[gmx-users] mpirun: cannot open .tpr file

[Ewaru]

Hi,

I'm trying to test mpirun, so I tried with the NPT equilibration. From the
tutorial of:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/07_equil2.html

I run this command: mpirun --np 10 --hostfile ~/hostfile mdrun_mpi -npme 3
-deffnm npt

and obtained an error saying "Cannot open file: npt.tpr". However, if I run
it with just mdrun, it goes fine. Can someone please advice what went wrong?
:( 

The output for the mpirun is as below:

NNODES=10, MYRANK=2, HOSTNAME=wizztjh-Presario-CQ42-Notebook-PC
NNODES=10, MYRANK=3, HOSTNAME=wizztjh-Presario-CQ42-Notebook-PC
NNODES=10, MYRANK=6, HOSTNAME=wizztjh-Presario-CQ42-Notebook-PC
NNODES=10, MYRANK=1, HOSTNAME=wizztjh-Presario-CQ42-Notebook-PC
NNODES=10, MYRANK=7, HOSTNAME=wizztjh-Presario-CQ42-Notebook-PC
NNODES=10, MYRANK=4, HOSTNAME=wizztjh-Presario-CQ42-Notebook-PC
NNODES=10, MYRANK=9, HOSTNAME=wizztjh-Presario-CQ42-Notebook-PC
NNODES=10, MYRANK=5, HOSTNAME=wizztjh-Presario-CQ42-Notebook-PC
NNODES=10, MYRANK=0, HOSTNAME=wizztjh-Presario-CQ42-Notebook-PC
NODEID=0 argc=5
NODEID=4 argc=5
NNODES=10, MYRANK=8, HOSTNAME=wizztjh-Presario-CQ42-Notebook-PC
NODEID=2 argc=5
NODEID=1 argc=5
NODEID=3 argc=5
 :-)  G  R  O  M  A  C  S  (-:

NODEID=5 argc=5
NODEID=9 argc=5
   NODEID=6 argc=5
NODEID=8 argc=5
Gromacs Runs One Microsecond At Cannonball Speeds

:-)  VERSION 4.5.4  (-:

Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
  Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, 
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, 
NODEID=7 argc=5
   Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, 
Michael Shirts, Alfons Sijbers, Peter Tieleman,

   Berk Hess, David van der Spoel, and Erik Lindahl.

   Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

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

  :-)  mdrun_mpi  (-:

Option Filename  Type Description

  -snpt.tpr  InputRun input file: tpr tpb tpa
  -onpt.trr  Output   Full precision trajectory: trr trj cpt
  -xnpt.xtc  Output, Opt. Compressed trajectory (portable xdr
format)
-cpinpt.cpt  Input, Opt.  Checkpoint file
-cponpt.cpt  Output, Opt. Checkpoint file
  -cnpt.gro  Output   Structure file: gro g96 pdb etc.
  -enpt.edr  Output   Energy file
  -gnpt.log  Output   Log file
-dhdl   npt.xvg  Output, Opt. xvgr/xmgr file
-field  npt.xvg  Output, Opt. xvgr/xmgr file
-table  npt.xvg  Input, Opt.  xvgr/xmgr file
-tablep npt.xvg  Input, Opt.  xvgr/xmgr file
-tableb npt.xvg  Input, Opt.  xvgr/xmgr file
-rerun  npt.xtc  Input, Opt.  Trajectory: xtc trr trj gro g96 pdb cpt
-tpinpt.xvg  Output, Opt. xvgr/xmgr file
-tpid   npt.xvg  Output, Opt. xvgr/xmgr file
 -einpt.edi  Input, Opt.  ED sampling input
 -eonpt.edo  Output, Opt. ED sampling output
  -jnpt.gct  Input, Opt.  General coupling stuff
 -jonpt.gct  Output, Opt. General coupling stuff
-ffout  npt.xvg  Output, Opt. xvgr/xmgr file
-devout npt.xvg  Output, Opt. xvgr/xmgr file
-runav  npt.xvg  Output, Opt. xvgr/xmgr file
 -pxnpt.xvg  Output, Opt. xvgr/xmgr file
 -pfnpt.xvg  Output, Opt. xvgr/xmgr file
-mtxnpt.mtx  Output, Opt. Hessian matrix
 -dnnpt.ndx  Output, Opt. Index file
-multidir   npt  Input, Opt., Mult. Run directory

Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-[no]version bool   no  Print version info and quit
-niceint0   Set the nicelevel
-deffnm  string npt Set the default filename for all file options
-xvg enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none
-[no]pd  bool   no  Use particle decompostion
-dd  vector 0 0 0   Domain decomposition grid, 0 is optimize
-npmeint3   Number of separate nodes to be used for PME, -1
is guess
-ddorder enum   interleave  DD node order: interleave, pp_pme or
cartesian
-[no]ddcheck bool   yes Check for all bonded interactions with DD
-rdd real   0   The maximum distance for bonded interactions
with
DD (nm), 0 is determi

Re: AW: AW: AW: AW: AW: AW: AW: [gmx-users] g_current

[Nilesh Dhumal]

Hello,

I run a 500ps simulation and save the trajectory each 3fs.

g_current work till 498ps and later it shows -nan.

Can you tell where is the problem

Nilesh


> Hi,
>  Now I've tested the version of g_current in 4.6 and for me it works fine.
> /Flo
>
>> -Ursprüngliche Nachricht-
>> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-
>> boun...@gromacs.org] Im Auftrag von Florian Dommert
>> Gesendet: Mittwoch, 27. Februar 2013 18:46
>> An: 'Discussion list for GROMACS users'
>> Betreff: AW: AW: AW: AW: AW: AW: AW: [gmx-users] g_current
>>
>> > -Ursprüngliche Nachricht-
>> > Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-
>> > boun...@gromacs.org] Im Auftrag von Nilesh Dhumal
>> > Gesendet: Mittwoch, 27. Februar 2013 17:38
>> > An: Discussion list for GROMACS users
>> > Betreff: Re: AW: AW: AW: AW: AW: AW: [gmx-users] g_current
>> >
>> > Hello,
>> >
>> > I am using g_current for first time. Now I am running additional
>> simulation and I
>> > will save trajectory at 2 fs.
>> >
>> > Is it possible to calculate contribution of rotational and translation
>> > to
>> dipole
>> > moment simultaneously with the simulation instead of saving the
>> > trajectory
>> at
>> > each 2fs?
>> >
>>
>> Hi,
>>
>>  This is one of my majors on my to do list, but currently not possible.
>> I
> think a
>> saving frequency of 0.05 ps should be fine.
>>
>> /Flo
>>
>>
>> > Nilesh
>> >
>> > > Hi,
>> > >
>> > >  Have you done a similar analysis with another IL system or is it
>> > > the first time you use g_current? Currently I am not able to figure
>> > > out what the problem is. However 2ps saving interval is quite long
>> > > for such a kind of analysis. A zero value of the translational
>> > > dipole moment hints to neutral molecules which should not be the
>> > > case for your system. What is written in the output of mj.xvg. Is
>> > > filled with zeros?
>> > >
>> > > /Flo
>> > >
>> > >
>> > >> -Ursprüngliche Nachricht-
>> > >> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-
>> > >> boun...@gromacs.org] Im Auftrag von Nilesh Dhumal
>> > >> Gesendet: Mittwoch, 27. Februar 2013 15:26
