[gmx-users] column no 1 , 2 and 3? of " hbnum.xvg " file? Re: gromacs.org_gmx-users Digest, Vol 157, Issue 135

[Adarsh V. K.]

So how can we conclude about column no 1 , 2 and 3 of " hbnum.xvg " file?

   2. Re: Third column of the " hbnum.xvg " file?...What is it
>   meant for ? (Erik Marklund)
>3. Re: Third column of the " hbnum.xvg " file?...What is it
>   meant for ? (Justin Lemkul)
> -
>
> Message: 2
> Date: Sat, 27 May 2017 18:44:19 +
> From: Erik Marklund 
> To: "gmx-us...@gromacs.org" 
> Subject: Re: [gmx-users] Third column of the " hbnum.xvg "
> file?...What is it meant for ?
>
> Hi Mark,
>
> Thinking out loud: ?Non-Hbonding pairs within 3.5 ??.
>
> Kind regards,
> Erik
>
> > On 27 May 2017, at 17:56, Mark Abraham  wrote:
> >
> > Hi,
> >
> > So what should we document in the help text as the meaning, so we don't
> > keep having emails about this?
> >
> > Mark
> >
> > On Sat, May 27, 2017 at 4:36 PM Erik Marklund 
> > wrote:
> >
> >>
> >>
> >> On 26 May 2017, at 22:12, David van der Spoel  >> > wrote:
> >>
> >> On 26/05/17 22:05, Erik Marklund wrote:
> >> ?Pairs within 0.35 nm?. They also don?t fulfil the angle criterion,
> which
> >> is why they are sometimes fewer than the hbonds.
> >>
> >> Therefore I would assume they are more instead.
> >>
> >>
> >> They sometimes are, but not necessarily. I pointed it out because
> >> sometimes people ask if g_hbond is buggy when they see that there are
> >> occasionally lower numbers in the third column, assuming that it
> contains
> >> all pairs within 3.5 ? regardless of angle which should more numeorus
> than
> >> the pairs that also fullfil the angle criterion. That?s not the meaning
> of
> >> the third column however.
> >>
> >> Kind regards,
> >> Erik
> >>
> >> On 26 May 2017, at 19:38, Adarsh V. K.  >> > wrote:
> >>
> >> Dear all,
> >>
> >> The 'gmx hbond' command returns a *.xvg file... viz. " hbnum.xvg "
> >>
> >> I would like to edit the file before viewing in 'Xmgrace'
> >>
> >> I opened the hbnum.xvg using 'gedit'. It shows following details (see
> >> below)
> >>
> >> Can you please tell me what is there in the third column of the file?
> >>
> >> -
> >> # gmx hbond is part of G R O M A C S:
> >> #
> >> # GROtesk MACabre and Sinister
> >> #
> >> @title "Hydrogen Bonds"
> >> @xaxis  label "Time (ps)"
> >> @yaxis  label "Number"
> >> @TYPE xy
> >> @ view 0.15, 0.15, 0.75, 0.85
> >> @ legend on
> >> @ legend box on
> >> @ legend loctype view
> >> @ legend 0.78, 0.8
> >> @ legend length 2
> >> @ s0 legend "Hydrogen bonds"
> >> @ s1 legend "Pairs within 0.35 nm"
> >>   02   7
> >>  10   2   5
> >>  20   4   3
> >>  30   3   2
> >>  40   3   3
> >>  50   5   1
> >>  60   3   6
> >>  70   3   6
> >>  80   2   3
> >>  90   5   1
> >> 100  3   3
> >> --
> >> Gromacs Users mailing list
> >>
>
> -
>
> Message: 3
> Date: Sat, 27 May 2017 14:46:21 -0400
> From: Justin Lemkul 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Third column of the " hbnum.xvg "
> file?...What is it meant for ?
> Message-ID: <0cbf8255-3416-b725-7afd-87d442905...@vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
> On 5/27/17 2:44 PM, Erik Marklund wrote:
> > Hi Mark,
> >
> > Thinking out loud: ?Non-Hbonding pairs within 3.5 ??.
> >
>
> I think it should be more explicit, and exactly what we always tell people:
>
> -num:  number of hydrogen bonds as a function of time. The second column
> contains the number of atom pairs that satisfy the distance criterion but
> not
> the angle criterion for hydrogen bonding.
>
> -Justin
>
> > Kind regards,
> > Erik
> >
> >> On 27 May 2017, at 17:56, Mark Abraham 
> wrote:
> >>
> >> Hi,
> >>
> >> So what should we document in the help text as the meaning, so we don't
> >> keep having emails about this?
> >>
> >> Mark
> >>
> >> On Sat, May 27, 2017 at 4:36 PM Erik Marklund  >
> >> wrote:
> >>
> >>>
> >>>
> >>> On 26 May 2017, at 22:12, David van der Spoel  >>> > wrote:
> >>>
> >>> On 26/05/17 22:05, Erik Marklund wrote:
> >>> ?Pairs within 0.35 nm?. They also don?t fulfil the angle criterion,
> which
> >>> is why they are sometimes fewer than the hbonds.
> >>>
> >>> Therefore I would assume they are more instead.
> >>>
> >>>
> >>> They sometimes are, but not necessarily. I pointed it out because
> >>> sometimes people ask if g_hbond is buggy when they see that there are
> >>> occasionally lower numbers in the third column, assuming that it
> contains
> >>> all pairs within 3.5 ? regardless of angle which should more numeorus
> than
> >>> the pairs that also fullfil the angle criterion. That?s not the
> mean

