[gmx-users] em ok, md wrong

[Liliya Shamova]

Hi everybody!

I made .top file for oxalic acid (OPLSAA ff), and energy mininization goes normally, but molecule becomes distorted after md in vacuo at 50 K (0K is still ok). I cannot understand what I'm doing wrong. 

Thanks in advance!

Liliya

oxalic_acid
    8
    1OXD     C1    1   7.752   9.727   5.820
    1OXD   O_31    2   8.626   8.893   5.820
    1OXD    OH1    3   8.016  11.053   5.820
    1OXD    HO1    4   9.001  11.076   5.820
    1OXD     C2    5   6.213   9.479   5.820
    1OXD   O_32    6   5.706   8.379   5.820
    1OXD    OH2    7   5.534  10.649   5.820
    1OXD    HO2    8   6.179  11.393   5.820
  14.25703  13.44165  11.64081   0.00000   0.00000   4.75234   0.00000  -4.75234   6.72083


;
;    Topology file for oxalic acid
;    Created by: Liliya Shamova
;    e-mail: lshamova at yahoo.com

; Include forcefield parameters
#include "ffoplsaa.itp"

[ moleculetype ]
; Name            nrexcl
OXD                    3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB    chargeB      massB
     1   opls_267      1    OXD     C1      1      0.520     12.011   ; qtot 
     2   opls_269      1    OXD   O_31      1     -0.440    15.9994   ; qtot 
     3   opls_268      1    OXD    OH1      1     -0.530    15.9994   ; qtot 
     4   opls_270      1    OXD    HO1      1      0.450      1.008   ; qtot 0
     5   opls_267      1    OXD     C2      2      0.520     12.011   ; qtot 
     6   opls_269      1    OXD   O_32      2     -0.440    15.9994   ; qtot 
     7   opls_268      1    OXD    OH2      2     -0.530    15.9994   ; qtot 
     8   opls_270      1    OXD    HO2      2      0.450      1.008   ; qtot 
     
[ bonds ]
;  ai    aj funct            c0            c1            c2            c3
    1     2     1 
    1     3     1 
    3     4     1
    1     5     1
    5     6     1
    5     7     1
    7     8     1

[ pairs ]
;  ai    aj funct            c0            c1            c2            c3
;    2     4     1
;    2     6     1
;    4     5     1
    2     7     1
;    1     8     1
    7     3     1
    3     6     1
;    6     8     1
;    7     4     1
;    3     8     1
    
[ angles ]
;  ai    aj    ak funct            c0            c1            c2            c3
    2     1     3     1 
    1     3     4     1
    2     1     5     1
    1     5     6     1
    6     5     7     1
    5     7     8     1
;    3     1     5     1
;    1     5     7     1
     
[ dihedrals ]
;  ai    aj    ak    al funct            c0            c1            c2            c3            c4            c5
    2     1     3     4     3;           5.5            0           -5.5             0             0            0 
;    2     1     5     6     3 ;           4           -0.8          -3.2             0             0            0
;    2     1     5     7     3  ;
    6     5     7     8     3   ;        5.5            0           -5.5             0             0            0 
    1     5     7     8     3    ;         7           -1.5          -5.5             0             0            0     
;    3     1     5     7     3  ;
;    3     1     5     6     3 ;
    4     3     1     5     3  ;           7           -1.5          -5.5             0             0            0  

;#define improper_CB14_CB12_CL4_CB16   180    4.6024     2
;#define improper_CB15_CB13_CL1_CB16   180    4.6024     2
; Include Position restraint file
;#ifdef POSRES
;#include "posre.itp"
;#endif

; Include water topology
;#ifdef FLEX_SPC
;#include "flexspc.itp"
;#else
;#include "spc.itp"
;#endif

;#ifdef POSRES_WATER
; Position restraint for each water oxygen
;[ position_restraints ]
;  i funct       fcx        fcy        fcz
;   1    1       1000       1000       1000
;#endif

[ system ]
; Name
oxalic_acid 

[ molecules ]
; Compound        #mols
OXD                1

;
;    User spoel (236)
;    Wed Nov  3 17:12:44 1993
;    Input file
;
title               =  full 50 K
cpp                 =  /usr/bin/cpp
;define              =  -DPOSRES
constraints         =  none
integrator          =  md
dt                  =  0.002    ; ps !
nsteps              =  10000    ; total 20 ps.
nstcomm             =  10       ; frequency for center of mass motion removal
comm_mode           =  Angular
nstxout             =  200      ;           to write coordinates
nstvout             =  1000     ;                    velocities
nstfout             =  0        ;                    forces
nstlog              =  100      ;
nstenergy           =  100
nstlist             =  0
ns_type             =  simple
pbc                 =  no
rlist               =  0
rcoulomb            =  0
rvdw                =  0
;SHAKE properties
;constraint_algorithm=  SHAKE
;shake_tol           =  0.0001
; Berendsen temperature coupling is on in one group
Tcoupl              =  berendsen
tc_grps             =  System
tau_t               =  0.1
ref_t               =  50
; Energy monitoring

; Pressure coupling is not on
Pcoupl              =  no
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is on at 50 K.
gen_vel             =  yes
gen_temp            =  50.0
gen_seed            =  173529


      
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