AW: [gmx-users] problem in creating forcefield.doc

[Rausch, Felix]

Hi.

You don't have to paste anything in there. Take an empty text document and 
write the text you like to name your force field like into the first line.
For example this

GROMOS 53A6 forcefield , extended to include Berger force field parameter.

Save it as forcefield.doc. That's all.

Good luck!

Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im 
Auftrag von Anushree Tripathi
Gesendet: Montag, 23. Januar 2012 08:52
An: Discussion list for GROMACS users
Betreff: Re: [gmx-users] problem in creating forcefield.doc

I have created one file named it as "forcefield.doc" and paste the contents of 
"forcefield.itp" into it and also include "lipid.itp file.The content of  my 
"forcefield.doc" file is given below:

#define _FF_GROMOS96
#define _FF_GROMOS53A6

[ defaults ]
; nbfunccomb-rulegen-pairsfudgeLJfudgeQQ
  11no1.01.0

#include "ffnonbonded.itp"
#include "ffbonded.itp"
#include "lipid.itp"

Let me know whether it is correct or not.
On Mon, Jan 23, 2012 at 12:17 PM, Mark Abraham 
mailto:mark.abra...@anu.edu.au>> wrote:
On 23/01/2012 5:13 PM, Anushree Tripathi wrote:

I am using gromacs 4.5.3 version and I am trying to follow the tutorials. For

 starting I am following the *KALP15 in DPPC*

 
tutorial(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html).





I am not getting the point that is given below :

Next, create a forcefield.doc file that contains a description of the force 
field parameters in it.  Mine contains something like:





GROMOS 53A6 forcefield , extended to include Berger force field parameter.



Please guide me for creating forcefield.doc.


Have a look at the contents of this file in the pre-supplied force fields. Then 
look at the normal output of pdb2gmx. The former is used in the latter to help 
you pick the force field you want to use.

Mark

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Re: [gmx-users] problem in creating forcefield.doc

[Mark Abraham]

On 23/01/2012 6:49 PM, Anushree Tripathi wrote:
I have created one file named it as "forcefield.doc" and paste the 
contents of "forcefield.itp" into it and also include "lipid.itp 
file.The content of  my "forcefield.doc" file is given below:


#define _FF_GROMOS96
#define _FF_GROMOS53A6

[ defaults ]
; nbfunccomb-rulegen-pairsfudgeLJfudgeQQ
  11no1.01.0

#include "ffnonbonded.itp"
#include "ffbonded.itp"
#include "lipid.itp"

Let me know whether it is correct or not.


No, it isn't.

Mark



On Mon, Jan 23, 2012 at 12:17 PM, Mark Abraham 
mailto:mark.abra...@anu.edu.au>> wrote:


On 23/01/2012 5:13 PM, Anushree Tripathi wrote:

/I am using gromacs 4.5.3 version and I am trying to follow the tutorials. 
For
//  starting I am following the *KALP15 in DPPC*
//  
tutorial(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html).


/I am not getting the point that is given below :
Next, create a|forcefield.doc|  file that contains a description of the 
force field parameters in it.  Mine contains something like:


GROMOS 53A6 forcefield , extended to include Berger force field parameter.

Please guide me for creating forcefield.doc.



Have a look at the contents of this file in the pre-supplied force
fields. Then look at the normal output of pdb2gmx. The former is
used in the latter to help you pick the force field you want to use.

Mark

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Re: [gmx-users] Gromacs and CHARMM silicate force field

[Mark Abraham]

On 23/01/2012 5:38 PM, Gianluca Interlandi wrote:
I would like to ask whether it is possible to use in Gromacs the 
CHARMM parameters for silicates. More generally, is it easy to convert 
CHARMM parameter and topology files to the gromacs format?


Probably, and yes. You will need to read the documentation of both 
carefully.


Mark
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[gmx-users] Partial charges of new RES in Charmm

[Steven Neumann]

Hi Gmx Users,

I am building a surface as a reperesentation of protein surface. In this
case I divide amino acids as: polar, nonpolar, positively charged and
negatively charged. Representation of 3 atoms constitutes one residue. I
created new residues (Charmm27) using exsiting charges:

e.g. Residue  - Negative [ NEG ]



[ NEG ]

[ atoms ]

CC   C0.34  0

OT1 OC -0.67 1

OT2  OC -0.67   2

[ bonds ]

CC OT1

CC OT2
Theses charges are taken from COO- group of terminal residue [ GLY ]. I am
able to find partial charges for Hydrophobic  (CH2). However, I cannot find
for positive representation of 3 atoms) for positive or hydrophilic
residues. They always come as 2 or 4 atoms giving positive (+1) of neutral
(hydrophilic).

My question: Can I create me own partial charges for given positive or
hydrophilic group? Is that ok for the force field? As different atoms in
different groups have different charges it should be fine in this case...

I will appreciate your response. Thank you!

Steven
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[gmx-users] problem in generation of tpr file

[Anushree Tripathi]

I am going through the Justin Lemku tutorial for KALP15 in DPPC.  I have
reached step three, when I try to generate a trp file for DPPC only by
means of :

grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr

I get the following warning:

Fatal error:
Atomtype OW not found

Any idea as to what causes this problem?
Please guide me.
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[gmx-users] regarding box dimension and number of solvent molecules

[priya thiyagarajan]

hello sir,

i like to know few informations regarding box dimension and setting
no.of.solvent molecules..

i want to run simulation for different number of protein molecules with
same number of water molecules..
 i used following commands
to increase the no.of molecules i used
genbox -nmol 100 -ci protein.pdb -box 15 15 15 -o protein100.pdb

then i set box type

editconf -f protein100.pdb -bt cubic -o prot100_box.pdb -box 15 15 15

to add water


genbox -cp prot100_box.pdb -cs spc216.gro -p topol.top -o
prot100_water.pdb  -maxsol 5



when i added  5 water molecules only half of my box is getting filled
by solvent molecules..


i tried 3 times.. i am gettin the same ...



can anyone tell me why its happening like this...


please help me with your answer..



thanking you,
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[gmx-users] a problem with grompp

[Banafsheh Mehrazma]

Dear all;
I am trying to constrain a double stranded DNA, I have made an index
file and a posre.itp file, and then when I wanted to run grompp
command I have encountered this:
...
Program grompp, VERSION 4.5.3
Source code file: toppush.c, line: 1526

Fatal error:
[ file posre_DNA.itp, line 318 ]:
Atom index (314) in position_restraints out of bounds (1-313).
This probably means that you have inserted topology section
"position_restraints"
in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right molecule.
...

and the following lines are some parts of my .mdp file;
..
title   = DNA NVT equilibration
define  = -DPOSRES_DNA  ; position restrain the DNA
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 75000 ; 2 * 75000 = 150 ps

; Temperature coupling is on
tcoupl  = V-rescale ; modified Berendsen thermostat
tc-grps = DNA   Water_and_ions
tau_t   = 0.1   0.1 ; time constant, in ps
ref_t   = 310   310 
.
 and my topl.top is the following lines;



; Include forcefield parameters
#include "amber99.ff/forcefield.itp"

; Include chain topologies
#include "topol_DNA_chain_A.itp"
#include "topol_DNA_chain_B.itp"

#ifdef POSRES_DNA
#include "posre_DNA.itp"
#endif

; Include water topology
#include "amber99.ff/tip3p.itp"

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

; Include topology for ions
#include "amber99.ff/ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound#mols
DNA_chain_A 1
DNA_chain_B 1
SOL 5580
NA  18

..


what do you suggest that I do to make it work?
Thank you
B.Mehrazma
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[gmx-users] Re: Partial charges of new RES in Charmm

[Steven Neumann]

Maybe in other words:

Can I create dipol in my aminoscids.rtp file which will be positively
charged (+1) - NH+

[ POS ]
 [atoms]
N   N   0.7 0
H   H   0.3 1
 [bonds]
N   H

Please, help whether this is not a mistake adding new residue with such
charges?