>> > >> An: Discussion list for GROMACS users
>> > >> Betreff: Re: AW: AW: AW: AW: AW: [gmx-users] g_current
>> > >>
>> > >> Hello,
>> > >>
>> > >> Yes. Segfault is solved. I saving velocites and coordinates at 2
>> ps.
>> > >>
>> > >> Nilesh
>> > >>
>> > >> > Hi,
>> > >> >
>> > >> >  At least the segfault is solved. However, the zero output of M_J
>> > >> > for your IL system is really strange. I'm thinking about a
>> > >> > reason, but I am currently not able to find one. How often do you
>> > >> > write out velocities and coordinates in your trr file?
>> > >> >
>> > >> > /Flo
>> > >> >
>> > >> >> -Ursprüngliche Nachricht-
>> > >> >> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-
>> > >> >> boun...@gromacs.org] Im Auftrag von Nilesh Dhumal
>> > >> >> Gesendet: Dienstag, 26. Februar 2013 17:50
>> > >> >> An: Discussion list for GROMACS users
>> > >> >> Betreff: Re: AW: AW: AW: AW: [gmx-users] g_current
>> > >> >>
>> > >> >> Hello,
>> > >> >>
>> > >> >> I didn't get any segmental fault if I use Gromacs Version 4.5.5.
>> > >> >>
>> > >> >>  g_current -f md.trr -s md.tpr -mc
>> > >> >>
>> > >> >> Program didn't write the mc.xvg
>> > >> >>
>> > >> >> Average translational dipole moment is zero.
>> > >> >>
>> > >> >> Average translational dipole moment M_J [enm] after 15001 frames
>> > >> >> (|M|^2):
>> > >> >> -0.00 -0.00 -0.00 (0.00)
>> > >> >>
>> > >> >> Can you tell where is the problem?
>> > >> >>
>> > >> >> Nilesh
>> > >> >>
>> > >> >> > Hi,
>> > >> >> > I am using the release branch of 4.5.
>> > >> >> >
>> > >> >> > /Flo
>> > >> >> >
>> > >> >> > ---
>> > >> >> > Florian Dommert
>> > >> >> > Dipl. Phys.
>> > >> >> >
>> > >> >> > Institut für Computerphysik
>> > >> >> > Universität Stuttgart
>> > >> >> > Allmandring 3
>> > >> >> > D-70569 Stuttgart
>> > >> >> >
>> > >> >> > Tel.: 0711-68563613
>> > >> >> > Fax: 0711-68563658
>> > >> >> >
>> > >> >> >
>> > >> >> >> -Ursprüngliche Nachricht-
>> > >> >> >> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-
>> > >> >> >> boun...@gromacs.org] Im Auftrag von Nilesh Dhumal
>> > >> >> >> Gesendet: Montag, 25. Februar 2013 15:35
>> > >> >> >> An: Discussion list for GROMACS users
>> > >> >> >> Betreff: Re: AW: AW: AW: [gmx-users] g_current
>> > >> >> >>
>> > >> >> >> Hello,
>> > >> >> >>
>> > >> >> >> Thanks.
>> > >> >> >>
>> > >> >> >> I will update Gromacs version. Can you tell which version you
>> > >> >> >> are using ?
>> > >> >> >>
>> > >> >> >> Nilesh
>> > >> >> >>
>> > >> >> >> > Hi,
>> > >> >> >> >
>> > >> >> >> >  Can you update your Gromacs version to an actual release
>> > >> >> >> > and check if the problem still occurs. It is very strange
>> > >> >> >> > that the Einstein-Helfand fit gives
>> > >> >> >> > 0 for sigma and M_J^2.
>> > >> >> >> >
>> > >> >> >> > Cheers,
>> > >> >> >> > Flo
>> > >> >> >> >
>> > >> >

[gmx-users] Re:Gromacs auxillary tools ideas

[lloyd riggs]

