Re: [gmx-users] Cut-offs in gromacs

[David van der Spoel]

Lum Nforbi wrote:

Dear all,
 
I did two md simulations of 200 particles each of a 
lennard-jones fluid. One of them gave me the correct pair distribution 
function for a lennard-jones fluid (converging to 1) and one did not 
(converging to zero). I have attached the .mdp files for both systems 
below. The barostats are different but I don't think this is the cause. 
I think that one worked because of the cut-off specifications (rlist, 
rvdw and rcoulomb), but I am not sure of the explanation of how the 
cut-off values can influence the shape of a pair distribution function. 
The fourier spacing in both parameter files are also different.
Please, if someone knows how these cut-off values and maybe 
fourier spacing could influence the shape of a pair distribution 
function, let me know the explanation.




If your rdf goes to zero you have a gas. Your box has probably expanded 
a lot. Please check the density.



.mdp file which gave the plot which converges to zero:

title= NPT simulation of a LJ FLUID
cpp  = /lib/cpp
include  = -I../top
define   =
integrator   = md ; a leap-frog algorithm for 
integrating Newton's equations of motion

dt   = 0.002  ; time-step in ps
nsteps   = 50 ; total number of steps; total 
time (1 ns)

nstcomm  = 1  ; frequency for com removal
nstxout  = 500; freq. x_out
nstvout  = 500; freq. v_out
nstfout  = 0  ; freq. f_out
nstlog   = 50 ; energies to log file
nstenergy= 50 ; energies to energy file
nstlist  = 10 ; frequency to update neighbour list
ns_type  = grid   ; neighbour searching type
rlist= 1.0; cut-off distance for the short 
range neighbour list
pbc  = xyz; Periodic boundary 
conditions:xyz, use periodic boundary conditions in all directions
periodic_molecules   = no ; molecules are finite, fast 
molecular pbc can be used

coulombtype  = PME; particle-mesh-ewald electrostatics
rcoulomb = 1.0; distance for the coulomb cut-off
vdw-type = Cut-off; van der Waals interactions
rvdw = 1.0; distance for the LJ or 
Buckingham cut-off
fourierspacing   = 0.12   ; max. grid spacing for the FFT 
grid for PME
fourier_nx   = 0  ; highest magnitude in reciprocal 
space when using Ewald
fourier_ny   = 0  ; highest magnitude in reciprocal 
space when using Ewald
fourier_nz   = 0  ; highest magnitude in reciprocal 
space when using Ewald

pme_order= 4  ; cubic interpolation order for PME
ewald_rtol   = 1e-5   ; relative strength of the 
Ewald-shifted direct potential
optimize_fft = yes; calculate optimal FFT plan for 
the grid at start up.

DispCorr = no ;
Tcoupl   = v-rescale  ; temp. coupling with vel. 
rescaling with a stochastic term.

tau_t= 0.1; time constant for coupling
tc-grps  = OXY; groups to couple separately to 
temp. bath

ref_t= 80 ; ref. temp. for coupling
Pcoupl   = berendsen  ; exponential relaxation pressure 
coupling (box is scaled every timestep)
Pcoupltype   = isotropic  ; box expands or contracts evenly 
in all directions (xyz) to maintain proper pressure

tau_p= 0.5; time constant for coupling (ps)
compressibility  = 4.5e-5 ; compressibility of solvent used 
in simulation

ref_p= 1.0; ref. pressure for coupling (bar)
gen_vel  = yes; generate velocities according to 
a Maxwell distr. at gen_temp

gen_temp = 80 ; temperature for Maxwell distribution
gen_seed = 173529 ; used to initialize random 
generator for random velocities


.mdp file which gave the plot which converges to 1:

title= NPT simulation of a LJ FLUID
cpp  = /lib/cpp
include  = -I../top
define   =
integrator   = md   ; a leap-frog algorithm for 
integrating Newton's equations of motion

dt   = 0.002; time-step in ps
nsteps   = 50   ; total number of steps; total 
time (1 ns)

nstcomm  = 1; frequency for com removal
nstxout  = 1000 ; freq. x_out
nstvout  = 1000 ; freq. v_out
nstfout  = 0; freq. f_out
nstlog   = 500  ; energies to log

Re: [gmx-users] writing forces in gromacs

[Amit Choubey]

Hi Berk.

Thanks a lot. I did not know that.

Amit

On Mon, Feb 22, 2010 at 11:57 PM, Berk Hess  wrote:

>  Hi,
>
> This note is printed when output files will be "large", large is defined as
> more than 2 GB.
> Not writing forces just gets you under this limit.
>
> Berk
>
> --
> Date: Mon, 22 Feb 2010 23:52:13 -0800
> From: kgp.a...@gmail.com
> To: gmx-users@gromacs.org
> Subject: [gmx-users] writing forces in gromacs
>
>
> Hi everyone,
>
> I had been trying to work with forces of the atoms and stumbled upon
> something weird.
>
> In my md.mdp file i ask to write forces with a certain frequency then the
> grompp shows a seemingly harmless note, the full md.mdp and extract of the
> grompp.out are as follows :-
>
> title   =  Yo
> cpp =  /usr/bin/cpp
> constraints =  none
> integrator  =  md
> dt  =  0.002 ; ps !
> nsteps  =  8500 ; total 17 ps.
> nstcomm =  0
> nstxout =  500
> nstvout =  500
> *nstfout =   500*
> nstlog  =  100
> nstenergy   =  10
> nstlist =  10
> ns_type =  grid
> rlist   =  1.3
> coulombtype=  Reaction-Field-zero
> rcoulomb=  1.0
> epsilon_rf=  0
> vdwtype=  Shift
> rvdw=  1.0
> rvdw_switch=  0.9
> Tcoupl  =  no
> energygrps  =   DPPC SOL
> Pcoupl  =  no
> gen_vel =  no
> lincs_iter=   2
>
> Ignoring obsolete mdp entry 'title'
> Ignoring obsolete mdp entry 'cpp'
> checking input for internal consistency...
> Opening library file
> /home/hpc-23/vedadi/gromacs-4.0.5/tmp/share/gromacs/top/ffgmx.itp
> Opening library file
> /home/hpc-23/vedadi/gromacs-4.0.5/tmp/share/gromacs/top/ffgmxnb.itp
> Opening library file
> /home/hpc-23/vedadi/gromacs-4.0.5/tmp/share/gromacs/top/ffgmxbon.itp
> Opening library file
> /home/hpc-23/vedadi/gromacs-4.0.5/tmp/share/gromacs/top/ff_dum.itp
> Generated 1369 of the 2211 non-bonded parameter combinations
> Opening library file
> /home/hpc-23/vedadi/gromacs-4.0.5/tmp/share/gromacs/top/spc.itp
> Excluding 3 bonded neighbours molecule type 'DPPC'
> Excluding 2 bonded neighbours molecule type 'SOL'
> processing coordinates...
> double-checking input for internal consistency...
> renumbering atomtypes...
> converting bonded parameters...
> initialising group options...
> processing index file...
> Opening library file
> /home/hpc-23/vedadi/gromacs-4.0.5/tmp/share/gromacs/top/aminoacids.dat
> Making dummy/rest group for T-Coupling containing 1933647 elements
> Making dummy/rest group for Acceleration containing 1933647 elements
> Making dummy/rest group for Freeze containing 1933647 elements
> Making dummy/rest group for VCM containing 1933647 elements
> Number of degrees of freedom in T-Coupling group rest is 3924894.00
> Making dummy/rest group for User1 containing 1933647 elements
> Making dummy/rest group for User2 containing 1933647 elements
> Making dummy/rest group for XTC containing 1933647 elements
> Making dummy/rest group for Or. Res. Fit containing 1933647 elements
> Making dummy/rest group for QMMM containing 1933647 elements
> T-Coupling   has 1 element(s): rest
> Energy Mon.  has 2 element(s): DPPC SOL
> Acceleration has 1 element(s): rest
> Freeze   has 1 element(s): rest
> User1has 1 element(s): rest
> User2has 1 element(s): rest
> VCM  has 1 element(s): rest
> XTC  has 1 element(s): rest
> Or. Res. Fit has 1 element(s): rest
> QMMM has 1 element(s): rest
> Checking consistency between energy and charge groups...
>
> *NOTE 1 [file nve.mdp, line unknown]:*
>   This run will generate roughly 2493 Mb of data
>
> writing run input file...
>
> There was 1 note
>
> gcq#197: "I Do It All the Time" (Magnapop)
>
>  :-)  G  R  O  M  A  C  S  (-:
>
>
>
> Now when i change nstfout to zero (no printing of forces) the note doesnt
> show up anymore.
>
> Also for the case with nstfout = 500 it seems that the forces are being
> read and written properly, I tried the g_traj tool to see the forces.
>
> Could someone clarify?
>
> Thank you,
> Amit Choubey
>
>
> --
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> you.
>
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[gmx-users] Re: 2. protein in dppc (edmund lee)

[Gerrit Groenhof]

Hi,

If I am allowed to do some advertisement:

you could try the tool g_membed  for inserting proteins as well

http://wwwuser.gwdg.de/~ggroenh/membed.html

Gerrit

gmx-users-requ...@gromacs.org wrote:
>2. protein in dppc (edmund lee)
>
> Date: Tue, 23 Feb 2010 15:55:36 +0800
> From: edmund lee 
> Subject: [gmx-users] protein in dppc
> To: 
> Message-ID: 
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> Dear Justin and all..
> I have been struggled for the pass few weeks...I follow the KALP-15 in DPPC 
> tutorials but I am using my own protein instead.
> I had successfully reached the step INFLATEGRO where 2 lipid removed from the 
> upper layer n 2 lipids removed from the lower layer. Then i updated my 
> topology with deducted 4 number of molecule of lipid.
> then I generated the strong_porse.itp using the following command:
> genrestr -f 1_newbox.gro -o strong_posre.itp -fc 10 10 10
> here is how the strong_posre.itp file look like[ position_restraints ];  i 
> funct   fcxfcyfcz   11 10 10 
> 10   21 10 10 10   31 10 
> 10 10   41 10 10 10   51 
> 10 10 1034831 10 10   
>   1034841 10 10 1034851 10 
> 10 1034861 10 10 10
> then i updated the topology (as shown below)
> ; Include Position restraint file#ifdef POSRES#include "posre.itp"#endif
> ; Strong position restraints for InflateGRO#ifdef STRONG_POSRES#include 
> "strong_posre.itp"#endif
> ; Include DPPC chain topology#include "dppc.itp"
> ; Include water topology#include "spc.itp"
> ; System specifications[ system ]128-Lipid DPPC Bilayer 
> [ molecules ]; molecule name nr.DPP124SOL   3655
>
>
>
> and I also add in the "define" line in the energyminimization.mdp file
> here is my em.mdp file 
> define   =-DSTRONG_POSRESintegrator = steepnsteps 
>   = 200constraints= noneemtol
> = 1000.0nstcgsteep= 10 ; do a steep every 10 steps of cgemstep
>  = 0.01 ; used with steepnstcomm  = 1coulombtype  
>   = PMEns_type= gridrlist   = 1.0rcoulomb 
>  = 1.0rvdw = 1.4Tcoupl  = 
> noPcoupl  = nogen_vel= nonstxout  
>= 0 ; write coords every # stepoptimize_fft  = yes
>
> HOWEVER, I get this error when I proceed to the grompp step.
> Fatal error:Syntax error - File strong_posre.itp, line 3Last line read:'[ 
> position_restraints ]'Invalid order for directive position_restraints
> Can anyone guide me in this?Yr comments and advices are appreciated.
> best regards
> edmund  
> _
>   