On Mon, Jan 23, 2012 at 9:31 AM, Steven Neumann wrote:

> Hi Gmx Users,
>
> I am building a surface as a reperesentation of protein surface. In this
> case I divide amino acids as: polar, nonpolar, positively charged and
> negatively charged. Representation of 3 atoms constitutes one residue. I
> created new residues (Charmm27) using exsiting charges:
>
> e.g. Residue  - Negative [ NEG ]
>
>
>
> [ NEG ]
>
> [ atoms ]
>
> CC   C0.34  0
>
> OT1 OC -0.67 1
>
> OT2  OC -0.67   2
>
> [ bonds ]
>
> CC OT1
>
> CC OT2
> Theses charges are taken from COO- group of terminal residue [ GLY ]. I am
> able to find partial charges for Hydrophobic  (CH2). However, I cannot find
> for positive representation of 3 atoms) for positive or hydrophilic
> residues. They always come as 2 or 4 atoms giving positive (+1) of neutral
> (hydrophilic).
>
> My question: Can I create me own partial charges for given positive or
> hydrophilic group? Is that ok for the force field? As different atoms in
> different groups have different charges it should be fine in this case...
>
> I will appreciate your response. Thank you!
>
> Steven
>
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Re: [gmx-users] Partial charges of new RES in Charmm

[Mark Abraham]

On 23/01/2012 8:31 PM, Steven Neumann wrote:

Hi Gmx Users,
I am building a surface as a reperesentation of protein surface. In 
this case I divide amino acids as: polar, nonpolar, positively charged 
and negatively charged. Representation of 3 atoms constitutes one 
residue. I created new residues (Charmm27) using exsiting charges:

e.g. Residue  - Negative [ NEG ]

[ NEG ]

[ atoms ]

CC   C0.34  0

OT1 OC -0.67 1

OT2  OC -0.67   2

[ bonds ]

CC OT1

CC OT2

Theses charges are taken from COO- group of terminal residue [ GLY ]. 
I am able to find partial charges for Hydrophobic  (CH2). However, I 
cannot find for positive representation of 3 atoms) for positive or 
hydrophilic residues. They always come as 2 or 4 atoms giving positive 
(+1) of neutral (hydrophilic).
My question: Can I create me own partial charges for given positive or 
hydrophilic group? Is that ok for the force field? As different atoms 
in different groups have different charges it should be fine in this 
case...


Since you'll need strong position restraints to keep your artificial 
surface intact, and have a heavy burden of proof that you have a valid 
model of something even without inventing partial charges for positive 
fragments, go ahead and invent anything you think might work... :-) The 
requirement of 3-atom fragments seems unduly restrictive.


Mark
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Re: [gmx-users] a problem with grompp

[Mark Abraham]

On 23/01/2012 10:13 PM, Banafsheh Mehrazma wrote:

Dear all;
I am trying to constrain a double stranded DNA, I have made an index
file and a posre.itp file, and then when I wanted to run grompp
command I have encountered this:
...
Program grompp, VERSION 4.5.3
Source code file: toppush.c, line: 1526

Fatal error:
[ file posre_DNA.itp, line 318 ]:
Atom index (314) in position_restraints out of bounds (1-313).
This probably means that you have inserted topology section
"position_restraints"
in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right molecule.


This is very likely to be literally what's wrong.


...

and the following lines are some parts of my .mdp file;
..
title   = DNA NVT equilibration
define  = -DPOSRES_DNA  ; position restrain the DNA
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 75000 ; 2 * 75000 = 150 ps

; Temperature coupling is on
tcoupl  = V-rescale ; modified Berendsen thermostat
tc-grps = DNA   Water_and_ions
tau_t   = 0.1   0.1 ; time constant, in ps
ref_t   = 310   310 
.
  and my topl.top is the following lines;



; Include forcefield parameters
#include "amber99.ff/forcefield.itp"

; Include chain topologies
#include "topol_DNA_chain_A.itp"
#include "topol_DNA_chain_B.itp"

#ifdef POSRES_DNA
#include "posre_DNA.itp"
#endif


Each [position_restraints] section can pertain only to the immediately 
foregoing [moleculetype], per the above error message. Break it up or 
move it accordingly.


Mark



; Include water topology
#include "amber99.ff/tip3p.itp"

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

; Include topology for ions
#include "amber99.ff/ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound#mols
DNA_chain_A 1
DNA_chain_B 1
SOL 5580
NA  18

..


what do you suggest that I do to make it work?
Thank you
B.Mehrazma


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Re: [gmx-users] regarding box dimension and number of solvent molecules

[Mark Abraham]

On 23/01/2012 9:27 PM, priya thiyagarajan wrote:

hello sir,

i like to know few informations regarding box dimension and setting 
no.of.solvent molecules..


i want to run simulation for different number of protein molecules 
with same number of water molecules..

 i used following commands
to increase the no.of molecules i used
genbox -nmol 100 -ci protein.pdb -box 15 15 15 -o protein100.pdb

then i set box type

editconf -f protein100.pdb -bt cubic -o prot100_box.pdb -box 15 15 15

to add water


genbox -cp prot100_box.pdb -cs spc216.gro -p topol.top -o 
prot100_water.pdb  -maxsol 5




when i added  5 water molecules only half of my box is getting 
filled by solvent molecules..




Go and work out how many water molecules at normal density you can have 
in a 15nm^3 box.


Mark
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Re: [gmx-users] problem in generation of tpr file

[Justin A. Lemkul]

Anushree Tripathi wrote:

I am going through the Justin Lemku tutorial for KALP15 in DPPC.  I have
reached step three, when I try to generate a trp file for DPPC only by
means of :

grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr

I get the following warning:

Fatal error:
Atomtype OW not found

Any idea as to what causes this problem?


You constructed the force field incorrectly by deleting or commenting out a line 
(or more) related to OW.  Re-check the instructions provided in the tutorial.


-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] About g_rms and the XPM file format

[Víctor]

Dear all,

I've been trying to do a rmsd matrix of  two different trajectories by
using g_rms (with -f traj1 and -f2 traj2). I'm wondering if the algorithm
g_rms uses does something like this:

for each frame f1 in traj1:
  for each frame f2 in traj2:
superimpose f1 , f2
calculateRMSD f1, f2

Or like this (as I've seen in some other rmsd matrix calculation scripts):

for each frame f in traj1:
  superimpose f with first frame

for each frame f1 in traj1:
  for each frame f2 in traj2:
calculateRMSD f1, f2

I've also been trying to convert the resulting xpm file to a readable file
in order to process it using python. Is there any tool to do this kind of
conversion?(Btw I've been trying to find this kind of tool with not much
luck). There's enough info on the file to be able to parse it easily, but
using a 3rd party tested tool would be more convenient.

Thanks!

-- 

Víctor Gil Sepúlveda
E. Informatica - FIB - UPC
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[gmx-users] Tabulated potentials

[Laura Leay]

All, 

I'm simulating a very small system of methane using tabulated
potentials. Charges are not modified and I'm using a cubic for values up
to 0.19 nm and the normal 6-12 LJ potential after that (the form the
cubic is such that the value and gradient at 0.19 nm is the same as for
the 6-12 LJ). 

