless they 
have solicited your inquiries. I know nothing about QMMM/MOPAC :-)

The best I can suggest is that you haven't made the MOPAC libs available in the 
default linking path. Please consult whatever installation documentation exists 
for this GROMACS/MOPAC hybrid.

Mark

- Original Message -
From: vidhya sankar 
Date: Wednesday, September 8, 2010 15:27
Subject: [gmx-users] reg compilation problem in Mopac gromacs
To: gmx-users@gromacs.org

---
| > Dear sir,  > thanks in advance >   When i type the following command in 
gromacs directory > ./configure --with-qmmm-mopac --disable-float > it 
configure successfully > but when i compile by make command i got the following 
error at the end of my compilation > 　 > libs/libgmxpreprocess_d.a 
../mdlib/.libs/libmd_d.a /root/gromacs-4.0.5/src/gmxlib/.libs/libgmx_d.a 
../gmxlib/.libs/libgmx_d.a -lnsl -lfftw3 -lm -lmopac -ltest  > 
../mdlib/.libs/libmd_d.a(qm_mopac.o): In function `call_mopac_SH': > 
qm_mopac.c:(.text+0x2a7): undefined reference to `domop_' > 
../mdlib/.libs/libmd_d.a(qm_mopac.o): In function `call_mopac': > 
qm_mopac.c:(.text+0x70b): undefined reference to `domop_' > 
../mdlib/.libs/libmd_d.a(qm_mopac.o): In function `init_mopac': > 
qm_mopac.c:(.text+0x964): undefined reference to `domldt_' > collect2: ld 
returned 1 exit status > make[3]: *** [grompp] Error 1 > make[3]: Leaving 
directory `/root/gromacs-4.0.5/src/kernel' > make[2]: *** [all-recursive] Error 
1 > make[2]: Leaving directory `/root/gromacs-4.0.5/src' > make[1]: *** [all] 
Error 2 > make[1]: Leaving directory `/root/gromacs-4.0.5/src' > make: *** 
[all-recursive] Error 1 > What should i do to avoid this error? i am expecting 
your reply > also when i use ./configure --without-qmmm-mopac --disable-float 
it compiles successfully |
---
> 
> -- 
> 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
-- 
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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Can't post? Read http://www.gromacs.org/Support/Mailing_Lists