[gmx-users] Analysis of a simulation

[sukesh chandra gain]

Dear All,

It is not clear from manual how to analyse my requirements after simulation.
Could you please help me in the following regards:

1> How to get the graph on "occupancy of hydrogen bond interactions of 
ligands throughout 5 ns simulation" and "occupancy of a particular 
salt-bridge throughout the simulation"  ?


2> I want to get a graph of the distances of some particular co-factor 
atoms and active site residues atoms throughout the simulation.
Suppose I want the distance graph between DPM:C9B and Arg7:CA for total 
simulation.


3> Average hydrogen bond distance between active site residues and ligand.

4> RMSD of some particular residues from its initial structure.

5> Total formal charge residing at active site  throughout the 
simulation (All +vely charge and -vely charge residues within 15 A 
radius of active site will be considered).


It would be a great help if you could kindly give some sample commands  
for these analysis.


Sorry for lots of questions.

Thank You.

Regards,
Sukesh


--
Sukesh Chandra Gain
TCS Innovation Labs
Tata Consultancy Services Ltd.
'Deccan Park', Madhapur
Hyderabad 500081
Phone:  +91 40 6667 3572

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Re: [gmx-users] indexing and new molecules

[Itamar Kass]

Hi Mark,

Thanks for the replay. I actually hold the modified force filed files in
the same directory in which I simulate, less mess in the system.

Cheers,
Itamar

-- 


"In theory, there is no difference between theory and practice. But, in
practice, there is." - Jan L.A. van de Snepscheut

===
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: itamar.k...@med.monash.edu.au


- Original Message -
From: Mark Abraham 
Date: Tuesday, February 16, 2010 4:51 pm
Subject: Re: [gmx-users] indexing and new molecules
To: Discussion list for GROMACS users 

On 02/16/10, Itamar Kass 
 wrote:Shalom
all,I am simulating a protein in which one of the residues
is chemicallymodified (non-natural) - so I had to add it into
aminoacids.dat.I found that when I analyse my results, and
use the index group of theprotein this amino acid does not count
unless the aminoacids.dat file isavailable in the same
folder.Such files are searched
for first in the local directory and then in $GMXLIB. So if you've used
"source /path/to/GMXRC" correctly and modified the
corresponding file, you'll be fine. If you have mu
ltiple installations, or multiple machines, you need to take some care,
of course.Now, I
don't think this is a bug - it is perfectly logic that in orderto
index the protein the program needs to know how amino acid lookslike. I just think this should be written
somewhere.Sure. There's a manual section that
discusses a small number of the environment variables that GROMACS uses,
but I don't know if this tidbit is there. It is not easy to write this
information somewhere where it will come to people's attention whene
ver it is needed.Mark

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Re: [gmx-users] indexing and new molecules

[Mark Abraham]

On 02/16/10, Itamar Kass   wrote:Shalom all,I am simulating a protein in which one of the residues is chemicallymodified (non-natural) - so I had to add it into aminoacids.dat.I found that when I analyse my results, and use the index group of theprotein this amino acid does not count unless the aminoacids.dat file isavailable in the same folder.Such files are searched for first in the local directory and then in $GMXLIB. So if you've used "source /path/to/GMXRC" correctly and modified the corresponding file, you'll be fine. If you have multiple installations, or multiple machines, you need to take some care, of course.Now, I don't think this is a bug - it is perfectly logic that in orderto index the protein the program needs to know how amino acid lookslike. I just think this should be written somewhere.Sure. There's a manual section that discusses a small number of the environment variables that GROMACS uses, but I don't know if this tidbit is there. It is not easy to write this information somewhere where it will come to people's attention whenever it is needed.Mark
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[gmx-users] indexing and new molecules

[Itamar Kass]

Shalom all,

I am simulating a protein in which one of the residues is chemically
modified (non-natural) - so I had to add it into aminoacids.dat.

I found that when I analyse my results, and use the index group of the
protein this amino acid does not count unless the aminoacids.dat file is
available in the same folder.

Now, I don't think this is a bug - it is perfectly logic that in order
to index the protein the program needs to know how amino acid looks
like. I just think this should be written somewhere.