Dear All,

I read a paper by Van der Groot and realized some tool regarding simple 
paersons r values, or correlation co-efficient by different names would be a 
great analytical asset for macromolecular biology.  Looking over the code, 
g:sham seems to have begun implicating such things but it loos like a caotic 
mess.  Basically, I used gnumeric, but MS excel also has functions, and you can 
take say a PC analysis, and run any other data set and see if it "Correlates", 
ie is an effect of or not related in any way too some other factor, in the case 
of PC, energy versus anything else.  All they need is say you take your 
Gaussian 10-300 trajectories as a mean in a spread sheet (ie 200-5000) data 
points in a column, and compare it with PC (or any other thing you want, 
although energy is about the most comprehensive), and it gives a linear 
correlation based on pearsons two column correlation of relation (circa 
1895)...it does allow say for a a PC, then taking several things like distance, 
hydro
 gen bonding means between 2 prtoeins, domain distance, inter protein 
movements, inter protein hydrogen bonding, LJ or coloumb, etc... and tells you 
which is the energy or correlation...would be a great asset...

And any competent programmer namless could do it in a week or two...as a 
gromacs tool...would add Bio more to funding sources...

Sincerely,

Stephan Watkins
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Re: [gmx-users] number of coordinates in coordinate file (system.gro, 10019) does not match topology (topol.top, 17093)

[Justin Lemkul]

On 3/2/13 1:42 AM, swati rana wrote:

Hi Justin,

Thanks a lot, that suggestion of yours helped. I am on the equilibration
step and its running but nothing is happening on the terminal its just
stagnant. Is it fine because its more than 17 hrs now. Is there some
problem.
After running the second command nothing is happening on the terminal.

grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr

mdrun -deffnm nvt

I am sorry as it is not a reasonable question to ask but i am just asking
out of curiosity and lack of time.



If you're trying to run an MD simulation in serial, you'll get terrible 
performance unless the system is very small (a few hundred atoms).  Most MD is 
conducted in parallel on high-performance computing clusters, or at the very 
least on a multi-core workstation, again using parallelization.


You won't get constant output in either case, since I/O is buffered and write 
intervals depend on what you specify in the .mdp file.  In any case, if you're 
getting poor performance, you're probably simply asking your computer to do 
something it's incapable of handling efficiently.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] removing number of sol

[Erik Marklund]

If you have a pdb file instead of a gro file then e.g. pymol might be  
useful.


Erik

On Mar 2, 2013, at 2:01 PM, gromacs query wrote:


Dear Erik,

I am new to Gromacs and used AMBER before, and I am exploring various
options in GROMACS too. Surely I will look in to g_select. Also as I  
was
using sed, one should include an extra space (using vi) in gro file  
just
before residue number and then can use sed to remove like this: sed - 
e '/
35SOL/d' -e '/ 36SOL/d' -e '/ 38SOL/d' -e '/ 39SOL/d' old.gro >  
new2.gro


But please note I included an extra space / 35SOL/d (instead of / 
35SOL/d)

by this sed will remove 35SOL not 135SOL.

regards,


On Fri, Mar 1, 2013 at 5:27 PM, Erik Marklund   
wrote:



Hi,

Then the problem lies in automating what molecules are to be removed,
right? Try g_select or look into trjorder.

Erik


On Mar 1, 2013, at 2:45 PM, gromacs query wrote:

Aha! thanks Erik (and Justin),


I really feel sorry 35 and 135 will be removed by sed. I must have  
given a
thought about that. So this was reason sed was over doing the  
things. Also

as you asked: They are random residue number water molecules so
not continuous and they were selected on the criteria based on X Y Z
coordinates (some space fixed and outlier waters are to be removed)

regards,


On Fri, Mar 1, 2013 at 3:09 PM, Erik Marklund 
wrote:



On Mar 1, 2013, at 2:08 PM, Erik Marklund wrote:


On Mar 1, 2013, at 1:58 PM, gromacs query wrote:


Dear Erik,



so you can filter out the unwanted residues there instead of  
using an





index file.