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Re: [gmx-users] Are you know the way for converting dl_poly input files to Gromacs inputs

[Florian Dommert]

Hello,

 at first I want to warn you the Lopes Force field for Ionic Liquids has some 
real defficiencies, especially in terms of reproducing correct dynamics. Now it 
depends on the counterion you want to use. For Ntf2 the is a force field from 
the Group of Ralf Ludwig, that give correct dynamics, statics and enthalpies of 
vaporization (DOI: 10.1002/cphc.200700552). Perhaps it is worth to try this 
force field.

Cheers,

Flo

On 23.02.2010, at 06:09, Mohammad Hossein Kowsari wrote:

> Dear Gromacs users,
>  
> I simulated several imidazolium-based ionic liquids by DL_POLY code which has 
> three input files: CONFIG, CONTROL, and FIELD. 
> the force field parameter (FIELD) used from the Canongia Lopes force fields, 
> e.g., (OPLS_AA / AMBER based):(JPC B, 2004, Vol. 108, 2038).
>  
> now, I like continuous my work on these ionic systems by GROMACS. have you 
> proper/simple way for converting DL_POLY input files to GROMACS inputs, 
> especially for inserting of Lopes force field parameters to the 
> topology/*.itp file of GROMACS.
> thanks for your help in advance
> Best Reagrds,
>  
> MHKowsari
> Isfahan University of Technology
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Dipl.-Phys.

Institute for Computational Physics

University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

Phone: +49(0)711/685-6-3613
Fax:   +49-(0)711/685-6-3658 

EMail: domm...@icp.uni-stuttgart.de
Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert



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[gmx-users] temperature

[shahab shariati]

Hi gromacs users

I want to run simulation of protein-dna interaction.

what is best for temperature in mdp file: 1) 300K (default) 2) 310k
(physiologic temperature)


Any help will highly appreciated!
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Re: [gmx-users] temperature

[Itamar Kass]

Hi Shahab,

The best temperature to use is 298K as this is the temperature in which
the force filed was parameterised. But, and this is a big but, I
speculate that any errors you might have during the simulation due to
the use of 310K is minimal and less then other inaccuracies in the force
field.

Best,
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
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| Victoria 3800
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| Tel: +61 3 9902 9376
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- Original Message -
From: shahab shariati 
Date: Tuesday, February 23, 2010 9:45 pm
Subject: [gmx-users] temperature
To: gmx-users@gromacs.org

> Hi gromacs users
> 
> I want to run simulation of protein-dna interaction.
> 
> what is best for temperature in mdp file: 1) 300K (default) 2) 310k
> (physiologic temperature)
> 
> 
> Any help will highly appreciated!
> 
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Re: [gmx-users] protein in dppc

[Justin A. Lemkul]

edmund lee wrote:

Dear Justin and all..

I have been struggled for the pass few weeks...
I follow the KALP-15 in DPPC tutorials but I am using my own protein 
instead.


I had successfully reached the step INFLATEGRO where 2 lipid removed 
from the upper layer n 2 lipids removed from the lower layer. Then i 
updated my topology with deducted 4 number of molecule of lipid.


then I generated the strong_porse.itp using the following command:

genrestr -f 1_newbox.gro -o strong_posre.itp -fc 10 10 10

here is how the strong_posre.itp file look like
[ position_restraints ]
;  i funct   fcxfcyfcz
   11 10 10 10
   21 10 10 10
   31 10 10 10
   41 10 10 10
   51 10 10 10
.


...
34831 10 10 10
34841 10 10 10
34851 10 10 10
34861 10 10 10

then i updated the topology (as shown below)

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Strong position restraints for InflateGRO
#ifdef STRONG_POSRES
#include "strong_posre.itp"
#endif

; Include DPPC chain topology
#include "dppc.itp"

; Include water topology
#include "spc.itp"

; System specifications
[ system ]
128-Lipid DPPC Bilayer 


[ molecules ]
; molecule name nr.
DPP124
SOL   3655




and I also add in the "define" line in the energyminimization.mdp file

here is my em.mdp file 


define   =-DSTRONG_POSRES
integrator = steep
nsteps   = 200
constraints= none
emtol= 1000.0
nstcgsteep= 10 ; do a steep every 10 steps of cg
emstep = 0.01 ; used with steep
nstcomm  = 1
coulombtype= PME
ns_type= grid
rlist   = 1.0
rcoulomb  = 1.0
rvdw = 1.4
Tcoupl  = no
Pcoupl  = no
gen_vel= no
nstxout = 0 ; write coords every # step
optimize_fft  = yes


HOWEVER, I get this error when I proceed to the grompp step.

Fatal error:
Syntax error - File strong_posre.itp, line 3
Last line read:
'[ position_restraints ]'
Invalid order for directive position_restraints

Can anyone guide me in this?
Yr comments and advices are appreciated.



You have several problems:

1. Your [molecules] directive makes no reference to the protein that should be 
present.
2. Your "strong_posre.itp" file looks like it refers to the whole system; it 
should have been created from the protein only.  You don't want to restrain 
everything in the system, anyway, and position restraints cannot be applied to a 
multiple molecule types in a single [position_restraints] directive.