Cheers,
Itamar

-- 


"In theory, there is no difference between theory and practice. But, in
practice, there is." - Jan L.A. van de Snepscheut

===
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: itamar.k...@med.monash.edu.au

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Re: [gmx-users] pbc option

[Mark Abraham]

On 02/16/10, Amit Choubey   wrote:Hi Everyone,I changed the gromacs source code a little bit and this change introduced some bias along x direction. Now i want to do a 'yz' pbc but gromacs has the option of pbc = xy only. Is there a quick tip to circumvent? I can always introduce the bias along z but its a little time taking job :)Rotate the simulation box?Mark
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[gmx-users] pbc option

[Amit Choubey]

Hi Everyone,

I changed the gromacs source code a little bit and this change introduced
some bias along x direction. Now i want to do a 'yz' pbc but gromacs has the
option of pbc = xy only. Is there a quick tip to circumvent? I can always
introduce the bias along z but its a little time taking job :)

Amit
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Re: [gmx-users] (no subject)

[Justin A. Lemkul]

Turtle Nedasing wrote:

What is coordination number and which  program generate  it?




That depends on your context, and there probably isn't a Gromacs program that 
generates it magically, but with a combination of tools to describe whatever 
criteria you're assigning, you might be able to get something close.


-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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Re: [gmx-users] number of adsorbed gas+silicon nanotube

[Justin A. Lemkul]

Turtle Nedasing wrote:

Hi , please answer my questions

1- for performed (MD) simulation to study adsorption gas on silicon 
nanotube  ,I used from  g_rdf and trjorder programs ,how I can measure 
adsorption coverage (number of adsorbed gas)on surface of the nanotube ?


Using g_dist -dist might be a start, defining some appropriate cutoff with the 
-dist option.




2-while running g_msd program ,in the option selected groups ,which one 
must select  :1-silicon nanotube or 2-gas molecules




Well, which one do you want the diffusion constant for?

-Justin

Thank you for attention  





--


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] How to select the molecules within a defined radius

[Teemu Murtola]

Hi,

On Mon, Feb 15, 2010 at 19:04, Saikat Banerjee  wrote:
> I selected a sphere at a fixed center and noted the
> number of water and DMSO molecules within that cut-off. I would like to know
> if there are any methods to do the same within GROMACS.

The development (git) version of Gromacs has for some time included a
tool called g_select, which should be able to do what you want.
There's only limited documentation, but 'g_select -select help' and
'g_select -select "help cmdline"' should give something to start with.
Your problem could be solved with something like

g_select -select 'resname DMSO and within 1.0 of (2.0, 2.0, 2.0)'
-seltype res_com -selrpos res_com -os

which gives you the number of DMSO centers of mass within 1 nm of the
given point as a function of time.

If you feel like testing it, any feedback is welcome.

- Teemu
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[gmx-users] pbc with nwall = 1

[toma0052]

Hello,
I want to study polymer adsorption onto a surface. To do so, I create 
a polymer-solvent system with a wall at z = 0 and use pbc = xy. This, 
however makes the system infinite in the z-direction. I was wondering if 
there was a way to create a periodic boundary at z = L such that when an 
atom crosses z = L the z-coordinate shifts to z = L/2 (rather than z=0 in 
normal pbc) but not the other way around. In this way I could have a 
portion of my system near the surface and a portion far from the surface 
which would represent the bulk. Is this possible? Would it require 
substantial modification to the code?


Thanks,
Mike
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Re: [gmx-users] How to select the molecules within a defined radius

[Saikat Banerjee]

>
>
> Saikat Banerjee wrote:


>> I am doing some simulations in binary solvent water and DMSO using ffG43a6
>> forcefield. I need to calculate the composition fluctuation of the solvent.
>> I have done that with hand-written codes using the trajectory files
>> generated by GROMACS. I selected a sphere at a fixed center and noted the
>> number of water and DMSO molecules within that cut-off. I would like to know
>> if there are any methods to do the same within GROMACS.
>>
>
> Have a look at:
>
> g_dist -dist
>
> -Justin
>
> Thanks for your reply. It could have been done with g_dist -dist or
trjorder -r. But the problem here is a bit different. I wanted to compute
the number of molecules within a cut-off from the center of the box, and not
from the center of mass of another atom.  So, the problem can be re-framed
as - is there any way to fix a dummy massless atom at the box centre ?