There are thousands of water to be removed so simple commands  
like sed

exhausts when I run it in loops. e.g. Just to say :

sed -e '/35SOL/d' -e '/36SOL/d' -e '/38SOL/d' -e '/39SOL/d' -e
'/40SOL/d'
-e '/41SOL/d' -e '/42SOL/d' -e '/43SOL/d' -e '/44SOL/d' -e '/ 
45SOL/d'

old.gro > new2.gro

this will remove such 10 residues but if you run this again and  
again

(in
text exe format) say 1000 times it exhausts some how and remove  
waters
which are not even mentioned in sed command! I have checked it  
many

times.
So I thought if index file could help me. But please reply for  
point 3:



First of all, that's not a safe way of removing waters. Note  
that both
SOL 35, SOL 135, ... will be removed by that command. Secondly,  
I'm sure
you can think of a better way of scripting it, using e.g. sed or  
awk. By

which criteria do you select the waters to be removed?



If its a contiguous chunk then it's dead simple.





3) Also once I get index file can editconf help to write a new gro





without the residues mentioned in index file?. I used this

editconf -f


my.gro -n index.ndx -o del.gro .



thanks,

This gave me del.gro having residues mentioned in index file.  
But I

want
del.gro file without the residues mentioned in index file.

On Fri, Mar 1, 2013 at 2:48 PM, Erik Marklund >

wrote:

The ndx format is really simple. You can easily script your way  
to a

new


index group as long as the selection of atoms can be automated.
Furthermore, the gro format is also simple, so you can filter  
out the

unwanted residues there instead of using an index file.

Erik


On Mar 1, 2013, at 1:42 PM, gromacs query wrote:

Dear All,


I know the residue numbers of SOL molecules (which are more  
than

thousands)
which I want to remove them from a gro file. I searched that  
make_ndx

can
be used make a index file to define residues. But It is a  
prompt

based
tool
and its difficult to type manually thousands of residue  
numbers.


1) Is there some way to feed the residue numbers to make_ndx?  
Or I

need to
make index file format my self by some scritpting Or is there  
is

rather
easier way of doing in gromacs.

2) Also is there any direct command which helps to remove a  
residue

number
directly from a gro file without using index file input; means
residue
defined in command itself?

3) Also once I get index file can editconf help to write a  
new gro

without
the residues mentioned in index file?. I used this editconf - 
f my.gro

-n
index.ndx -o del.gro .

This gave me del.gro having residues mentioned in index file.  
But I

want
del.gro file without the residues mentioned in index file.


regards,
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Re: [gmx-users] do_dssp

[Erik Marklund]

Hi,

I'll try out the 2.1.0 with do_dssp and see if there's something  
problematic with this new version. Good thing you brought it up.


Erik

On Mar 1, 2013, at 6:24 PM, Miguel Ángel Mompeán García wrote:


Hi Erik,

Since I read in the mailing list that nobody had asked about 2.1.0,  
just
decided to try an older version before going into the trouble  
itself...

Kind of coward, I know, but the troubles with that version are already
reported so that  I thought things would be easier :)
Thank-you a lot for your comments



2013/3/1 Erik Marklund 


Interesting. Perhaps there are new issues with 2.1.0. Did you try to
execute the command yourself?

Erik


On Mar 1, 2013, at 5:16 PM, Miguel Ángel Mompeán García wrote:

The issue I mentioned was with dssp-2.1.0.  I changed to 2.0.1 and it

works
fine. However, when converting the xpm to eps I get I plot very  
small,
where one barely can see the colour code and the legend is sooo  
big. Does

anyone know how to change that?





2013/3/1 Erik Marklund 

What happens if you execute the command (/usr/local/bin/dssp/ -i  
ddQ3PqtX

-o ddR1HavD) in your terminal?