The potential is different for each pair interaction so I have specified
separate tables for the C-C and H-H interaction leaving the default
table.xvg to deal with the H-C interactions. So in my mdp file I've
specified:
  coulombtype = Cut-off
  vdw-type = user
  energygrps = CT HC ;(consistent with the conf.gro file)
  energygrp_table = HC HC CT CT

My table files are:
- table.xvg
- table_CT_CT.xvg
- table_HC_HC.xvg

I have specified an index file for the system, the hydrogens and the
carbons in the file index.ndx.

Each table file gives values down to 3.0 nm with 0.002 nm spacing. I am
using gromacs version 4.0.7 single precision.


However when I try and grompp and run the simulation using:
  grompp -v -n index.ndx
  mdrun -v table table.xvg

I get the following error:

  Tables in file table.xvg not long enough for cut-off:
should be at least 1.90 nm


I've compared my table files to the examples given in gromacs's own
topology directory and the increments between each data point is exactly
the same (0.002 nm). I've also checked that the increments for each of
my table files are consistently 0.002 nm. I'm not sure what else to
check to resolve this error.

Help please.


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Re: [gmx-users] About g_rms and the XPM file format

[Tsjerk Wassenaar]

Hi Victor,

By default it does this:

> for each frame f in traj1:
>   superimpose f with first frame
>
> for each frame f1 in traj1:
>   for each frame f2 in traj2:
>     calculateRMSD f1, f2

But there's a hidden option -fitall that gives you the other. Check

g_rms -h -hidden

> I've also been trying to convert the resulting xpm file to a readable file
> in order to process it using python. Is there any tool to do this kind of
> conversion?(Btw I've been trying to find this kind of tool with not much
> luck). There's enough info on the file to be able to parse it easily, but
> using a 3rd party tested tool would be more convenient.

I posted a python script some while ago to do:

http://lists.gromacs.org/pipermail/gmx-users/2010-October/054557.html

Hope it helps,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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[gmx-users] multiple molecules in a box

[Turgay Cakmak]

Hi gromacs users,

I have two different molecules, lets say A and B. I want to put 5 A
molecules and 5 B molecules in the same box.
I carried out the following steps.
   1)  For both A and B, I used *genbox* with *-nmol* flag separetely
and obtained the A_multiple and the B_multiple structure files.
   2)  Using *cat* command, I concatanated two structure files (A_multiple,
B_multiple) to get system.gro.
   3)  Using the *pdb2gmx*, I got conf.gro and topol.top of system..

But, I am not sure if this is the correct way? Because, when I look the
conf.gro at VMD, I saw that some part of the A molecule and B molecule had
overlapped.

Could anybody help me please?

Turgay
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Re: [gmx-users] About g_rms and the XPM file format

[Víctor]

Thanks a lot, your answer has been very useful!

Btw, do you know why is the default matrix used more often than the other?
(I see that It's faster, but maybe there's another reason)

On Mon, Jan 23, 2012 at 3:39 PM, Tsjerk Wassenaar  wrote:

> Hi Victor,
>
> By default it does this:
>
> > for each frame f in traj1:
> >   superimpose f with first frame
> >
> > for each frame f1 in traj1:
> >   for each frame f2 in traj2:
> > calculateRMSD f1, f2
>
> But there's a hidden option -fitall that gives you the other. Check
>
> g_rms -h -hidden
>
> > I've also been trying to convert the resulting xpm file to a readable
> file
> > in order to process it using python. Is there any tool to do this kind of
> > conversion?(Btw I've been trying to find this kind of tool with not much
> > luck). There's enough info on the file to be able to parse it easily, but
> > using a 3rd party tested tool would be more convenient.
>
> I posted a python script some while ago to do:
>
> http://lists.gromacs.org/pipermail/gmx-users/2010-October/054557.html
>
> Hope it helps,
>
> Tsjerk
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
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-- 

Víctor Gil Sepúlveda
E. Informatica - FIB - UPC
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[gmx-users] force field

[lina]

Hi,

which gromacs force field shares the high "quasi-compatibility" with
the amber force field.

I checked the heme only exists in gromos and the charmn

while gbsa only shows in amber and oplsaa,

truth is that I don't know how to get the gbsa parameter for heme,

Thanks for any suggestions,

Best regards,
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Re: [gmx-users] multiple molecules in a box

[Justin A. Lemkul]

Turgay Cakmak wrote:

Hi gromacs users,
 
I have two different molecules, lets say A and B. I want to put 5 A 
molecules and 5 B molecules in the same box.

I carried out the following steps.
   1)  For both A and B, I used *genbox* with *-nmol* flag separetely 
and obtained the A_multiple and the B_multiple structure files.
   2)  Using *cat* command, I concatanated two structure files 
(A_multiple, B_multiple) to get system.gro.

   3)  Using the *pdb2gmx*, I got conf.gro and topol.top of system..
 
But, I am not sure if this is the correct way? Because, when I look the 
conf.gro at VMD, I saw that some part of the A molecule and B molecule 
had overlapped.
 
Could anybody help me please?
 


An alternate procedure:

1. Run pdb2gmx on a single molecule of A and a single molecule of B
2. Convert the two resulting .top files into .itp files (see the manual or wiki 
for the differences) and construct a simple .top that #includes these

3. Build your system for molecule A as you did before
4. Insert 5 molecules of B into the A system to avoid clashes

This way you avoid a lot of topological redundancy and eliminate clashes.

-Justin


Turgay



--


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] Implicit solvent model in Gromacs

[lina]

On Mon, Jan 23, 2012 at 10:01 AM, Gianluca Interlandi
 wrote:
> Dear gromacs users list,
>
> I noticed that gromacs can perform simulations with an implicit solvent
> model using a GBSA method. Is it compatible with the CHARMM22 force field?

look for gbsa.itp showed

amber03.ff/forcefield.itp
amber03.ff/gbsa.itp
amber94.ff/forcefield.itp
amber94.ff/gbsa.itp
amber96.ff/forcefield.itp
amber96.ff/gbsa.itp
amber99.ff/forcefield.itp
amber99.ff/gbsa.itp
amber99sb.ff/forcefield.itp
amber99sb.ff/gbsa.itp
amber99sb-ildn.ff/forcefield.itp
amber99sb-ildn.ff/gbsa.itp
amberGS.ff/forcefield.itp
amberGS.ff/gbsa.itp
oplsaa.ff/forcefield.itp
oplsaa.ff/gbsa.itp

seems not.

>
> Thanks,
>
>     Gianluca
>
> -
> Gianluca Interlandi, PhD gianl...@u.washington.edu
>                    +1 (206) 685 4435
>                    http://artemide.bioeng.washington.edu/
>
> Postdoc at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
> -
> --
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Re: [gmx-users] Implicit solvent model in Gromacs

[Justin A. Lemkul]

lina wrote:

On Mon, Jan 23, 2012 at 10:01 AM, Gianluca Interlandi
 wrote:

Dear gromacs users list,

I noticed that gromacs can perform simulations with an implicit solvent
model using a GBSA method. Is it compatible with the CHARMM22 force field?


look for gbsa.itp showed

amber03.ff/forcefield.itp
amber03.ff/gbsa.itp
amber94.ff/forcefield.itp
amber94.ff/gbsa.itp
amber96.ff/forcefield.itp
amber96.ff/gbsa.itp
amber99.ff/forcefield.itp
amber99.ff/gbsa.itp
amber99sb.ff/forcefield.itp
amber99sb.ff/gbsa.itp
amber99sb-ildn.ff/forcefield.itp
amber99sb-ildn.ff/gbsa.itp
amberGS.ff/forcefield.itp
amberGS.ff/gbsa.itp
oplsaa.ff/forcefield.itp
oplsaa.ff/gbsa.itp

seems not.