> Thanking you,
>>
>> Saikat
>>
>> --
>> ---
>> Saikat Banerjee
>> Integrated Ph.D student
>> Prof B. Bagchi's group
>> Room no. 210
>> Solid State and Structural Chemistry Unit (SSCU)
>> Indian Institute of Science
>> Bangalore-560012
>> ---
>>
>>
> --
> 
>
> 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] (no subject)

[Turtle Nedasing]

What
is coordination number and which  program
generate  it?


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[gmx-users] number of adsorbed gas+silicon nanotube

[Turtle Nedasing]

Hi , please answer my questions

1- for performed (MD)
simulation to study adsorption gas on silicon
nanotube  ,I used from  g_rdf and trjorder programs ,how I can measure
adsorption coverage (number of adsorbed gas)on surface of the nanotube ?

2-while running g_msd program ,in
the option selected groups ,which one must select  :1-silicon nanotube or 2-gas 
molecules


Thank you for attention   


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Re: [gmx-users] Problems wtih g_wham

[Jennifer Casey]

Thank you so much!  I appreciate the help, and the good news is actually
great news.

Jenny

On Sun, Feb 14, 2010 at 12:45 PM, Jochen Hub  wrote:

> Jennifer Casey wrote:
>
>> Hello,
>>
>> I am trying to create a PMF for the sodium cation and iodine anion in the
>> presence of THF.  I have been following the umbrella sampling tutorial on
>> the gromacs website, and everything has been working out.  I have finally
>> created 14 different equilibriation simulations, whose starting
>> configurations were obtained form a pull simulation with pull_rate = 0.06.
>>  To get the 14 different equilibriated runs, I left the pull code on, but I
>> just made pull_rate = 0.00.  I have created a list of the .tpr files and the
>> pullf[].xvg files, and I tried to use g_wham.  The error I got was as
>> follows:  "This is not a tpr of an umbrella simulation.  Found ir.ePul; =
>> cylinder."  Has anyone else found this error?  I was not even using
>> cylinder, I was using distance.
>>
>
> Hi Jennifer,
>
> the error message is indeed wrong and should have been "Found ir.ePull =
> constaint" (epullg_names should have been epull_names, one "g" too much in
> gmx_wham.c). I have submitted a bugzilla for that. But the problem was, that
> you did not do umbrella sampling. For umbrella sampling, you restrain the
> system with a (normally harmonic) restraint along the reaction coordinate,
> using "pull = umbrella". You have constrained the system at a fixed position
> along the reaction coordinate, which is not umbrella sampling. However, now
> comes the good news, you can still compute the PMF via the mean forces.
> Average the forces in pullf (after some equilibration), and integrate the
> mean forces (e.g. with g_analyze), giving the potential of mean force (PMF).
> That technique is called something like constrained something calculation or
> so, don't remember exactly.
>
> If you still want to do umbrella sampling, you'll have to do the simulation
> again with pull = umbrella and then use g_wham to get the PMF.
>
> Best wishes,
>
> Jochen
>
>
>
>
>
>
>> I have attached my original pull  .mdp file, and the .mdp file used in the
>> 14 equilibration runs.
>>
>> I appreciate any help.
>>
>> Thanks,
>> Jenny
>>
>
>
> --
> ---
> Dr. Jochen Hub
> Molecular Biophysics group
> Dept. of Cell & Molecular Biology
> Uppsala University. Box 596, 75124 Uppsala, Sweden.
> Phone: +46-18-4714451 Fax: +46-18-511755
> ---
>
>
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Re: [gmx-users] How to select the molecules within a defined radius

[Justin A. Lemkul]

Saikat Banerjee wrote:

Hi all,

I am doing some simulations in binary solvent water and DMSO using 
ffG43a6 forcefield. I need to calculate the composition fluctuation of 
the solvent. I have done that with hand-written codes using the 
trajectory files generated by GROMACS. I selected a sphere at a fixed 
center and noted the number of water and DMSO molecules within that 
cut-off. I would like to know if there are any methods to do the same 
within GROMACS.


