R: Re: R: RE: R: RE: R: RE: R:[gmx-users] Tabulated potential - Problem
albitauro at virgilio.it
albitauro at virgilio.it
Tue Oct 6 12:29:55 CEST 2009
Hi,
Here's my mdp file:
*********************************+
title = Martini
integrator = md
tinit = 0.0
dt = 0.03
nsteps = 200000
nstcomm = 1
nstxout = 1000
nstvout = 1000
nstfout = 0
nstlog = 1000
nstenergy = 100
nstxtcout = 1000
xtc_precision = 100
energygrps = NN
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.4
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2
DispCorr = No
tcoupl = Berendsen
tau_t = 0.1
tc-grps = NN
ref_t = 100
gen_vel = yes
gen_temp = 300
gen_seed = 473529
constraints = none
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 4
lincs_warnangle = 30
***********************************
and my top file:
*************************
#include "martini_v21.itp"
#include "nn_num.itp"
[ system ]
NN CHAIN
[ molecules ]
NN 1
**************************
where the nn_num.itp looks like:
************************************
;
; Topology file for NN
;
;
[ moleculetype ]
; Name nrexcl
NN 1
[atoms]
; id
1 C1 1 NN S01 1 0.0
2 P4 1 NN P02 2 0.0
3 C1 1 NN B03 3 0.0
4 P4 1 NN P04 4 0.0
5 C1 1 NN B05 5 0.0
..............................
[bonds]
; i j funct table_nr force.c.
1 2 8 0 1.0
2 3 8 0 1.0
3 4 8 0 1.0
4 5 8 0 1.0
5 6 8 0 1.0
6......................
.................................
[angles]
; i j k funct r0 force.c.
1 2 3 2 180.000 25.000
2 3 4 2 180.000 25.000
3 4 5 2 180.000 25.000
4 5 6 2 180.000 25.000
5 6 7 2 180.000 25.000
6 7 8 2 180.000
.........................................
************************************************
Thank you
AM
----Messaggio originale----
Da: Mark.Abraham at anu.edu.au
Data: 5-ott-2009 11.19 PM
A: "Discussion list for GROMACS users"<gmx-users at gromacs.org>
Ogg: Re: R: RE: R: RE: R: RE: R:[gmx-users] Tabulated potential - Problem
albitauro at virgilio.it wrote:
> Hi,
> I came back to my original stretching potential in tabulated form and I
> have still problems...
> when running a geometry optimization the results are like that:
>
> *************************************************
> ^MStep 635, Epot=2.259501e+02, Fnorm=4.086e+00, Fmax=1.886e+01 (atom 34)
> ^MStep 636, Epot=2.259499e+02, Fnorm=3.847e+00, Fmax=1.992e+01 (atom 33)
> ^MStep 637, Epot=2.259495e+02, Fnorm=1.002e+01, Fmax=5.408e+01 (atom 33)
> ^MStep 638, Epot=2.259449e+02, Fnorm=1.026e+01, Fmax=4.098e+01 (atom 34)
> ^MStep 639, Epot=2.259393e+02, Fnorm=2.193e+01, Fmax=1.159e+02 (atom 35)
> ^MStep 640, Epot=2.259364e+02, Fnorm=1.469e+01, Fmax=7.064e+01 (atom 34)
> ^MStep 641, Epot=2.259335e+02, Fnorm=1.281e+01, Fmax=7.154e+01 (atom 34)
> ^MStep 642, Epot=2.259315e+02, Fnorm=5.803e+00, Fmax=2.861e+01 (atom 35)
> ^MStep 643, Epot=2.259314e+02, Fnorm=6.332e+00, Fmax=3.116e+01 (atom 34)
> ^MStep 644, Epot=2.259310e+02, Fnorm=3.550e+00, Fmax=1.502e+01 (atom 34)
>
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 0.1
> ************************************************************************************
>
> as if the system is frozen. My system here is an isolated, linear and
> finite-length chain.
> When running an md simulation I got the error:
>
> -------------------------------------------------------
> Program mdrun_mpi, VERSION 4.0.5
> Source code file: bondfree.c, line: 1772
>
> Fatal error:
> A tabulated bond interaction table number 0 is out of the table range: r
> 1.815411, between table indices 1815 and 1816, table length 1001
> -------------------------------------------------------
>
> The tabulated potential is uniformly spaced, the bond type is 8 to
> exclude LJ interaction between bonded atoms, nrexcl=1 to include 1-3
> interactions (as required by MARTINI force field).
That seems like it should work.
> The same system does
> not have any problem when running simulation with an harmonic stretching
> potential in both numerical and analytical form.
> Does anyone have any suggestion for possible solutions or error in the
> input?
Running gmxcheck between various .tpr files may be instructive, e.g. one
file may have many more nonbonded interactions, or such. Otherwise,
posting your .mdp file and the start of your .top may help us spot a
problem.
Mark
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