Erik

On Mar 1, 2013, at 1:06 PM, Miguel Ángel Mompeán García wrote:

I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error  
you

got:



dssp cmd='/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD > /dev/ 
null 2>

/dev/null'
Reading frame   0 time0.000
Back Off! I just backed up ddQ3PqtX to ./#ddQ3PqtX.1#

---
Program do_dssp, VERSION 4.6
Source code file: /usr/local/bin/gromacs-4.6/
src/tools/gmx_do_dssp.c,

line:
667

Fatal error:
Failed to execute command: Try specifying your dssp version with  
the

-ver
option.

How can I fix that?

Thanks







2013/1/15 James Starlight 

Justin, thanks both options works perfect.




James

2013/1/15 Justin Lemkul :




On 1/15/13 7:13 AM, James Starlight wrote:



Justin,


I  want to obtain timescale on X as well as number of  
residues on Y
on the xmp graph . By  default that graph has not legend so  
it's hard

to analyse it .


The legends are printed in the .xvg header.  I've never had a

problem
plotting its contents (though they are usually somewhat  
unclear when


plotted


together) with xmgrace -nxy scount.xvg



By the way have you forced with some problems with dppc ?  
Simetimes



I've obtain error like


There are 286 residues in your selected group
dssp cmd='/usr/local/bin/dssp -i dd42GVbd -o ddpu8ln2 > /dev/ 
null 2>

/dev/null'
Reading frame   0 time0.000
Back Off! I just backed up dd42GVbd to ./#dd42GVbd.1


Fatal error:
Failed to execute command: Try specifying your dssp version  
with the

-ver option.

and I dont know how to fix it.

I'm using gromacs-4.6-beta 3 with dssp 2.0.3


Since dssp changed its command line options, Gromacs had to  
adapt as


well.


The error tells you to use the -ver option; you should do so.

Version 2
should be the default, so check to make sure you're actually  
using

that
version and not the old dssp.


-Justin

--
====


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin 
>




====

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[gmx-users] implicit solvent

[aixintiankong]

//www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
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>Message: 3
>Date: Sat, 2 Mar 2013 21:21:04 +0800 (CST)
>From: "congchen" 
>Subject: [gmx-users] Semiisotropic pressure coupling problem
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[gmx-users] Semiisotropic pressure coupling problem

[congchen]

 

Dear Gromacs users,
  I am doing a simulation on CO2/water interface. Two separate simulations (NPT) have been done sucessfully for pure CO2 and pure water systems. Then two CO2 gro files and one water gro files were connected into one single gro files for CO2/water interface (CO2/water/CO2).
  The CO2/water system was simulated in NVT ensemble first with water molecules fixed in positions for 500ps,  and then the position constraints were removed and further 500ps simulation run were made. The temperature were coupled with v-rescale method and the average value was exactly the same as the target temperature. The CO2/water system was further simulated in NPT ensemble for 3000ps, but the result seems quite bad. The average values of temperature and pressure are 344.7K and -6.89249e+02 bar, respectively, which are quite different from the targets.
  The reason may be that the system is far from equilibrium, but the simulation time for 3ns is enough for my opinion.
  I would be grateful if anyone could give me some advice. The .mdp file is listed as follows.
title    = chcwaaa;;; run control;;integrator   = md   ;a leap-frog integrator for integrating Newton's equations of motiontinit    = 0    ; default, starting time for your rundt   = 0.001    ; time step for integration, default 0.001 psnsteps   = 300   ; maximum number of steps to integrate or minimize, -1 is no maximuminit-step    = 0    ; the starting step. t=tinit + dt(init-step + i)comm-mode    = Linear   ; remove center of mass translation; Angular: remove center of mass translation and rotation around the center of massnstcomm  = 100  ; frequency for center of mass motion removalcomm-grps    = system ; groups for center of mass motion removal, default is the whole system;;; output control;;nstxout  = 5000 ; frequency to write coordinates to output trajectory file, the last coordinates are always writtennstvout  = 5000 ; frequency to write velocities to output trajectorynstfout  = 0    ; frequency to write forces to output trajectorynstlog   = 5000 ; frequency to write energies to log filenstcalcenergy    = 100  ; default, frequency for calculating energies.nstenergy    = 300  ; frequency to write energies to energy file, should be a multiple of nstcalcenergynstxtcout    = 300  ; frequency to write coordinates to xtc trajectoryxtc-precision    = 1000 ; precision to write to xtc trajectory, defaultxtc-grps = system   ; default the whole systemenergygrps   = system   ; groups to write to energy file;;; neighbor searching;;cutoff-scheme    = Verlet   ; generate a pair list with buffering.nstlist  = 10   ; default, frequency to update the neighbor listns-type  = grid ; make a grid in the box and only check atoms in neighboring grid cells when constructing a new neighbor list.pbc  = xyzperiodic-molecules   = no   ; molecules are finite, defaultverlet-buffer-drift  = 0.005    ; This sets the target energy drift per particle caused by the Verlet buffer, which indirectly sets rlist.rlist    = 1  ; With cutoff-scheme=Verlet, this is by default set by the verlet-buffer-drift option and the value of rlist is ignorednstcalclr    = 1;;; electrostatics;;coulombtype  = PME  ;Fast smooth Particle-Mesh Ewald (SPME) electrostaticscoulomb-modifier = Potential-shift-Verletrcoulomb = 1.6  ;distance for the Coulomb cut-off ;;; vdw;;vdwtype  = Cut-offvdw-modifier = Potential-shift-Verletrvdw = 1.6DispCorr = EnerPres  ;apply long range dispersion corrections for Energy and Pressure ;;; Ewald;;fourierspacing   = 0.12  ;pme-order    = 4ewald-rtol   