[gmx-users] Genion error

[‪Mohammad Roostaie‬ ‪]

Hi All, when I wanted to add ions to the system, I got this error:
Fatal error:No line with moleculetype 'SOL' found the [ molecules ] section of 
file 'gr.top'For more information and tips for troubleshooting, please check 
the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors
However, there is 'SOL' molecule type in the [ molecules ] section of the 
topology file. Can you please help me to solve this problem?
Thanks,Mohammad
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Re: [gmx-users] column no 1 , 2 and 3? of " hbnum.xvg " file? Re: gromacs.org_gmx-users Digest, Vol 157, Issue 135

[David van der Spoel]

On 28/05/17 09:30, Adarsh V. K. wrote:

So how can we conclude about column no 1 , 2 and 3 of " hbnum.xvg " file?


As it says in the legend:
@ s0 legend "Hydrogen bonds"
@ s1 legend "Pairs within 0.35 nm"

Note that s1 does NOT include s0.



   2. Re: Third column of the " hbnum.xvg " file?...What is it

  meant for ? (Erik Marklund)
   3. Re: Third column of the " hbnum.xvg " file?...What is it
  meant for ? (Justin Lemkul)
-

Message: 2
Date: Sat, 27 May 2017 18:44:19 +
From: Erik Marklund 
To: "gmx-us...@gromacs.org" 
Subject: Re: [gmx-users] Third column of the " hbnum.xvg "
file?...What is it meant for ?

Hi Mark,

Thinking out loud: ?Non-Hbonding pairs within 3.5 ??.

Kind regards,
Erik


On 27 May 2017, at 17:56, Mark Abraham  wrote:

Hi,

So what should we document in the help text as the meaning, so we don't
keep having emails about this?

Mark

On Sat, May 27, 2017 at 4:36 PM Erik Marklund 
wrote:




On 26 May 2017, at 22:12, David van der Spoel mailto:sp...@xray.bmc.uu.se>> wrote:

On 26/05/17 22:05, Erik Marklund wrote:
?Pairs within 0.35 nm?. They also don?t fulfil the angle criterion,

which

is why they are sometimes fewer than the hbonds.

Therefore I would assume they are more instead.


They sometimes are, but not necessarily. I pointed it out because
sometimes people ask if g_hbond is buggy when they see that there are
occasionally lower numbers in the third column, assuming that it

contains

all pairs within 3.5 ? regardless of angle which should more numeorus

than

the pairs that also fullfil the angle criterion. That?s not the meaning

of

the third column however.

Kind regards,
Erik

On 26 May 2017, at 19:38, Adarsh V. K. mailto:adarsh_p13008...@nitc.ac.in>> wrote:

Dear all,

The 'gmx hbond' command returns a *.xvg file... viz. " hbnum.xvg "

I would like to edit the file before viewing in 'Xmgrace'

I opened the hbnum.xvg using 'gedit'. It shows following details (see
below)

Can you please tell me what is there in the third column of the file?

-
# gmx hbond is part of G R O M A C S:
#
# GROtesk MACabre and Sinister
#
@title "Hydrogen Bonds"
@xaxis  label "Time (ps)"
@yaxis  label "Number"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "Hydrogen bonds"
@ s1 legend "Pairs within 0.35 nm"
  02   7
 10   2   5
 20   4   3
 30   3   2
 40   3   3
 50   5   1
 60   3   6
 70   3   6
 80   2   3
 90   5   1
100  3   3
--
Gromacs Users mailing list



-

Message: 3
Date: Sat, 27 May 2017 14:46:21 -0400
From: Justin Lemkul 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Third column of the " hbnum.xvg "
file?...What is it meant for ?
Message-ID: <0cbf8255-3416-b725-7afd-87d442905...@vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed


On 5/27/17 2:44 PM, Erik Marklund wrote:

Hi Mark,

Thinking out loud: ?Non-Hbonding pairs within 3.5 ??.