-Justin


best regards

edmund


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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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[gmx-users] (no subject)

[Antonia V .]

Dear all,

I am simulating a two component system and I want to calculate the g(r) of the 
centers of mass of the one component. 
Using the command,

g_rdf -f traj.xtc -rdf mol_com

I get an rdf which doesn't obtain the value one at long distances. How can I 
change that?

thank you for your help,
Antonia
  
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[gmx-users] ffamber94 with gromacs 4.0.3

[Carla Jamous]

Hi,
please does anyone know if the ffamber94 force-field is compatible with
gromacs version 4.0?
Because I used to use it with gromacs 3.3.3 but now that I'm trying with
gromacs 4, I'm having some error messages.

Thank you
Carla
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Re: [gmx-users] ffamber94 with gromacs 4.0.3

[Justin A. Lemkul]

Carla Jamous wrote:

Hi,
please does anyone know if the ffamber94 force-field is compatible with 
gromacs version 4.0?
Because I used to use it with gromacs 3.3.3 but now that I'm trying with 
gromacs 4, I'm having some error messages.




There is no problem at all using ffamber under Gromacs 4.0.x.  If you want help, 
though, you'll have to provide a lot more information - what you're doing 
(command line) and what the exact error message(s) is (are).


-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] hydrogen bond autocorrelation function c(t),

[leila karami]

Hi

In hydrogen bond autocorrelation function c(t), correlation of what quantity
of hydrogen bond  is considered?

thanks
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Re: [gmx-users] hydrogen bond autocorrelation function c(t),

[Justin A. Lemkul]

leila karami wrote:

Hi
 
In hydrogen bond autocorrelation function c(t), correlation of what 
quantity of hydrogen bond  is considered?
 
thanks




There is a reason Gromacs tools frequently print out a message saying "please 
read and cite the following reference."  I would suggest you start with the 
paper g_hbond informs you of.


-Justin

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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] rdf not equal to one

[Antonia V .]

Dear all,

I am simulating a two component system (which form two completely separated 
phases) and I want to calculate the g(r) of the centers of mass of the one 
component. 
Using the command,

g_rdf -f traj.xtc -rdf mol_com

I get an rdf which doesn't obtain the value one at long distances. How can I 
change that?

thank you for your help,
Antonia   
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[gmx-users] problem in npt pr for pope

[Mahnam]

In God We Trust
Hello everyone 
We have a problem for equilibrate the system with a protein within 
POPE. we have searched mailing list , we dident any good note. We have used 
pope.pdb from Dr. Tielemans website. We have inserted our protein into pope 
and minimized it and equilibrated it with NVT ensemble for 2 ns, and 
temperture was stable, but when we want to equilibrate our system 
with NPT ensemble it dosen't accept lincs algoritm and says :
" presure coupling more than 1% " and also " box was shifted at least 10 
time. 
here is our npt file for position reastrant:
constraints =  all-bonds
define  =  -DPOSRES  -DPOSRES_pop
integrator  =  md
dt  =  0.002; ps 
nsteps  =  250; .
nstcomm =  1
comm_mode   =  Linear
comm_grps   =  upper lower SOL
nstxout =  250
nstvout =  1000
nstfout =  0
nstlog  =  10
nstenergy   =  10
nstlist =  1
ns_type =  grid
rlist   =  1
coulombtype =  cut-off
rcoulomb=  1.4
rvdw=  1.4
fourierspacing  =  0.12
fourier_nx  =  0
fourier_ny  =  0
fourier_nz  =  0
pme_order   =  4
ewald_rtol  =  1e-5
optimize_fft=  yes
niter   = 20
pbc = xyz 
nstcgsteep   = 1000
nbfgscorr= 10
vdwtype = cut-off
DispCorr=  EnerPres
freezegrps   = Protein
freezedim= Y Y Y
emtol= 100
emstep   = 0.01
energygrps  = Protein 
energygrp_excl  = Protein  Protein
; Berendsen temperature coupling is on in three groups
Tcoupl  =  Nose-Hoover
tau_t   =  0.1  0.1  0.1   
tc-grps  =  Protein  POP  bulk   
ref_t   =  100100   100
; Pressure coupling is  on
Pcoupl  =  Berendsen 
Pcoupltype  =  semiisotropic
tau_p   =  1  1  
compressibility =  4.5e-05  4.5e-05  
ref_p   =  1   1  
; Generate velocites is on at 300 K.
gen_vel =  yes
gen_temp=  100.0
gen_seed=  173529
constraint-algorithm =lincs 
lincs_iter  = 1
lincs_order = 4

whould you please gide me

Many thanks in advance for your help and your reply.
Yours truly 
Karim Mahnam
Institute of  Biochemistry  and  Biophysics (IBB)
Tehran University 
P.O.box 13145-1384
Tehran 
Iran 
http://www.ibb.ut.ac.ir/
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[gmx-users] problem in g_rdf using only x and y

[Rebeca García Fandiño]

Hi,
I am trying to calculate g_rdf using only the x and y components of the 
distance (gromacs 4.0.4):

g_rdf -f trajectory.xtc -s production1.tpr -n index.ndx -o rdf_Na_xy.xvg -com 
-norm -pbc -xy and the calculations stays at the window:

Select a group: 1
Selected 1: 'UNK'
Select a group: 4
Selected 4: 'Na'
Reading frame   0 time0.000   

for days...(I had to kill it after 4 days).

Using the same order without -xy takes only 10 minutes.