Re: [gmx-users] removing number of sol

[gromacs query]

Dear Erik,

I am new to Gromacs and used AMBER before, and I am exploring various
options in GROMACS too. Surely I will look in to g_select. Also as I was
using sed, one should include an extra space (using vi) in gro file just
before residue number and then can use sed to remove like this: sed -e '/
35SOL/d' -e '/ 36SOL/d' -e '/ 38SOL/d' -e '/ 39SOL/d' old.gro > new2.gro

But please note I included an extra space / 35SOL/d (instead of /35SOL/d)
by this sed will remove 35SOL not 135SOL.

regards,


On Fri, Mar 1, 2013 at 5:27 PM, Erik Marklund  wrote:

> Hi,
>
> Then the problem lies in automating what molecules are to be removed,
> right? Try g_select or look into trjorder.
>
> Erik
>
>
> On Mar 1, 2013, at 2:45 PM, gromacs query wrote:
>
>  Aha! thanks Erik (and Justin),
>>
>> I really feel sorry 35 and 135 will be removed by sed. I must have given a
>> thought about that. So this was reason sed was over doing the things. Also
>> as you asked: They are random residue number water molecules so
>> not continuous and they were selected on the criteria based on X Y Z
>> coordinates (some space fixed and outlier waters are to be removed)
>>
>> regards,
>>
>>
>> On Fri, Mar 1, 2013 at 3:09 PM, Erik Marklund 
>> wrote:
>>
>>
>>> On Mar 1, 2013, at 2:08 PM, Erik Marklund wrote:
>>>
>>>
>>>  On Mar 1, 2013, at 1:58 PM, gromacs query wrote:

 Dear Erik,

>
> so you can filter out the unwanted residues there instead of using an
>
>>
>>>  index file.
>>
>
> There are thousands of water to be removed so simple commands like sed
> exhausts when I run it in loops. e.g. Just to say :
>
> sed -e '/35SOL/d' -e '/36SOL/d' -e '/38SOL/d' -e '/39SOL/d' -e
> '/40SOL/d'
> -e '/41SOL/d' -e '/42SOL/d' -e '/43SOL/d' -e '/44SOL/d' -e '/45SOL/d'
> old.gro > new2.gro
>
> this will remove such 10 residues but if you run this again and again
> (in
> text exe format) say 1000 times it exhausts some how and remove waters
> which are not even mentioned in sed command! I have checked it many
> times.
> So I thought if index file could help me. But please reply for point 3:
>
>
 First of all, that's not a safe way of removing waters. Note that both
 SOL 35, SOL 135, ... will be removed by that command. Secondly, I'm sure
 you can think of a better way of scripting it, using e.g. sed or awk. By
 which criteria do you select the waters to be removed?