I think it should be more explicit, and exactly what we always tell people:

-num:  number of hydrogen bonds as a function of time. The second column
contains the number of atom pairs that satisfy the distance criterion but
not
the angle criterion for hydrogen bonding.

-Justin


Kind regards,
Erik


On 27 May 2017, at 17:56, Mark Abraham 

wrote:


Hi,

So what should we document in the help text as the meaning, so we don't
keep having emails about this?

Mark

On Sat, May 27, 2017 at 4:36 PM Erik Marklund 


wrote:




On 26 May 2017, at 22:12, David van der Spoel mailto:sp...@xray.bmc.uu.se>> wrote:

On 26/05/17 22:05, Erik Marklund wrote:
?Pairs within 0.35 nm?. They also don?t fulfil the angle criterion,

which

is why they are sometimes fewer than the hbonds.

Therefore I would assume they are more instead.


They sometimes are, but not necessarily. I pointed it out because
sometimes people ask if g_hbond is buggy when they see that there are
occasionally lower numbers in the third column, assuming that it

contains

all pairs within 3.5 ? regardless of angle which should more numeorus

than

the pairs that also fullfil the angle criterion. That?s not the

meaning of

the third column however.

Kind regards,
Erik

On 26 May 2017, at 19:38, Adarsh V. K. mailto:adarsh_p13008...@nitc.ac.in>> wrote:

Dear all,

The 'gmx hbond' command returns a *.xvg file... viz. " hbnum.xvg "

I would like to edit the file before viewing in 'Xmgrace'

I opened the hbnum.xvg using 'gedit'. It shows following details (see
below)

Can you please tell me what is there in the third column of the file?

[gmx-users] appropriate tau-p for surface tension coupling

[Ali Shomali]

Hello to all dear gromacs users
I'm simulating a monolayer using pcouple= surface tension and as manual
says my converged area per lipid and surface tension are very much
dependable on the value of tau-p , so can some one help me how can I make
sure that my tau-p value is OK?
thanks
Ali
mdp script:
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 500 ;  (10 ns)
dt= 0.001 ; 1 fs
; Output control
nstxout = 10 ; save coordinates every 0.2 ps
nstvout = 10 ; save velocities every 0.2 ps
nstenergy = 500 ; save energies every 0.2 ps
nstlog = 1000 ; update log file every 0.2 ps
; Bond parameters
continuation = yes; Restarting after NVT
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds; all bonds (even heavy atom-H bonds)
constrained
lincs_iter = 1; accuracy of LINCS
lincs_order = 4; also related to accuracy
; Neighborsearching
cutoff-scheme = Verlet
ns_type = grid ; search neighboring grid cels
nstlist = 10; 10 fs
rlist = 1.4 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm)
rvdw = 1.4 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4; cubic interpolation
vdwtype = Cut-off
; Temperature coupling is on
tcoupl =  berendsen; More accurate thermostat
tc-grps =  SOL OCT ; three coupling groups - more accurate
tau_t = 0.5 0.5  ; time constant, in ps
ref_t = 300 300; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl = berendsen; Pressure coupling on in NPT
pcoupltype = surface-tension; uniform scaling of x-y box vectors,
independent z
tau_p = 1.0 1.0; time constant, in ps
ref_p = 800 1.0; reference pressure, x-y, z (in bar)
compressibility = 4.5e-5 0 ; isothermal compressibility, bar^-1
; Periodic boundary conditions
pbc= xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no ; Velocity generation is off
; COM motion removal
; These options remove motion of the protein/bilayer relative to the
solvent/ions
nstcomm = 10
comm-mode   = Linear
comm-grps   = SOL OCT
-- 
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* Please search the archive at 
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* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

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[gmx-users] Invalid directive impropers

[Saeed Nasiri]

Dear all

I created the topol.top and itp files for a specific molecules manually,
but the "grompp" could not  read the improper dihedral. I checked th
tutorials and previous emails, but I did not find about this problem or how
to defined the improper dihedral.