Have a look at:

g_dist -dist

-Justin



Thanking you,

Saikat

--
---
Saikat Banerjee
Integrated Ph.D student
Prof B. Bagchi's group
Room no. 210
Solid State and Structural Chemistry Unit (SSCU)
Indian Institute of Science
Bangalore-560012
---



--


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] How to select the molecules within a defined radius

[Saikat Banerjee]

Hi all,

I am doing some simulations in binary solvent water and DMSO using ffG43a6
forcefield. I need to calculate the composition fluctuation of the solvent.
I have done that with hand-written codes using the trajectory files
generated by GROMACS. I selected a sphere at a fixed center and noted the
number of water and DMSO molecules within that cut-off. I would like to know
if there are any methods to do the same within GROMACS.

Thanking you,

Saikat

-- 
---
Saikat Banerjee
Integrated Ph.D student
Prof B. Bagchi's group
Room no. 210
Solid State and Structural Chemistry Unit (SSCU)
Indian Institute of Science
Bangalore-560012
---
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Re: [gmx-users] Poor load balancing

[Carsten Kutzner]

Hi,

18 seconds real time is a bit short for such a test. You should run
at least several minutes. The performance you can expect depends
a lot on the interconnect you are using. You will definitely need a 
really low-latency interconnect if you have less then 1000 atoms
per core. 

Carsten


On Feb 15, 2010, at 3:13 PM, Deniz KARASU wrote:

> Hi All,
> 
> I'm trying to d.lzm gromacs benchmarks with 64 node machine, but   dynamic 
> load balancing performance is very low. 
> 
> Any suggestion will be of great help.
> 
> Thanks.
> 
> Deniz KARASU
> 

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Re: [gmx-users] pbc whole

[Justin A. Lemkul]

Carla Jamous wrote:

Hi everyone,
I'm using this command to extract my protein and my ligand from the 
trajectory.


trjconv -f prot_md60ns.xtc -s prot_md50.tpr -fit rot+trans -pbc whole -n 
prot_wat.ndx -o prot_ligand_60ns.xtc < grps >& outtrj


Before, I had a problem with residues of my protein showing at the other 
end of the box, when I display my .xtc with VMD.

the "-pbc whole" fixed it.

However, now I have another issue: my ligand is at the other end of the 
box. So please can anyone tell me what can I do to fix that and get a 
reasonable RMSD value?




You may need several more iterations of trjconv (one rarely does the trick), 
employing -pbc nojump, -pbc cluster, and/or -center.  For protein-ligand 
complexes, I have often found that the combination of:


trjconv -pbc mol -ur compact -center

(centering on "Protein")

does the trick.  And it makes molecules whole, as well :)  I think there are 
also some breakdowns (documented somewhere in the list archive) when applying 
-fit and -pbc in the same step.  I believe it is recommended to fix PBC first, 
then applying any sort of fitting in a separate, subsequent step.


-Justin


Thank you
Carla



--


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] pbc whole

[Carla Jamous]

Hi everyone,
I'm using this command to extract my protein and my ligand from the
trajectory.

trjconv -f prot_md60ns.xtc -s prot_md50.tpr -fit rot+trans -pbc whole -n
prot_wat.ndx -o prot_ligand_60ns.xtc < grps >& outtrj

Before, I had a problem with residues of my protein showing at the other end
of the box, when I display my .xtc with VMD.
the "-pbc whole" fixed it.

However, now I have another issue: my ligand is at the other end of the box.
So please can anyone tell me what can I do to fix that and get a reasonable
RMSD value?

Thank you
Carla
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[gmx-users] Poor load balancing

[Deniz KARASU]

Hi All,

I'm trying to d.lzm gromacs benchmarks with 64 node machine, but   dynamic
load balancing performance is very low.

Any suggestion will be of great help.

Thanks.