It's called gb.itp in the charmm27.ff subdirectory.

-Justin


Thanks,

Gianluca

-
Gianluca Interlandi, PhD gianl...@u.washington.edu
   +1 (206) 685 4435
   http://artemide.bioeng.washington.edu/

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-
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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] About g_rms and the XPM file format

[lina]

On Mon, Jan 23, 2012 at 9:56 PM, Víctor  wrote:
> Dear all,
>
> I've been trying to do a rmsd matrix of  two different trajectories by using
> g_rms (with -f traj1 and -f2 traj2). I'm wondering if the algorithm g_rms
> uses does something like this:
>
> for each frame f1 in traj1:
>   for each frame f2 in traj2:
>     superimpose f1 , f2
>     calculateRMSD f1, f2
>
> Or like this (as I've seen in some other rmsd matrix calculation scripts):
>
> for each frame f in traj1:
>   superimpose f with first frame
>
> for each frame f1 in traj1:
>   for each frame f2 in traj2:
>     calculateRMSD f1, f2
>
> I've also been trying to convert the resulting xpm file to a readable file

BTW, xpm file is readable.
try:
more xpm or other tools your preferred to read.


> in order to process it using python. Is there any tool to do this kind of
> conversion?(Btw I've been trying to find this kind of tool with not much
> luck). There's enough info on the file to be able to parse it easily, but
> using a 3rd party tested tool would be more convenient.
>
> Thanks!
>
> --
>
> Víctor Gil Sepúlveda
> E. Informatica - FIB - UPC
>
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] About g_rms and the XPM file format

[Víctor]

Yes, thanks. My first impulse was to do a python script to do the
conversion, but Tsjerk Wassenaar's script works neat :)

On Mon, Jan 23, 2012 at 5:10 PM, lina  wrote:

> On Mon, Jan 23, 2012 at 9:56 PM, Víctor 
> wrote:
> > Dear all,
> >
> > I've been trying to do a rmsd matrix of  two different trajectories by
> using
> > g_rms (with -f traj1 and -f2 traj2). I'm wondering if the algorithm g_rms
> > uses does something like this:
> >
> > for each frame f1 in traj1:
> >   for each frame f2 in traj2:
> > superimpose f1 , f2
> > calculateRMSD f1, f2
> >
> > Or like this (as I've seen in some other rmsd matrix calculation
> scripts):
> >
> > for each frame f in traj1:
> >   superimpose f with first frame
> >
> > for each frame f1 in traj1:
> >   for each frame f2 in traj2:
> > calculateRMSD f1, f2
> >
> > I've also been trying to convert the resulting xpm file to a readable
> file
>
> BTW, xpm file is readable.
> try:
> more xpm or other tools your preferred to read.
>
>
> > in order to process it using python. Is there any tool to do this kind of
> > conversion?(Btw I've been trying to find this kind of tool with not much
> > luck). There's enough info on the file to be able to parse it easily, but
> > using a 3rd party tested tool would be more convenient.
> >
> > Thanks!
> >
> > --
> >
> > Víctor Gil Sepúlveda
> > E. Informatica - FIB - UPC
> >
> > --
> > 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!
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-- 

Víctor Gil Sepúlveda
E. Informatica - FIB - UPC
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Re: [gmx-users] Implicit solvent model in Gromacs

[lina]

On Tue, Jan 24, 2012 at 12:08 AM, Justin A. Lemkul  wrote:
>
>
> lina wrote:
>>
>> On Mon, Jan 23, 2012 at 10:01 AM, Gianluca Interlandi
>>  wrote:
>>>
>>> Dear gromacs users list,
>>>
>>> I noticed that gromacs can perform simulations with an implicit solvent
>>> model using a GBSA method. Is it compatible with the CHARMM22 force
>>> field?
>>
>>
>> look for gbsa.itp showed
>>
>> amber03.ff/forcefield.itp
>> amber03.ff/gbsa.itp
>> amber94.ff/forcefield.itp
>> amber94.ff/gbsa.itp
>> amber96.ff/forcefield.itp
>> amber96.ff/gbsa.itp
>> amber99.ff/forcefield.itp
>> amber99.ff/gbsa.itp
>> amber99sb.ff/forcefield.itp
>> amber99sb.ff/gbsa.itp
>> amber99sb-ildn.ff/forcefield.itp
>> amber99sb-ildn.ff/gbsa.itp
>> amberGS.ff/forcefield.itp
>> amberGS.ff/gbsa.itp
>> oplsaa.ff/forcefield.itp
>> oplsaa.ff/gbsa.itp
>>
>> seems not.
>>
>
> It's called gb.itp in the charmm27.ff subdirectory.

Thanks. your information is very helpful. I know the answer asked on
another thread.

>
> -Justin
>
>
>>> Thanks,
>>>
>>>    Gianluca
>>>
>>> -
>>> Gianluca Interlandi, PhD gianl...@u.washington.edu
>>>                   +1 (206) 685 4435
>>>                   http://artemide.bioeng.washington.edu/
>>>
>>> Postdoc at the Department of Bioengineering
>>> at the University of Washington, Seattle WA U.S.A.
>>> -
>>> --
>>> gmx-users mailing list    gmx-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!
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>>> interface
>>> or send it to gmx-users-requ...@gromacs.org.
>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
> --
> 
>
> 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] Molecular Modelling Workshop 2012 in Erlangen, Germany

[Harald Lanig]

Dear list subscribers,

this year, the traditional Molecular Modelling Workshop in Erlangen 
(formerly known as "Darmstadt workshop") takes place on


March, Monday 12th to Wednesday 14th, 2012.

Starting on Monday after lunch should allow to avoid travelling on 
weekend keeping the expenses at a minimum.


### Plenary Speakers ###
We are very happy to announce that three leading experts in their field 
have agreed to give a plenary talk at the meeting:


   Prof. Tim Clark
   University of Erlangen-Nuernberg

   Prof. Peter Comba
   University of Heidelberg

   Prof. Francesco Gervasio
   Spanish National Cancer Research Center

### Bursaries available ###
There are a limited number of MGMS-DS travel bursaries for
students available upon request. Please apply for all support
to mmws[*]mgms-ds.de

### Poster and Lecture Awards ###
As in the past years, there will be two Poster Awards of EUR 100,-- each
and three Lecture Awards for the best talks:

1st Winner: Travel bursary to the Young Modellers Forum in the United
Kingdom (travel expenses are reimbursed up to EUR 500)
2nd Winner: EUR 200,-- travel expenses reimbursement
3rd Winner: EUR 100,-- travel expenses reimbursement

Only undergraduate and graduate research students qualify for the
poster and lecture awards.

As every year, an interesting and successful workshop depends on your
contributions. Therefore let me invite you to submit talks and/or poster
titles via the registration form accessible on the workshop Web site
http://www.chemie.uni-erlangen.de/ccc/conference/mmws12/
This Web site will provide all necessary information about the meeting!

The deadline for all submissions is February 24th, 2012.

I am looking forward to meeting you in Erlangen soon!
-Harald Lanig

--

 Dr. Harald LanigUniversitaet Erlangen/Nuernberg
 Computer-Chemie-Centrum Naegelsbachstr. 25, D-91052 Erlangen

 Phone +49(0)9131-85 26525   harald DOT lanig AT chemie.uni-erlangen.de
 Fax   +49(0)9131-85 26565   http://www.chemie.uni-erlangen.de/lanig


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[gmx-users] PSF file in martini force field

[Li, Hualin]

Hi all,

I am running Gromacs on the system of several proteins on the membrane 
using martini force field.From the output files, if I want to generate the PSF 
files from them , is there any easy way to do it please?