Any help will highly appreciated.
*

*gmx_mpi grompp -f minim.mdp -c M1M2_solv.gro -p topol.top -o em.tpr*
  :-) GROMACS - gmx grompp, VERSION 5.1.2 (-:

GROMACS is written by:
 Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar
Bjelkmar
 Aldert van Buuren   Rudi van Drunen Anton Feenstra   Sebastian Fritsch
  Gerrit Groenhof   Christoph Junghans   Anca HamuraruVincent Hindriksen
 Dimitrios KarkoulisPeter KassonJiri Kraus  Carsten Kutzner
Per Larsson  Justin A. Lemkul   Magnus Lundborg   Pieter Meulenhoff
   Erik Marklund  Teemu Murtola   Szilard Pall   Sander Pronk
   Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
   Peter TielemanTeemu Virolainen  Christian WennbergMaarten Wolf
   and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:  gmx grompp, VERSION 5.1.2
Executable:   /usr/local/gromacs/bin/gmx_mpi
Data prefix:  /usr/local/gromacs
Command line:
  gmx_mpi grompp -f minim.mdp -c M1M2_solv.gro -p topol.top -o em.tpr


Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#

NOTE 1 [file minim.mdp]:
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
  that with the Verlet scheme, nstlist has no effect on the accuracy of
  your simulation.

Setting the LD random seed to 3819485409
Generated 105 of the 105 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 105 of the 105 1-4 parameter combinations























*ERROR 1 [file M1.itp, line 224]:  Invalid directive impropersERROR 2 [file
M1.itp, line 226]:  No default Proper Dih. typesERROR 3 [file M1.itp, line
227]:  No default Proper Dih. typesERROR 4 [file M1.itp, line 229]:  No
default Proper Dih. typesERROR 5 [file M1.itp, line 231]:  No default
Proper Dih. typesERROR 6 [file M1.itp, line 232]:  No default Proper Dih.
types*

---
Program gmx grompp, VERSION 5.1.2
Source code file:
/home/home/gromacs-5.1.2/src/gromacs/gmxpreprocess/toppush.c, line: 1353

Fatal error:
Atomtype opls_111 not found
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Halting program gmx grompp
--
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.



topol.top#
#inM2ude "ff_M1.itp"
#inM2ude "M1.itp"
#inM2ude "M2.itp"

; InM2ude water topology
#inM2ude "oplsaa.ff/tip3p.itp"

[system]
M1 M2

[molecules]
M11
M2  1

SOL   858
SOL   858
###ff_M1.itp###
[ defaults ]
; nbfunccomb-rulegen-pairsfudgeLJfudgeQQ
 13   yes0.5  0.5

[ atomtypes ]

;nameat.nummasschargeptypeV(c6)
W(c12)
C1612.011-0.17A3.500.27614
C2612.0110.01A3.500.27614
CE612.011-0.05A3.500.27614
CS612.011-0.12A3.500.27614
CT612.011-0.18A3.500.27614
CR612.011-0.11A3.550.29288
CW612.011-0.13A3.550.29288
HA11.0080.21A2.420.12552
HCR11.0080.21A2.420.12552
HCW11.0080.21A2.420.12552
HC11.0080.06A2.500.12552
H111.0080.13A2.500.12552
NA714.007   

Re: [gmx-users] Genion error

[Justin Lemkul]

On 5/28/17 3:43 AM, ‪Mohammad Roostaie‬ ‪ wrote:

Hi All, when I wanted to add ions to the system, I got this error:
Fatal error:No line with moleculetype 'SOL' found the [ molecules ] section of 
file 'gr.top'For more information and tips for troubleshooting, please check 
the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors
However, there is 'SOL' molecule type in the [ molecules ] section of the 
topology file. Can you please help me to solve this problem?


Upload your topology to a file-sharing service and provide the URL to access it. 
 There's no way to know what's going on (and I recall giving some previous 
advice about line endings - have you checked this?)


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Invalid directive impropers

[Justin Lemkul]

On 5/28/17 3:40 PM, Saeed Nasiri wrote:

Dear all

I created the topol.top and itp files for a specific molecules manually,
but the "grompp" could not  read the improper dihedral. I checked th
tutorials and previous emails, but I did not find about this problem or how
to defined the improper dihedral.



There's no such thing as a [impropers] directive.  They're just [dihedrals] with 
an appropriate function type.  See Table 5.5 in the PDF manual.