Deniz KARASU

Log file opened on Sat Feb 13 17:23:37 2010
Host: d077.uybhm.itu.edu.tr  pid: 20157  nodeid: 0  nnodes:  64
The Gromacs distribution was built Thu Sep 10 11:45:26 EEST 2009 by
mds.fa...@lnode1.uybhm.itu.edu.tr (Linux
2.6.18-53.1.14.el5_lustre.1.6.5.1smp x86_64)


 :-)  G  R  O  M  A  C  S  (-:

 Good ROcking Metal Altar for Chronical Sinners

:-)  VERSION 4.0.5  (-:


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

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

:-)  /AKDENIZ/HOME005/users/mds.fatma/rs/software/bin/mdrun  (-:


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 435-447
  --- Thank You ---  


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
Berendsen
GROMACS: Fast, Flexible and Free
J. Comp. Chem. 26 (2005) pp. 1701-1719
  --- Thank You ---  


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
  --- Thank You ---  


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
  --- Thank You ---  

parameters of the run:
   integrator   = md
   nsteps   = 5000
   init_step= 0
   ns_type  = Grid
   nstlist  = 5
   ndelta   = 2
   nstcomm  = 1
   comm_mode= Linear
   nstlog   = 0
   nstxout  = 0
   nstvout  = 0
   nstfout  = 0
   nstenergy= 0
   nstxtcout= 0
   init_t   = 0
   delta_t  = 0.004
   xtcprec  = 1000
   nkx  = 0
   nky  = 0
   nkz  = 0
   pme_order= 4
   ewald_rtol   = 1e-05
   ewald_geometry   = 0
   epsilon_surface  = 0
   optimize_fft = FALSE
   ePBC = xyz
   bPeriodicMols= FALSE
   bContinuation= FALSE
   bShakeSOR= FALSE
   etc  = Berendsen
   epc  = No
   epctype  = Isotropic
   tau_p= 1
   ref_p (3x3):
  ref_p[0]={ 0.0e+00,  0.0e+00,  0.0e+00}
  ref_p[1]={ 0.0e+00,  0.0e+00,  0.0e+00}
  ref_p[2]={ 0.0e+00,  0.0e+00,  0.0e+00}
   compress (3x3):
  compress[0]={ 0.0e+00,  0.0e+00,  0.0e+00}
  compress[1]={ 0.0e+00,  0.0e+00,  0.0e+00}
  compress[2]={ 0.0e+00,  0.0e+00,  0.0e+00}
   refcoord_scaling = No
   posres_com (3):
  posres_com[0]= 0.0e+00
  posres_com[1]= 0.0e+00
  posres_com[2]= 0.0e+00
   posres_comB (3):
  posres_comB[0]= 0.0e+00
  posres_comB[1]= 0.0e+00
  posres_comB[2]= 0.0e+00
   andersen_seed= 815131
   rlist= 0.9
   rtpi = 0.05
   coulombtype  = Cut-off
   rcoulomb_switch  = 0
   rcoulomb = 1.4
   vdwtype  = Cut-off
   rvdw_switch  = 0
   rvdw = 1.4
   epsilon_r= 1
   epsilon_rf   = 1
   tabext   = 1
   implicit_solvent = No
   gb_algorithm = Still
   gb_epsilon_solvent   = 80
   nstgbradii   = 1
   rgbradii = 2
   gb_saltconc  = 0
   gb_obc_alpha = 1
   gb_obc_beta  = 0.8
   gb_obc_gamma = 4.85
   sa_surface_tension   = 2.092
   DispCorr = No
   free_energy  = no
   init_lambda  = 0
   sc_alpha = 0
   sc_power = 0
   sc_sigma = 0.3
   delta_lambda = 0
   nwall= 0
   wall_type= 9-3
   wall_atomtyp

Re: [gmx-users] problem with the translate option of editconf

[Erik Marklund]

Ozge Engin skrev:

Hi all,

I am trying to translate the peptide within the simulation box. I have 
a box with dimensions of 3.8 3.0 3.0 nm^3, and I want to put the 
peptide on top of the box. In order to that I used the following 
command line:


editconf -f pep.pdb -box 3.8 3.0 3.0 -translate 0 0 1.5 -o trans.pdb

The peptide is not translated, but sitting at the center of the box. 
Why is the case? Any suggestions?


Thanks in advance

--
Ozge Engin


Because -c is implied by -box. excerpt form editconf -h output:

-[no]c   bool   no  Center molecule in box (implied by -box and -d)

You'll have to do the -box and the -translate in two sequential passes 
through editconf.