>>> If its a contiguous chunk then it's dead simple.
>>>
>>>
>>>
>>>
  3) Also once I get index file can editconf help to write a new gro
>
>>
  without the residues mentioned in index file?. I used this
>>> editconf -f
>>>
>> my.gro -n index.ndx -o del.gro .
>
>
> thanks,
>
> This gave me del.gro having residues mentioned in index file. But I
> want
> del.gro file without the residues mentioned in index file.
>
> On Fri, Mar 1, 2013 at 2:48 PM, Erik Marklund 
> wrote:
>
> The ndx format is really simple. You can easily script your way to a
> new
>
>> index group as long as the selection of atoms can be automated.
>> Furthermore, the gro format is also simple, so you can filter out the
>> unwanted residues there instead of using an index file.
>>
>> Erik
>>
>>
>> On Mar 1, 2013, at 1:42 PM, gromacs query wrote:
>>
>> Dear All,
>>
>>
>>> I know the residue numbers of SOL molecules (which are more than
>>> thousands)
>>> which I want to remove them from a gro file. I searched that make_ndx
>>> can
>>> be used make a index file to define residues. But It is a prompt
>>> based
>>> tool
>>> and its difficult to type manually thousands of residue numbers.
>>>
>>> 1) Is there some way to feed the residue numbers to make_ndx? Or I
>>> need to
>>> make index file format my self by some scritpting Or is there is
>>> rather
>>> easier way of doing in gromacs.
>>>
>>> 2) Also is there any direct command which helps to remove a residue
>>> number
>>> directly from a gro file without using index file input; means
>>> residue
>>> defined in command itself?
>>>
>>> 3) Also once I get index file can editconf help to write a new gro
>>> without
>>> the residues mentioned in index file?. I used this editconf -f my.gro
>>> -n
>>> index.ndx -o del.gro .
>>>
>>> This gave me del.gro having residues mentioned in index file. But I
>>> want
>>> del.gro file without the residues mentioned in index file.
>>>
>>>
>>> regards,
>>> --
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[gmx-users] Fw:some waters in active site of receptor

[aixintiankong]

Dear,
there are three waters in active site of receptor,mediating the binding of 
ligand with target protein. i want to study the three waters how to affect the 
binding of ligand with target protein and the contribution to the stability of 
the system.
   In order to avoid the three waters exchange with the solvent waters, can i 
do the ligand-receptor in the implicit solvent. i will prepare two  diffrent 
recepor mode. The one is not water in active site and the other retain waters 
in the active site. my ideal is good or not?
 








 Forwarding messages 
From: aixintiankong 
Date: 2013-02-16 23:54:51
To: gmx-users@gromacs.org
Subject: some waters in active site of receptor

Dear,
 there are three waters in active site of receptor, mediating the binding 
of ligand with target protein. i want to study the three waters how to affect 
the binding of ligand with target protein and the contribution to the stability 
of the system.
 In order to study the role of the waters, i want to compare some diffrent 
system models. The first model have all a waters in active site ,the second 
model have two waters and the third have one water , the fourth have none water 
in acitve site. however, i don't know how to construct simulation models  of 
those. when i use the genbox program to add solvent to my system,  i find there 
are many other waters being added to the active site and i think the waters 
which are added by genbox program  maybe replace the initial three waters and 
then i can't study the waters in active site.
 please hlpe me and then tell me how to do it
Thank you very much!





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