Is there anything wrong with the commands I am using? Or maybe is there a bug 
in the -xy option?

Thank you very much for your help, in advance.

Best wishes,

Rebeca Garcia.
  
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RE: [gmx-users] problem in g_rdf using only x and y

[Berk Hess]

Hi,

I fixed this bug in 4.0.7.

Berk

From: rega...@hotmail.com
To: gmx-users@gromacs.org
Date: Tue, 23 Feb 2010 15:40:07 +
Subject: [gmx-users] problem in g_rdf using only x and y








Hi,
I am trying to calculate g_rdf using only the x and y components of the 
distance (gromacs 4.0.4):

g_rdf -f trajectory.xtc -s production1.tpr -n index.ndx -o rdf_Na_xy.xvg -com 
-norm -pbc -xy and the calculations stays at the window:

Select a group: 1
Selected 1: 'UNK'
Select a group: 4
Selected 4: 'Na'
Reading frame   0 time0.000   

for days...(I had to kill it after 4 days).

Using the same order without -xy takes only 10 minutes.

Is there anything wrong with the commands I am using? Or maybe is there a bug 
in the -xy option?

Thank you very much for your help, in advance.

Best wishes,

Rebeca Garcia.
  
¿Quieres tener a tus amigos de Facebook en Messenger?  ¡Clic AQUÍ!  
  
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RE: [gmx-users] problem in g_rdf using only x and y

[Rebeca García Fandiño]

Hi,
thank you very much for your answer. However, I have tried with the 4.0.7 
version, and the problem continues, and it is just the same. I have the 
trajectory and tpr file obtained with the 4.0.4 version. Do you think it cares, 
or maybe is it another problem?
Cheers,
Rebeca.

From: g...@hotmail.com
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] problem in g_rdf using only x and y
Date: Tue, 23 Feb 2010 16:47:43 +0100








Hi,

I fixed this bug in 4.0.7.

Berk

From: rega...@hotmail.com
To: gmx-users@gromacs.org
Date: Tue, 23 Feb 2010 15:40:07 +
Subject: [gmx-users] problem in g_rdf using only x and y








Hi,
I am trying to calculate g_rdf using only the x and y components of the 
distance (gromacs 4.0.4):

g_rdf -f trajectory.xtc -s production1.tpr -n index.ndx -o rdf_Na_xy.xvg -com 
-norm -pbc -xy and the calculations stays at the window:

Select a group: 1
Selected 1: 'UNK'
Select a group: 4
Selected 4: 'Na'
Reading frame   0 time0.000   

for days...(I had to kill it after 4 days).

Using the same order without -xy takes only 10 minutes.

Is there anything wrong with the commands I am using? Or maybe is there a bug 
in the -xy option?

Thank you very much for your help, in advance.

Best wishes,

Rebeca Garcia.
  
¿Quieres tener a tus amigos de Facebook en Messenger?  ¡Clic AQUÍ!  
  
New Windows 7: Find the right PC for you. Learn more.   
  
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Re: [gmx-users] problem in g_rdf using only x and y

[Justin A. Lemkul]

Rebeca García Fandiño wrote:

Hi,
thank you very much for your answer. However, I have tried with the 
4.0.7 version, and the problem continues, and it is just the same. I 
have the trajectory and tpr file obtained with the 4.0.4 version. Do you 
think it cares, or maybe is it another problem?


I think there is a problem in g_rdf, not a 4.0.4 vs 4.0.7 issue.  I was actually 
about to report this problem, myself.  I have simulations that I did with 
version 4.0.7, and the RDF analysis hung the exact same way as you reported.


-Justin


Cheers,
Rebeca.


From: g...@hotmail.com
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] problem in g_rdf using only x and y
Date: Tue, 23 Feb 2010 16:47:43 +0100

Hi,

I fixed this bug in 4.0.7.

Berk


From: rega...@hotmail.com
To: gmx-users@gromacs.org
Date: Tue, 23 Feb 2010 15:40:07 +
Subject: [gmx-users] problem in g_rdf using only x and y

Hi,
I am trying to calculate g_rdf using only the x and y components of the 
distance (gromacs 4.0.4):


g_rdf -f trajectory.xtc -s production1.tpr -n index.ndx -o rdf_Na_xy.xvg 
-com -norm -pbc -xy and the calculations stays at the window:


Select a group: 1
Selected 1: 'UNK'
Select a group: 4
Selected 4: 'Na'
Reading frame   0 time0.000  


for days...(I had to kill it after 4 days).

Using the same order without -xy takes only 10 minutes.

Is there anything wrong with the commands I am using? Or maybe is there 
a bug in the -xy option?


Thank you very much for your help, in advance.

Best wishes,

Rebeca Garcia.


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New Windows 7: Find the right PC for you. Learn more. 



Navega con el navegador más seguro de todos. ¡Descárgatelo ya! 





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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] ffamber94 with gromacs 4.0.3

[deisy yurley rodriguez sarmiento]

Yes, the force field Amber94 is compatible with Gromacs 4.0, i use that
combination...you should are very careful whit the instalation.