   Thanks in advance.

Regards,
Hualin--
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[gmx-users] PSF file in martini force field

[Li, Hualin]

Hi all,

I am running Gromacs on the system of several proteins on the membrane 
using martini force field.From the output files, if I want to generate the PSF 
files from them , is there any easy way to do it please?

   Thanks in advance.

Regards,
Hualin--
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Re: [gmx-users] About g_rms and the XPM file format

[Víctor]

I've having some problems with use of the option '-fitall'.

The command I'm using is:
g_rms -hidden -fitall -s ../topol_amber.tpr -f ../amber99sb_skip10.xtc -f2
../amber99sb_skip10.xtc -m rmsd.xpm

But a diff with the rmsd.xpm file I got without using '-fitall' reveals
that the files are identical.

Furthermore, the rmsd.xpm file represents a non-symetric matrix, which is
not what I expected... Anyone has a clue of what's happening?

Thanks in advance,
Víctor

On Mon, Jan 23, 2012 at 5:12 PM, Víctor wrote:

> Yes, thanks. My first impulse was to do a python script to do the
> conversion, but Tsjerk Wassenaar's script works neat :)
>
> On Mon, Jan 23, 2012 at 5:10 PM, lina  wrote:
>
>> On Mon, Jan 23, 2012 at 9:56 PM, Víctor 
>> wrote:
>> > Dear all,
>> >
>> > I've been trying to do a rmsd matrix of  two different trajectories by
>> using
>> > g_rms (with -f traj1 and -f2 traj2). I'm wondering if the algorithm
>> g_rms
>> > uses does something like this:
>> >
>> > for each frame f1 in traj1:
>> >   for each frame f2 in traj2:
>> > superimpose f1 , f2
>> > calculateRMSD f1, f2
>> >
>> > Or like this (as I've seen in some other rmsd matrix calculation
>> scripts):
>> >
>> > for each frame f in traj1:
>> >   superimpose f with first frame
>> >
>> > for each frame f1 in traj1:
>> >   for each frame f2 in traj2:
>> > calculateRMSD f1, f2
>> >
>> > I've also been trying to convert the resulting xpm file to a readable
>> file
>>
>> BTW, xpm file is readable.
>> try:
>> more xpm or other tools your preferred to read.
>>
>>
>> > in order to process it using python. Is there any tool to do this kind
>> of
>> > conversion?(Btw I've been trying to find this kind of tool with not much
>> > luck). There's enough info on the file to be able to parse it easily,
>> but
>> > using a 3rd party tested tool would be more convenient.
>> >
>> > Thanks!
>> >
>> > --
>> >
>> > Víctor Gil Sepúlveda
>> > E. Informatica - FIB - UPC
>> >
>> > --
>> > 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!
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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
>>
>
>
>
> --
>
> Víctor Gil Sepúlveda
> E. Informatica - FIB - UPC
>



-- 

Víctor Gil Sepúlveda
E. Informatica - FIB - UPC
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[gmx-users] Installing & uninstalling of gromacs

[Spring buds]

Dear Gromacs users,

Greetings!!!

I am very new users and I am trying to install grmacs 4.5.5 or 3.3.3 for
past four days. But still I am not able to. So I would like to ask some
questions which are below.


1.My laptop is a dual core, which means two processors?.So should I need to
install MPI?

2.I installed gromacs 4.5.5 with mistakes. To remove installing, I used the
"which gromacs" and it shows as "/usr/bin/which: no mdrun in
(/usr/kerberos/bin:/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/home/Malai/bin)".
However, I used "rm -rf /usr/local/gromacs" to remove installing I still
can see tha gromacs files with red background in "/usr/local/bin". Could
you tell me I removed the gromacs installing?

3.Could you please tell me the very simple steps for installatios, since I
am a novice.

Many thanks in advance for your time and help.

Huang Malai
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Re: [gmx-users] Installing & uninstalling of gromacs

[lina]

On 24 Jan, 2012, at 1:53, Spring buds  wrote:

> Dear Gromacs users,
> 
> Greetings!!!
> 
> I am very new users and I am trying to install grmacs 4.5.5 or 3.3.3 for past 
> four days. But still I am not able to. So I would like to ask some questions 
> which are below.
> 
> 
> 1.My laptop is a dual core, which means two processors?.So should I need to 
> install MPI?
> 
--enable threads 

> 2.I installed gromacs 4.5.5 with mistakes. To remove installing, I used the 
> "which gromacs" and it shows as "/usr/bin/which: no mdrun in 
> (/usr/kerberos/bin:/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/home/Malai/bin)".
>  However, I used "rm -rf /usr/local/gromacs" to remove installing I still can 
> see tha gromacs files with red background in "/usr/local/bin". Could you tell 
> me I removed the gromacs installing?

You have not.  

> 
> 3.Could you please tell me the very simple steps for installatios, since I am 
> a novice. 

http://www.gromacs.org/Downloads/Installation_Instructions

> 
> Many thanks in advance for your time and help.
> 
> Huang Malai
> -- 
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Re: [gmx-users] PSF file in martini force field

[Mark Abraham]

On 24/01/2012 4:20 AM, Li, Hualin wrote:

Hi all,

 I am running Gromacs on the system of several proteins on the membrane 
using martini force field.From the output files, if I want to generate the PSF 
files from them , is there any easy way to do it please?


No GROMACS utilities will write a PSF for CHARMM input. Consult the 
CHARMM documentation.


Mark
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Re: [gmx-users] force field

[Mark Abraham]

On 24/01/2012 2:58 AM, lina wrote:

Hi,

which gromacs force field shares the high "quasi-compatibility" with
the amber force field.


Force fields are not designed for compatibility, and the exceptions to 
this are very rare.



I checked the heme only exists in gromos and the charmn

while gbsa only shows in amber and oplsaa,

truth is that I don't know how to get the gbsa parameter for heme,


Apparently, you want to run an implicit solvation simulation on heme 
using AMBER. That may or may not be possible, or easy, depending what 
has already been done. Start here 
http://www.google.com.au/search?q=heme+amber+force+field and see what 
you find.


Mark
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RE: [gmx-users] PSF file in martini force field

[Li, Hualin]

Hi,Mark,

 Thank you very much for your answer.  In this case , if I want to know 
about the protein structure(like bonding, angles...), Is there any method I can 
use please? The difficult part in this question may be that I have more than 
one proteins in the same output file(GRO),  I know some tcl script may draw the 
protein structure in CG  model (including bonding and secondary structures) one 
protein by one protein, but is there any method to draw the structure for all 
the proteins at the same time?

Thanks again.
--Hualin 

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of Mark Abraham [mark.abra...@anu.edu.au]
Sent: Monday, January 23, 2012 3:22 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] PSF file in martini force field

On 24/01/2012 4:20 AM, Li, Hualin wrote:
> Hi all,
>
>  I am running Gromacs on the system of several proteins on the membrane 
> using martini force field.From the output files, if I want to generate the 
> PSF files from them , is there any easy way to do it please?

No GROMACS utilities will write a PSF for CHARMM input. Consult the
CHARMM documentation.