--
---
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys

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Re: [gmx-users] problem with the translate option of editconf

[Justin A. Lemkul]

Ozge Engin wrote:

Hi all,

I am trying to translate the peptide within the simulation box. I have a 
box with dimensions of 3.8 3.0 3.0 nm^3, and I want to put the peptide 
on top of the box. In order to that I used the following command line:


editconf -f pep.pdb -box 3.8 3.0 3.0 -translate 0 0 1.5 -o trans.pdb

The peptide is not translated, but sitting at the center of the box. Why 
is the case? Any suggestions?


The use of -box implies -c, so either use -noc or set the center explicitly with 
-center instead of -translate.


-Justin



Thanks in advance

--
Ozge Engin
★☆



--


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] problem with the translate option of editconf

[Ozge Engin]

Hi all,

I am trying to translate the peptide within the simulation box. I have a box
with dimensions of 3.8 3.0 3.0 nm^3, and I want to put the peptide on top of
the box. In order to that I used the following command line:

editconf -f pep.pdb -box 3.8 3.0 3.0 -translate 0 0 1.5 -o trans.pdb

The peptide is not translated, but sitting at the center of the box. Why is
the case? Any suggestions?

Thanks in advance

-- 
Ozge Engin
★☆
-- 
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SV: [gmx-users] spc vs. flex_spc

[Sarah Witzke]

Thank you very much for your quick answer Berk!



Fra: gmx-users-boun...@gromacs.org på vegne af Berk Hess
Sendt: ma 15-02-2010 10:56
Til: Discussion list for GROMACS users
Emne: RE: [gmx-users] spc vs. flex_spc


Hi,

flex_spc is not a reliable water model, never use it for MD.
You should only use it when your initial configuration is so bad that energy
minimization with normal, rigid water molecules crashes.
However, the deviations are so small that after a few picoseconds of MD
with normal spc there will be no memory of the flex_spc initial structure.

Berk

> Date: Mon, 15 Feb 2010 10:38:40 +0100
> From: sawi...@student.sdu.dk
> To: gmx-users@gromacs.org
> Subject: [gmx-users] spc vs. flex_spc
> 
> Dear gmx-users,
> 
> I am wondering whether or not there is a good reason to use flex_spc during 
> energy minimisation and spc during production run? I guess one would not use 
> flex_spc during a production run as this would decrease the time step needed 
> quite a lot - but is it a good idea to use during EM as the system easier 
> relaxes?
> I know that strictly this is not a gromacs related issue, but if you could 
> say just 'yes' or 'no', I would very much appreciate it.
> 
> Thank you for all your help and quick answers,
> Sarah
> -- 
> 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/search before posting!
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> www interface or send it to gmx-users-requ...@gromacs.org.
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New Windows 7: Simplify what you do everyday. Find the right PC for you. 
  
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RE: [gmx-users] spc vs. flex_spc

[Berk Hess]

Hi,

flex_spc is not a reliable water model, never use it for MD.
You should only use it when your initial configuration is so bad that energy
minimization with normal, rigid water molecules crashes.
However, the deviations are so small that after a few picoseconds of MD
with normal spc there will be no memory of the flex_spc initial structure.

Berk

> Date: Mon, 15 Feb 2010 10:38:40 +0100
> From: sawi...@student.sdu.dk
> To: gmx-users@gromacs.org
> Subject: [gmx-users] spc vs. flex_spc
> 
> Dear gmx-users,
>  
> I am wondering whether or not there is a good reason to use flex_spc during 
> energy minimisation and spc during production run? I guess one would not use 
> flex_spc during a production run as this would decrease the time step needed 
> quite a lot - but is it a good idea to use during EM as the system easier 
> relaxes?
> I know that strictly this is not a gromacs related issue, but if you could 
> say just 'yes' or 'no', I would very much appreciate it.
>  
> Thank you for all your help and quick answers,
> Sarah
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
  
_
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[gmx-users] spc vs. flex_spc

[Sarah Witzke]

Dear gmx-users,
 
I am wondering whether or not there is a good reason to use flex_spc during 
energy minimisation and spc during production run? I guess one would not use 
flex_spc during a production run as this would decrease the time step needed 
quite a lot - but is it a good idea to use during EM as the system easier 
relaxes?
I know that strictly this is not a gromacs related issue, but if you could say 
just 'yes' or 'no', I would very much appreciate it.
 
Thank you for all your help and quick answers,
Sarah
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