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Re: [gmx-users] problem in npt pr for pope

[Justin A. Lemkul]

Mahnam wrote:

In God We Trust
Hello everyone
We have a problem for equilibrate the system with a protein within
POPE. we have searched mailing list , we dident any good note. We have 
used pope.pdb from Dr. Tielemans website. We have inserted our protein 
into pope and minimized it and equilibrated it with NVT ensemble for 2 
ns, and temperture was stable, but when we want to equilibrate our system

with NPT ensemble it dosen't accept lincs algoritm and says :
" *presure coupling more than 1% *" and also "* box was shifted at least 
10 time*.

here is our npt file for position reastrant:
constraints =  all-bonds
define  =  -DPOSRES  -DPOSRES_pop
integrator  =  md
dt  =  0.002; ps
nsteps  =  250; .
nstcomm =  1
comm_mode   =  Linear
comm_grps   =  upper lower SOL
nstxout =  250
nstvout =  1000
nstfout =  0
nstlog  =  10
nstenergy   =  10
nstlist =  1
ns_type =  grid
rlist   =  1
coulombtype =  cut-off


I can see no logical reason to use plain cutoff electrostatics, especially for a 
membrane protein system.  The artifacts are well-documented.  You should be 
using PME.  I don't know if this is the root cause of your problem, but it 
certainly won't lead to correct results.



rcoulomb=  1.4
rvdw=  1.4
fourierspacing  =  0.12
fourier_nx  =  0
fourier_ny  =  0
fourier_nz  =  0
pme_order   =  4
ewald_rtol  =  1e-5
optimize_fft=  yes
niter   = 20
pbc = xyz
nstcgsteep   = 1000
nbfgscorr= 10
vdwtype = cut-off
DispCorr=  EnerPres
freezegrps   = Protein
freezedim= Y Y Y
emtol= 100
emstep   = 0.01
energygrps  = Protein
energygrp_excl  = Protein  Protein


What happens if you do not freeze your protein?  Perhaps there are unresolved 
clashes that freezing is keeping in place.


-Justin


; Berendsen temperature coupling is on in three groups
Tcoupl  =  Nose-Hoover
tau_t   =  0.1  0.1  0.1  
tc-grps  =  Protein  POP  bulk  
ref_t   =  100100   100   
; Pressure coupling is  on

Pcoupl  =  Berendsen
Pcoupltype  =  semiisotropic
tau_p   =  1  1 
compressibility =  4.5e-05  4.5e-05 
ref_p   =  1   1 
; Generate velocites is on at 300 K.

gen_vel =  yes
gen_temp=  100.0
gen_seed=  173529
constraint-algorithm =lincs
lincs_iter  = 1
lincs_order = 4
 
whould you please gide me
 
Many thanks in advance for your help and your reply.

Yours truly
Karim Mahnam
Institute of  Biochemistry  and  Biophysics (IBB)
Tehran University
P.O.box 13145-1384
Tehran
Iran
http://www.ibb.ut.ac.ir/



--


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] Inconsisten shift Error

[teklebrh]

 Hi Justin,

I just checked this error on the archive list but could not found a  
reasonable answer ..


I have done the energy minimization and it is ok Fmax less than 100

but when I start equilibrating my system I got the following error..

=
 There were 2 inconsistent shifts. Check your topology

Warning: 1-4 interaction between 18851 and 18856 at distance 42.558  
which is larger than the 1-4 table size 1.900 nm


These are ignored for the rest of the simulation

This usually means your system is exploding,

if not, you should increase table-extension in your mdp file

or with user tables increase the table size

Segmentation fault



My nvt.mdp file


;
;   ; LINES STARTING WITH ';' ARE COMMENTS

title   = NVT equlibration  ; Title of run
cpp = /usr/bin/cpp ; location of cpp on linux
; The following lines tell the program the standard locations where to  
find certain files


; VARIOUS PREPROCESSING OPTIONS
; Preprocessor information: use cpp syntax.
; e.g.: -I/home/joe/doe -I/home/mary/hoe
include  =
; e.g.: -DI_Want_Cookies -DMe_Too
define   = -DPOSRES

; RUN CONTROL PARAMETERS
integrator   = md
; Start time and timestep in ps
tinit= 0
dt   = 0.002
nsteps   = 15000
; For exact run continuation or redoing part of a run
; Part index is updated automatically on checkpointing (keeps files separate)
simulation_part  = 1
init_step= 0
; mode for center of mass motion removal
comm-mode= Linear
; number of steps for center of mass motion removal
nstcomm  = 1
; group(s) for center of mass motion removal
comm-grps=

; LANGEVIN DYNAMICS OPTIONS
; Friction coefficient (amu/ps) and random seed
bd-fric  = 0
ld-seed  = 1993

; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol= 100
emstep   = 0.01
; Max number of iterations in relax_shells
niter= 20
; Step size (ps^2) for minimization of flexible constraints
fcstep   = 0
; Frequency of steepest descents steps when doing CG
nstcgsteep   = 1000
nbfgscorr= 10

; TEST PARTICLE INSERTION OPTIONS
rtpi = 0.05

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout  = 100
nstvout  = 100
nstfout  = 100
; Output frequency for energies to log file and energy file
nstlog   = 100
nstenergy= 100
; Output frequency and precision for xtc file
nstxtcout= 100
xtc-precision= 1000
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps =
; Selection of energy groups
energygrps   =

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist  = 10
; ns algorithm (simple or grid)
ns-type  = Grid
; Periodic boundary conditions: xyz, no, xy
pbc  = xyz
periodic_molecules   = no
; nblist cut-off
rlist= 0.9

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = PME
rcoulomb-switch  = 0
rcoulomb = 0.9
; Relative dielectric constant for the medium and the reaction field
epsilon_r= 1
epsilon_rf   = 1
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths
rvdw-switch  = 0
rvdw = 0.9
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = no
; Extension of the potential lookup tables beyond the cut-off
table-extension  = 1
; Seperate tables between energy group pairs
energygrp_table  =
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters
pme_order= 4
ewald_rtol   = 1e-05
ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = no

; IMPLICIT SOLVENT ALGORITHM
implicit_solvent = No

; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm = Still
; Frequency of calculating the Born radii inside rlist
nstgbradii   = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii = 2
; Dielectric coefficient of the implicit solvent
gb_epsilon_solvent   = 80
; Salt concentration in M for Gener

[gmx-users] Re: Inconsisten shift Error

[Justin A. Lemkul]

tekle...@ualberta.ca wrote:

 Hi Justin,

I just checked this error on the archive list but could not found a 
reasonable answer ..