Mark
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Re: [gmx-users] PSF file in martini force field

[Mark Abraham]

On 24/01/2012 8:39 AM, Li, Hualin wrote:

Hi,Mark,

  Thank you very much for your answer.  In this case , if I want to know 
about the protein structure(like bonding, angles...), Is there any method I can 
use please?


g_bond and g_angle allow you to measure bond lengths and angles of atoms 
in well chosen index groups.



  The difficult part in this question may be that I have more than one proteins 
in the same output file(GRO),  I know some tcl script may draw the protein 
structure in CG  model (including bonding and secondary structures) one protein 
by one protein, but is there any method to draw the structure for all the 
proteins at the same time?


With suitable modification to their heuristics for guessing where bonds 
occur, various visualization packages can be useful. The GROMACS webpage 
has some suggestions.


Mark



 Thanks again.
--Hualin

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of Mark Abraham [mark.abra...@anu.edu.au]
Sent: Monday, January 23, 2012 3:22 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] PSF file in martini force field

On 24/01/2012 4:20 AM, Li, Hualin wrote:

Hi all,

  I am running Gromacs on the system of several proteins on the membrane 
using martini force field.From the output files, if I want to generate the PSF 
files from them , is there any easy way to do it please?

No GROMACS utilities will write a PSF for CHARMM input. Consult the
CHARMM documentation.

Mark
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[gmx-users] Monte Carlo with Gromacs and implicit solvent

[Gianluca Interlandi]

Hi!

I would like to use gromacs to perform Monte Carlo simulations in implicit 
solvent of a protein near a surface. The protein is treated as a rigid 
body whereas the surface is fix.


I see that there are plans to code MC into gromacs:

http://www.gromacs.org/Developer_Zone/Programming_Guide/Monte_Carlo

Is there a preliminary version?

If not, I wonder whether anybody has tried to do MC with gromacs using IMD 
and MDDriver:


http://www.baaden.ibpc.fr/projects/mddriver/

Besides this. Is there an easy way to obtain the force field energy of a 
system using gromacs? Would I have to run a 0-steps MD and read out the 
energy? I know that this would have a big overhead in a MC simulation, but 
it might be worth trying.


Thanks,

 Gianluca

-
Gianluca Interlandi, PhD gianl...@u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-
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Re: [gmx-users] Monte Carlo with Gromacs and implicit solvent

[Rodrigo Faccioli]

Hi,

Although I don't work with MC simulation, I have used Gromacs to obtain
energies and others protein features in my Evolutionary Algorithms (EA).

In general lines, I created a script that calls Gromacs programs and the
output of these programs, such as g_energy (I read its xvg file), I stored
it at a specific file which is read by my algorithm and its values are put
into my data structure. I call Gromacs either implicit or explicit
solvent.

My project is working with EA until now. However, the integration with
GROMACS is able to work with other kind of algorithms such as MC. Actually,
we have idea to work with MC. But, I don't know when it will be possible.
If you want, we can talk about join these work.

Best regards,

--
Rodrigo Antonio Faccioli
Ph.D Student in Electrical Engineering
University of Sao Paulo - USP
Engineering School of Sao Carlos - EESC
Department of Electrical Engineering - SEL
Intelligent System in Structure Bioinformatics
http://laips.sel.eesc.usp.br
Phone: 55 (16) 3373-9366 Ext 229
Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5


On Mon, Jan 23, 2012 at 11:39 PM, Gianluca Interlandi <
gianl...@u.washington.edu> wrote:

> Hi!
>
> I would like to use gromacs to perform Monte Carlo simulations in implicit
> solvent of a protein near a surface. The protein is treated as a rigid body
> whereas the surface is fix.
>
> I see that there are plans to code MC into gromacs:
>
> http://www.gromacs.org/**Developer_Zone/Programming_**Guide/Monte_Carlo
>
> Is there a preliminary version?
>
> If not, I wonder whether anybody has tried to do MC with gromacs using IMD
> and MDDriver:
>
> http://www.baaden.ibpc.fr/**projects/mddriver/
>
> Besides this. Is there an easy way to obtain the force field energy of a
> system using gromacs? Would I have to run a 0-steps MD and read out the
> energy? I know that this would have a big overhead in a MC simulation, but
> it might be worth trying.
>
> Thanks,
>
> Gianluca
>
> --**---
> Gianluca Interlandi, PhD gianl...@u.washington.edu
>+1 (206) 685 4435
>
> http://artemide.bioeng.**washington.edu/
>
> Postdoc at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
> --**---
> --
> 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/Searchbefore
>  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] Monte Carlo with Gromacs and implicit solvent

[Gianluca Interlandi]

Thanks Enrico!

Just wondering. How fast is it? Calling gromacs must have a lot of 
overhead. Also, do you call mdrun or does g_energy evaluate the energy?


Gianluca

On Tue, 24 Jan 2012, Rodrigo Faccioli wrote:


Hi,

Although I don't work with MC simulation, I have used Gromacs to obtain 
energies and others
protein features in my Evolutionary Algorithms (EA).

In general lines, I created a script that calls Gromacs programs and the output 
of these
programs, such as g_energy (I read its xvg file), I stored it at a specific 
file which is
read by my algorithm and its values are put into my data structure. I call 
Gromacs either
implicit or explicit solvent. 

My project is working with EA until now. However, the integration with GROMACS 
is able to
work with other kind of algorithms such as MC. Actually, we have idea to work 
with MC. But,
I don't know when it will be possible. If you want, we can talk about join 
these work.

Best regards,

--
Rodrigo Antonio Faccioli
Ph.D Student in Electrical Engineering
University of Sao Paulo - USP
Engineering School of Sao Carlos - EESC
Department of Electrical Engineering - SEL
Intelligent System in Structure Bioinformatics
http://laips.sel.eesc.usp.br
Phone: 55 (16) 3373-9366 Ext 229
Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5


On Mon, Jan 23, 2012 at 11:39 PM, Gianluca Interlandi 
 wrote:
  Hi!

  I would like to use gromacs to perform Monte Carlo simulations in implicit
  solvent of a protein near a surface. The protein is treated as a rigid 
body
  whereas the surface is fix.

  I see that there are plans to code MC into gromacs:

  http://www.gromacs.org/Developer_Zone/Programming_Guide/Monte_Carlo

  Is there a preliminary version?

  If not, I wonder whether anybody has tried to do MC with gromacs using 
IMD and
  MDDriver:

  http://www.baaden.ibpc.fr/projects/mddriver/

  Besides this. Is there an easy way to obtain the force field energy of a 
system
  using gromacs? Would I have to run a 0-steps MD and read out the energy? 
I know
  that this would have a big overhead in a MC simulation, but it might be 
worth
  trying.

  Thanks,

      Gianluca

  -
  Gianluca Interlandi, PhD gianl...@u.washington.edu
                     +1 (206) 685 4435
                     http://artemide.bioeng.washington.edu/

  Postdoc at the Department of Bioengineering
  at the University of Washington, Seattle WA U.S.A.
  -
  --
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  send it to gmx-users-requ...@gromacs.org.
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-
Gianluca Interlandi, PhD gianl...@u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
--- 
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Re: [gmx-users] Monte Carlo with Gromacs and implicit solvent

[Rodrigo Faccioli]

Hi Gianluca,

Thanks your question.

All steps to obtain a generation with 200 individuals, on average, is 6
minutes for 1VII, example. In each generation I must  converted my proteins
Dihedral to Cartesian representation, compute the energies, choose the
individuals which will go to reproduction, save previous population. This
test was using one core of a conventional Desktop computer.

The proteins, that I have tested my algorithm, vary from 20 to 56 amino
acids.