-Justin


Any help will highly appreciated.
*

*gmx_mpi grompp -f minim.mdp -c M1M2_solv.gro -p topol.top -o em.tpr*
   :-) GROMACS - gmx grompp, VERSION 5.1.2 (-:

 GROMACS is written by:
  Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar
Bjelkmar
  Aldert van Buuren   Rudi van Drunen Anton Feenstra   Sebastian Fritsch
   Gerrit Groenhof   Christoph Junghans   Anca HamuraruVincent Hindriksen
  Dimitrios KarkoulisPeter KassonJiri Kraus  Carsten Kutzner
 Per Larsson  Justin A. Lemkul   Magnus Lundborg   Pieter Meulenhoff
Erik Marklund  Teemu Murtola   Szilard Pall   Sander Pronk
Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
Peter TielemanTeemu Virolainen  Christian WennbergMaarten Wolf
and the project leaders:
 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:  gmx grompp, VERSION 5.1.2
Executable:   /usr/local/gromacs/bin/gmx_mpi
Data prefix:  /usr/local/gromacs
Command line:
   gmx_mpi grompp -f minim.mdp -c M1M2_solv.gro -p topol.top -o em.tpr


Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#

NOTE 1 [file minim.mdp]:
   With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
   that with the Verlet scheme, nstlist has no effect on the accuracy of
   your simulation.

Setting the LD random seed to 3819485409
Generated 105 of the 105 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 105 of the 105 1-4 parameter combinations























*ERROR 1 [file M1.itp, line 224]:  Invalid directive impropersERROR 2 [file
M1.itp, line 226]:  No default Proper Dih. typesERROR 3 [file M1.itp, line
227]:  No default Proper Dih. typesERROR 4 [file M1.itp, line 229]:  No
default Proper Dih. typesERROR 5 [file M1.itp, line 231]:  No default
Proper Dih. typesERROR 6 [file M1.itp, line 232]:  No default Proper Dih.
types*

---
Program gmx grompp, VERSION 5.1.2
Source code file:
/home/home/gromacs-5.1.2/src/gromacs/gmxpreprocess/toppush.c, line: 1353

Fatal error:
Atomtype opls_111 not found
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Halting program gmx grompp
--
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.



topol.top#
#inM2ude "ff_M1.itp"
#inM2ude "M1.itp"
#inM2ude "M2.itp"

; InM2ude water topology
#inM2ude "oplsaa.ff/tip3p.itp"

[system]
M1 M2

[molecules]
M11
M2  1

SOL   858
SOL   858
###ff_M1.itp###
[ defaults ]
; nbfunccomb-rulegen-pairsfudgeLJfudgeQQ
  13   yes0.5  0.5

[ atomtypes ]

;nameat.nummasschargeptypeV(c6)
W(c12)
 C1612.011-0.17A3.500.27614
 C2612.0110.01A3.500.27614
 CE612.011-0.05A3.500.27614
 CS612.011-0.12A3.500.27614
 CT612.011-0.18A3.500.27614
 CR612.011-0.11A3.550.29288
 CW612.011-0.13A3.550.29288
 HA11.0080.21A2.420.12552
 HCR11.0080.21A2.420.1255

[gmx-users] Regarding centering the molecule/protein during Simulation

[Dilip H N]

Hello,
I have ran a md simulation of a amino-acid with solvent mixture. Now i view
the trajectory in vmd and see tht the amino-acid moves sometimes toward the
edge of the box,sometimes towards the corners and so on...
 Now how can i centre only the amino-acid to the centre of the box and rest
(ie.,solvent mixture) to move as it is..ie., if i view the trajectory in
vmd i want to fix only the amino-acid to be in centre,whereas the solvent
mixtures to move around during the trajectory...
How can i do this,...??

Thank you...

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



   Sent with Mailtrack

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Re: [gmx-users] Regarding centering the molecule/protein during Simulation

[Saumyak Mukherjee]

Hi Dilip,

To fix the amino acid at the centre of the box first you have to use -c
flag with editconf. Later, during simulation you have to use
define=-dposres in the mdp file. This will include the position restrain
defined in the posre.itp file generated during the use of pdb2gmx.

Best,
Saumyak

On 29 May 2017 at 10:59, Dilip H N  wrote:

> Hello,
> I have ran a md simulation of a amino-acid with solvent mixture. Now i view
> the trajectory in vmd and see tht the amino-acid moves sometimes toward the
> edge of the box,sometimes towards the corners and so on...
>  Now how can i centre only the amino-acid to the centre of the box and rest
> (ie.,solvent mixture) to move as it is..ie., if i view the trajectory in
> vmd i want to fix only the amino-acid to be in centre,whereas the solvent
> mixtures to move around during the trajectory...
> How can i do this,...??
>
> Thank you...
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
>
>
>
>    Sent with Mailtrack
>  referral=cy16f01.di...@nitk.edu.in&idSignature=22>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>



-- 

*Saumyak Mukherjee*

Junior Research Fellow
Prof. Biman Bagchi's Group
Solid State and Structural Chemistry Unit
Indian Institute of Science
Bangalore - 560012

Mob : 8017292426
Alternative e-mail : saumyakmukher...@gmail.com
smukher...@sscu.iisc.ernet.in

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