I have done the energy minimization and it is ok Fmax less than 100

but when I start equilibrating my system I got the following error..

=
 There were 2 inconsistent shifts. Check your topology

Warning: 1-4 interaction between 18851 and 18856 at distance 42.558 
which is larger than the 1-4 table size 1.900 nm


These are ignored for the rest of the simulation

This usually means your system is exploding,



Here's the usual advice:

http://www.gromacs.org/Documentation/Terminology/Blowing_Up




tcoupl   = V-rescale ; modified berendsen thermostat
; Groups to couple separately
tc-grps  = PAP TOL


What are PAP and TOL?  Are they of sufficient size to justify their own 
temperature coupling groups?


http://www.gromacs.org/Documentation/Terminology/Thermostats

Other than that, you'll have to give some information about what your system is, 
how you built it, and what parameters (force field) you're using.


-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] hydrogen bond autocorrelation function c(t),

[Erik Marklund]

leila karami skrev:

Hi
 
In hydrogen bond autocorrelation function c(t), correlation of what 
quantity of hydrogen bond  is considered?
 
thanks

Its existence.

Erik

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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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[gmx-users] Reducing distance between atoms! PULL

[Алексей Раевский]

Sorry, I want to ask the same question I had a week ago. I need your advice
in COM PULL.

This is a part of article which describes methodology "...with respect to
the atomic distance between the carbonyl carbon of the substrate and the
oxygen atom of the identified nucleophilic water, a constrained MD
simulation was performed to investigate the mechanisms of the approach of
the water molecule. This simulation was started by using a harmonic
potential as the distance constraint, where the force constant was set to 5
kcal/mol å2. When the atomic distance was not reduced any further, despite
the presence of the harmonic potential in the MD simulation (at about 470
ps), the force constant was increased up to 200 kcal/mol å2; this was
exploited to mimic the first phase of a nucleophilic attack..all together
about 1ns"

and

"The atomic distance is 3.4 A, suggesting that this water molecule acts as a
nucleophile in the post-transfer editing reaction.."

I have to reduce distance between oxygen of H2O and carbon during
simulation, but H2O must be free enough for revolution around C. Index file
is ready for it. This is part of mdp.

; COM PULLING

; Pull type: no, umbrella, constraint or constant_force

pull = umbrella

; Pull geometry: distance, direction, cylinder or position

pull_geometry = distance

; Select components for the pull vector. default: Y Y Y

pull_dim = Y Y Y

; Cylinder radius for dynamic reaction force groups (nm)

pull_r1 = 1

; Switch from r1 to r0 in case of dynamic reaction force

pull_r0 = 1.5

pull_constr_tol = 1e-06

pull_start = yes

pull_nstxout = 1

pull_nstfout = 1

; Number of pull groups

pull_ngroups = 1

; Group name, weight (default all 1), vector, init, rate (nm/ps),
kJ/(mol*nm^2)

pull_group0 = C

pull_weights0 =

pull_pbcatom0 = 0

pull_group1 = H2O

pull_weights1 =

pull_pbcatom1 = 0

pull_vec1 = 0.0 0.0 1.0

pull_init1 = 3.4

pull_rate1 = 0.02

pull_k1 = 837

pull_kB1 = 837

Is everything ok with pull_vec1, pull_init1, pull_rate1 (if I put 0 atoms
will stay without any movement, but I suggest it will cause another result),
pull (umbrella is harmonical, constrains - no) and pull_geometry (in the
article was mentioned "distance" instead of "direction") ???

I did experiments with different changes in parameters...Waiting for your
comments. Thanks
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Re: [gmx-users] Re: Inconsisten shift Error

[Justin A. Lemkul]

tekle...@ualberta.ca wrote:


Hi Justin,

My system is -- simulation a polymer (called PAP) in toluene (TOL)... to 
see the aggregation behavior of the molecule in TOL.


the PAP molecule contains 55 atoms...

I inserted 8 PAP molecule in a Toluene . it works fine.

Energy minimization  it works fine (to the entire system)



Define "fine" - what were the values of the potential energy and maximum force?


I am using the ffgmx force field.



Why?  This force field has long been deprecated.


I used a 10 X 10 X 10 both with a total of 29749 atoms in the box..

when I start equilibrating my system using NVT ... I got that error.

Initially I used the berendsen thermostat and got an error of 
segmentation fault but I changed the thermostat as recommended in the 
error to V-rescaling and got this error...




For initial equilibration, either should be fine, but the fact that the system 
crashes suggests that there is something physically unrealistic about the 
system.  Change nstxout to 1 and try to capture some frames of what's going 
wrong, to see where the crash starts.  Otherwise, consider how you developed the 
parameters for both PAP and TOL - did you validate them?  Are they appropriate?


-Justin


That is it..

Regards,

Rob







Quoting "Justin A. Lemkul" :




tekle...@ualberta.ca wrote:

Hi Justin,

I just checked this error on the archive list but could not found a 
reasonable answer ..


I have done the energy minimization and it is ok Fmax less than 100

but when I start equilibrating my system I got the following error..