Best regards,

--
Rodrigo Antonio Faccioli
Ph.D Student in Electrical Engineering
University of Sao Paulo - USP
Engineering School of Sao Carlos - EESC
Department of Electrical Engineering - SEL
Intelligent System in Structure Bioinformatics
http://laips.sel.eesc.usp.br
Phone: 55 (16) 3373-9366 Ext 229
Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5


On Tue, Jan 24, 2012 at 12:36 AM, Gianluca Interlandi <
gianl...@u.washington.edu> wrote:

> Thanks Enrico!
>
> Just wondering. How fast is it? Calling gromacs must have a lot of
> overhead. Also, do you call mdrun or does g_energy evaluate the energy?
>
> Gianluca
>
>
> On Tue, 24 Jan 2012, Rodrigo Faccioli wrote:
>
>  Hi,
>>
>> Although I don't work with MC simulation, I have used Gromacs to obtain
>> energies and others
>> protein features in my Evolutionary Algorithms (EA).
>>
>> In general lines, I created a script that calls Gromacs programs and the
>> output of these
>> programs, such as g_energy (I read its xvg file), I stored it at a
>> specific file which is
>> read by my algorithm and its values are put into my data structure. I
>> call Gromacs either
>> implicit or explicit solvent.
>>
>> My project is working with EA until now. However, the integration with
>> GROMACS is able to
>> work with other kind of algorithms such as MC. Actually, we have idea to
>> work with MC. But,
>> I don't know when it will be possible. If you want, we can talk about
>> join these work.
>>
>> Best regards,
>>
>> --
>> Rodrigo Antonio Faccioli
>> Ph.D Student in Electrical Engineering
>> University of Sao Paulo - USP
>> Engineering School of Sao Carlos - EESC
>> Department of Electrical Engineering - SEL
>> Intelligent System in Structure Bioinformatics
>> http://laips.sel.eesc.usp.br
>> Phone: 55 (16) 3373-9366 Ext 229
>> Curriculum Lattes - 
>> http://lattes.cnpq.br/**1025157978990218
>> Public Profile - 
>> http://br.linkedin.com/pub/**rodrigo-faccioli/7/589/a5
>>
>>
>> On Mon, Jan 23, 2012 at 11:39 PM, Gianluca Interlandi <
>> gianl...@u.washington.edu> wrote:
>>  Hi!
>>
>>  I would like to use gromacs to perform Monte Carlo simulations in
>> implicit
>>  solvent of a protein near a surface. The protein is treated as a
>> rigid body
>>  whereas the surface is fix.
>>
>>  I see that there are plans to code MC into gromacs:
>>
>>  http://www.gromacs.org/**Developer_Zone/Programming_**
>> Guide/Monte_Carlo
>>
>>  Is there a preliminary version?
>>
>>  If not, I wonder whether anybody has tried to do MC with gromacs
>> using IMD and
>>  MDDriver:
>>
>>  
>> http://www.baaden.ibpc.fr/**projects/mddriver/
>>
>>  Besides this. Is there an easy way to obtain the force field energy
>> of a system
>>  using gromacs? Would I have to run a 0-steps MD and read out the
>> energy? I know
>>  that this would have a big overhead in a MC simulation, but it might
>> be worth
>>  trying.
>>
>>  Thanks,
>>
>>  Gianluca
>>
>>  --**---
>>  Gianluca Interlandi, PhD gianl...@u.washington.edu
>> +1 (206) 685 4435
>> 
>> http://artemide.bioeng.**washington.edu/
>>
>>  Postdoc at the Department of Bioengineering
>>  at the University of Washington, Seattle WA U.S.A.
>>  --**---
>>  --
>>  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/Searchbefore
>>  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
>>
>>
>>
>>
>>
> --**---
> Gianluca Interlandi, PhD gianl...@u.washington.edu
>+1 (206) 685 4435
>
> http

Re: [gmx-users] Installing & uninstalling of gromacs

[Spring buds]

Hi lina,

Thanks for reply. could you tell me how to remove completly the gromacs
installation?

On Tue, Jan 24, 2012 at 2:31 AM, lina  wrote:

> On 24 Jan, 2012, at 1:53, Spring buds  wrote:
>
> > Dear Gromacs users,
> >
> > Greetings!!!
> >
> > I am very new users and I am trying to install grmacs 4.5.5 or 3.3.3 for
> past four days. But still I am not able to. So I would like to ask some
> questions which are below.
> >
> >
> > 1.My laptop is a dual core, which means two processors?.So should I need
> to install MPI?
> >
> --enable threads
>
> > 2.I installed gromacs 4.5.5 with mistakes. To remove installing, I used
> the "which gromacs" and it shows as "/usr/bin/which: no mdrun in
> (/usr/kerberos/bin:/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/home/Malai/bin)".
> However, I used "rm -rf /usr/local/gromacs" to remove installing I still
> can see tha gromacs files with red background in "/usr/local/bin". Could
> you tell me I removed the gromacs installing?
>
> You have not.
>
> >
> > 3.Could you please tell me the very simple steps for installatios, since
> I am a novice.
>
> http://www.gromacs.org/Downloads/Installation_Instructions
>
> >
> > Many thanks in advance for your time and help.
> >
> > Huang Malai
> > --
> > 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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> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>
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Re: [gmx-users] Installing & uninstalling of gromacs

[lina]

On Tue, Jan 24, 2012 at 11:42 AM, Spring buds  wrote:
> Hi lina,
>
> Thanks for reply. could you tell me how to remove completly the gromacs
> installation?

Which commands have you issued?

try make uninstall in the directory where you used make install
before. like Path_to//gromacs-4.5.5
and then make distclean
for a totally clear re-installation, removed the /gromac-4.5.5 and
re-untar the gromacs-4.5.5.tar.gz

before that, further check the lib and bin have totally removed or not.

Which OS you are working on?

>
>
> On Tue, Jan 24, 2012 at 2:31 AM, lina  wrote:
>>
>> On 24 Jan, 2012, at 1:53, Spring buds  wrote:
>>
>> > Dear Gromacs users,
>> >
>> > Greetings!!!
>> >
>> > I am very new users and I am trying to install grmacs 4.5.5 or 3.3.3 for
>> > past four days. But still I am not able to. So I would like to ask some
>> > questions which are below.
>> >
>> >
>> > 1.My laptop is a dual core, which means two processors?.So should I need
>> > to install MPI?
>> >
>> --enable threads
>>
>> > 2.I installed gromacs 4.5.5 with mistakes. To remove installing, I used
>> > the "which gromacs" and it shows as "/usr/bin/which: no mdrun in
>> > (/usr/kerberos/bin:/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/home/Malai/bin)".
>> > However, I used "rm -rf /usr/local/gromacs" to remove installing I still 
>> > can
>> > see tha gromacs files with red background in "/usr/local/bin". Could you
>> > tell me I removed the gromacs installing?
>>
>> You have not.
>>
>> >
>> > 3.Could you please tell me the very simple steps for installatios, since
>> > I am a novice.
>>
>> http://www.gromacs.org/Downloads/Installation_Instructions
>>
>> >
>> > Many thanks in advance for your time and help.
>> >
>> > Huang Malai
>> > --
>> > gmx-users mailing list    gmx-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 list    gmx-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 list    gmx-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!
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Re: [gmx-users] Installing & uninstalling of gromacs

[Spring buds]

On Tue, Jan 24, 2012 at 11:49 AM, lina  wrote:

> On Tue, Jan 24, 2012 at 11:42 AM, Spring buds 
> wrote:
> > Hi lina,
> >
> > Thanks for reply. could you tell me how to remove completly the gromacs
> > installation?
>
> Which commands have you issued?
>

I used "rm -rf /usr/local/gromacs" but still I can see the gromacs
files in /usr/local/bin. How to remove here?