=
There were 2 inconsistent shifts. Check your topology

Warning: 1-4 interaction between 18851 and 18856 at distance 42.558 
which is larger than the 1-4 table size 1.900 nm


These are ignored for the rest of the simulation

This usually means your system is exploding,



Here's the usual advice:

http://www.gromacs.org/Documentation/Terminology/Blowing_Up




tcoupl   = V-rescale ; modified berendsen thermostat
; Groups to couple separately
tc-grps  = PAP TOL


What are PAP and TOL?  Are they of sufficient size to justify their 
own temperature coupling groups?


http://www.gromacs.org/Documentation/Terminology/Thermostats

Other than that, you'll have to give some information about what your 
system is, how you built it, and what parameters (force field) you're 
using.


-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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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] ffamber94 with gromacs 4.0.3

[Mark Abraham]

On 24/02/2010 12:56 AM, Justin A. Lemkul wrote:



Carla Jamous wrote:

Hi,
please does anyone know if the ffamber94 force-field is compatible
with gromacs version 4.0?
Because I used to use it with gromacs 3.3.3 but now that I'm trying
with gromacs 4, I'm having some error messages.



There is no problem at all using ffamber under Gromacs 4.0.x. If you
want help, though, you'll have to provide a lot more information - what
you're doing (command line) and what the exact error message(s) is (are).


...and do yourself a favour and update to GROMACS 4.0.7 - there have 
been many bugs fixed since 4.0.3


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

[Mark Abraham]

On 24/02/2010 12:23 AM, Antonia V. wrote:

Dear all,

I am simulating a two component system and I want to calculate the g(r)
of the centers of mass of the one component.
Using the command,

g_rdf -f traj.xtc -rdf mol_com

I get an rdf which doesn't obtain the value one at long distances. How
can I change that?


Use a better model physics? Simulate longer? You haven't given anywhere 
near enough information for us to tell...


Mark
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[gmx-users] water simulation

[Amit Choubey]

Hi everyone,

I am afraid this is not really a gromacs related question. Could anyone
refer me to a review paper which discusses about simulating water? Does any
of them gives a comparative and complete study of molecular dynamics with
water , answering questions like which water model to use, how to deal with
coulomb interaction, what should be the cutoff value (if cutoff is used) . I
have not been able to find one with complete story. Is anyone aware of such
a publication.

Thank you,
Amit
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Re: [gmx-users] water simulation

[Justin A. Lemkul]

Amit Choubey wrote:

Hi everyone,

I am afraid this is not really a gromacs related question. Could anyone 
refer me to a review paper which discusses about simulating water? Does 
any of them gives a comparative and complete study of molecular dynamics 
with water , answering questions like which water model to use, how to 
deal with coulomb interaction, what should be the cutoff value (if 
cutoff is used) . I have not been able to find one with complete story. 
Is anyone aware of such a publication.




The first Google result if you search for "water models" is:

http://www1.lsbu.ac.uk/water/models.html

There are tons of references there.  I'm sure they will lead you in the right 
direction.  Which water model to use also often depends on the parameterization 
scheme of the force field you want to use.


-Justin


Thank you,
Amit



--


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] Query about g_hbond

[naimah haron naimah]

Dear gmx-users...

I am new to gromacs, I am trying to obtain the intermolecular hydrogen bonds 
formed during 10ns simulation of 125 ionic liquid (tetraethylammonium 
L-Lysinate). I use OPLS-AA force field for this simulation. When I do this by 
using g_hbond and selecting the LYS group, I am getting hydrogen bonds at all. 
The angle that I get is 0.33 degree, number of hydrogen bonds = 160.13, and the 
distance for hydrogen bond =0.16 nm.


This is the command I am using:

g_hbond -f mixture_mdpr_compilefile.trr -s mixture_mdpr_ext1.tpr -n index.ndx 
-num hbnum.xvg -dist hbdist.xvg -ang hbang.xvg -hbn hbond.ndx -d 500 -e 1 
-a 30 -r 0.35 

This is the output that I obtain :

No option -sel
Reading file mixture_mdpr_ext1.tpr, VERSION 3.3.3 (double precision)
Specify 2 groups to analyze :
Group 0 (System) has   6500 elements
Group 1 ( N) has   3625 elements
Group 2 (   LYS) has   2875 elements

Select a group: 2
Selected 2: 'LYS'
Select a group: 2
Selected 2: 'LYS'
Calculating hydrogen bonds in LYS (2875 atoms)
Found 250 donors and 500 acceptors 
trn version: GMX_trn_file (single precision)
Reading frame   2000 time  500.000
Will do grid-seach on 9x9x9 grid, rcut=0.35
Last frame4 time 1.00
Found 2353 different hydrogen bonds in trajectory
Found 2271 different atom-pairs within hydrogen bonding distance
Merging hbonds with Acceptor and Donor swapped
250/250
-Reduced number of hbonds from 2353 to 1783
-Reduced number of distances from 2271 to 2271
Average number of hbonds per timeframe 160.130 out of 62500 possible

gcq#44: "May the Force Be With You" (Star Wars)

My question is; 
1) Is it correct the command that I used to get the number of hydrogen bonding, 
angle and distance for hydrogen bonding?
2) Is it reasonable the value for number of hydrogen bonding, angle and 
distance for hydrogen bonding that I calculate?

Thanks 

IMA


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[gmx-users] Converting Gromacs output files to dl_poly output files.

[naimah haron naimah]

 Dear Gromacs users,

I simulated ionic liquids by GROMACS code. The force field that I used was 
OPLS-AA. 
Now, I like continuous my work on these ionic systems by DL_POLY code. Have 
anyone know the 
proper/simple way for converting GROMACS output files to DL_POLY output.
Thanks

IMA



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