> try make uninstall in the directory where you used make install
> before. like Path_to//gromacs-4.5.5
> and then make distclean
> for a totally clear re-installation, removed the /gromac-4.5.5 and
>
re-untar the gromacs-4.5.5.tar.gz
>
> before that, further check the lib and bin have totally removed or not.
>

Sure. I will do now

>
> Which OS you are working on?
>

Linux (CentOS 5.7)

Thanks a lot.

>
> >
> >
> > On Tue, Jan 24, 2012 at 2:31 AM, lina  wrote:
> >>
> >> On 24 Jan, 2012, at 1:53, Spring buds  wrote:
> >>
> >> > Dear Gromacs users,
> >> >
> >> > Greetings!!!
> >> >
> >> > I am very new users and I am trying to install grmacs 4.5.5 or 3.3.3
> for
> >> > past four days. But still I am not able to. So I would like to ask
> some
> >> > questions which are below.
> >> >
> >> >
> >> > 1.My laptop is a dual core, which means two processors?.So should I
> need
> >> > to install MPI?
> >> >
> >> --enable threads
> >>
> >> > 2.I installed gromacs 4.5.5 with mistakes. To remove installing, I
> used
> >> > the "which gromacs" and it shows as "/usr/bin/which: no mdrun in
> >> >
> (/usr/kerberos/bin:/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/home/Malai/bin)".
> >> > However, I used "rm -rf /usr/local/gromacs" to remove installing I
> still can
> >> > see tha gromacs files with red background in "/usr/local/bin". Could
> you
> >> > tell me I removed the gromacs installing?
> >>
> >> You have not.
> >>
> >> >
> >> > 3.Could you please tell me the very simple steps for installatios,
> since
> >> > I am a novice.
> >>
> >> http://www.gromacs.org/Downloads/Installation_Instructions
> >>
> >> >
> >> > Many thanks in advance for your time and help.
> >> >
> >> > Huang Malai
> >> > --
> >> > 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
> >> 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
> > www interface or send it to gmx-users-requ...@gromacs.org.
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> --
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] Monte Carlo with Gromacs and implicit solvent

[Rodrigo Faccioli]

Hi Gianluca,

I forgot to say that the step of compute the energies is considered from
pdb2gmx until g_energy.

Sorry about my oblivion.

Best regards,

--
Rodrigo Antonio Faccioli
Ph.D Student in Electrical Engineering
University of Sao Paulo - USP
Engineering School of Sao Carlos - EESC
Department of Electrical Engineering - SEL
Intelligent System in Structure Bioinformatics
http://laips.sel.eesc.usp.br
Phone: 55 (16) 3373-9366 Ext 229
Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5


On Tue, Jan 24, 2012 at 1:07 AM, Rodrigo Faccioli <
rodrigo_facci...@uol.com.br> wrote:

> Hi Gianluca,
>
> Thanks your question.
>
> All steps to obtain a generation with 200 individuals, on average, is 6
> minutes for 1VII, example. In each generation I must  converted my proteins
> Dihedral to Cartesian representation, compute the energies, choose the
> individuals which will go to reproduction, save previous population. This
> test was using one core of a conventional Desktop computer.
>
> The proteins, that I have tested my algorithm, vary from 20 to 56 amino
> acids.
>
> Best regards,
>
> --
> Rodrigo Antonio Faccioli
> Ph.D Student in Electrical Engineering
> University of Sao Paulo - USP
> Engineering School of Sao Carlos - EESC
> Department of Electrical Engineering - SEL
> Intelligent System in Structure Bioinformatics
> http://laips.sel.eesc.usp.br
> Phone: 55 (16) 3373-9366 Ext 229
> Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
> Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5
>
>
> On Tue, Jan 24, 2012 at 12:36 AM, Gianluca Interlandi <
> gianl...@u.washington.edu> wrote:
>
>> Thanks Enrico!
>>
>> Just wondering. How fast is it? Calling gromacs must have a lot of
>> overhead. Also, do you call mdrun or does g_energy evaluate the energy?
>>
>> Gianluca
>>
>>
>> On Tue, 24 Jan 2012, Rodrigo Faccioli wrote:
>>
>>  Hi,
>>>
>>> Although I don't work with MC simulation, I have used Gromacs to obtain
>>> energies and others
>>> protein features in my Evolutionary Algorithms (EA).
>>>
>>> In general lines, I created a script that calls Gromacs programs and the
>>> output of these
>>> programs, such as g_energy (I read its xvg file), I stored it at a
>>> specific file which is
>>> read by my algorithm and its values are put into my data structure. I
>>> call Gromacs either
>>> implicit or explicit solvent.
>>>
>>> My project is working with EA until now. However, the integration with
>>> GROMACS is able to
>>> work with other kind of algorithms such as MC. Actually, we have idea to
>>> work with MC. But,
>>> I don't know when it will be possible. If you want, we can talk about
>>> join these work.
>>>
>>> Best regards,
>>>
>>> --
>>> Rodrigo Antonio Faccioli
>>> Ph.D Student in Electrical Engineering
>>> University of Sao Paulo - USP
>>> Engineering School of Sao Carlos - EESC
>>> Department of Electrical Engineering - SEL
>>> Intelligent System in Structure Bioinformatics
>>> http://laips.sel.eesc.usp.br
>>> Phone: 55 (16) 3373-9366 Ext 229
>>> Curriculum Lattes - 
>>> http://lattes.cnpq.br/**1025157978990218
>>> Public Profile - 
>>> http://br.linkedin.com/pub/**rodrigo-faccioli/7/589/a5
>>>
>>>
>>> On Mon, Jan 23, 2012 at 11:39 PM, Gianluca Interlandi <
>>> gianl...@u.washington.edu> wrote:
>>>  Hi!
>>>
>>>  I would like to use gromacs to perform Monte Carlo simulations in
>>> implicit
>>>  solvent of a protein near a surface. The protein is treated as a
>>> rigid body
>>>  whereas the surface is fix.
>>>
>>>  I see that there are plans to code MC into gromacs:
>>>
>>>  http://www.gromacs.org/**Developer_Zone/Programming_**
>>> Guide/Monte_Carlo
>>>
>>>  Is there a preliminary version?
>>>
>>>  If not, I wonder whether anybody has tried to do MC with gromacs
>>> using IMD and
>>>  MDDriver:
>>>
>>>  
>>> http://www.baaden.ibpc.fr/**projects/mddriver/
>>>
>>>  Besides this. Is there an easy way to obtain the force field energy
>>> of a system
>>>  using gromacs? Would I have to run a 0-steps MD and read out the
>>> energy? I know
>>>  that this would have a big overhead in a MC simulation, but it
>>> might be worth
>>>  trying.
>>>
>>>  Thanks,
>>>
>>>  Gianluca
>>>
>>>  --**---
>>>  Gianluca Interlandi, PhD gianl...@u.washington.edu
>>> +1 (206) 685 4435
>>> 
>>> http://artemide.bioeng.**washington.edu/
>>>
>>>  Postdoc at the Department of Bioengineering
>>>  at the University of Washington, Seattle WA U.S.A.
>>>  --**---
>>>

[gmx-users] regarding boxtype and numer of solvent molecules..

[priya thiyagarajan]

hello sir,
Thanks for your kind reply..

15 boxtype accomodates 105046 solvent molecules..

but i need to run simulation by keeping  number of water molecules constant
and changing number of protein molecules..

thanking you,
-- 
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