[gmx-users] distance_restraints

[maggin]

Hi, all

I use GMX4.5.5,  GROMOS96 53a6 force field ro simulation 1dx0.pdb, I use two
steps energy minimization (steep and cg ) in vacuum as follows:

1. pdb2gmx -f 1dx0.pdb -o xxx.gro -ignh -ter -water  spce  -ss  -p xxx.top

2. editconf -f xxx.gro -o xxx.pdb -c -d 0.9 -bt cubic 

3.grompp -f em.mdp -c xxx.pdb -p xxx.top -o xxx.tpr

4.mdrun -v -s xxx.tpr -nt 2 -deffnm em_xxx

5.grompp_d -f cg.mdp -c em_xxx.gro -p xxx.top -o xxx.tpr

6.mdrun_d -v -s xxx.tpr -nt 2 -deffnm cg_xxx

steep is no problem, while cg have some warnings:

Step 143, Epot=-1.190781e+04, Fnorm=3.680e+01, Fmax=7.027e+02 (atom 217)
Step 144, Epot=-1.190936e+04, Fnorm=2.620e+01, Fmax=2.688e+02 (atom 217)
Step 145, Epot=-1.191034e+04, Fnorm=2.618e+01, Fmax=2.276e+02 (atom 277)
Step 146, Epot=-1.191235e+04, Fnorm=3.672e+01, Fmax=4.235e+02 (atom 277)
Step 147, Epot=-1.192020e+04, Fnorm=6.482e+01, Fmax=8.288e+02 (atom 219)
Step 148, Epot=-1.196346e+04, Fnorm=1.315e+02, Fmax=1.971e+03 (atom 378)

Step -1, time -0.002 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000694, max 0.004189 (between atoms 296 and 297)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step -1, time -0.002 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.009008, max 0.056534 (between atoms 1 and 4)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    181    182   31.3    0.1000   0.1000      0.1000
    685    688   37.8    0.1000   0.1051      0.1000
    262    263   41.0    0.1000   0.1000      0.1000
      1      4   39.2    0.1000   0.1057      0.1000
Step 149, Epot=-1.197948e+04, Fnorm=1.069e+02, Fmax=1.271e+03 (atom 218)
Step 150, Epot=-1.198617e+04, Fnorm=6.868e+01, Fmax=9.492e+02 (atom 218)
Step 151, Epot=-1.199312e+04, Fnorm=6.069e+01, Fmax=8.678e+02 (atom 378)
Step 152, Epot=-1.199645e+04, Fnorm=2.884e+01, Fmax=3.323e+02 (atom 378)
Step 153, Epot=-1.199771e+04, Fnorm=2.482e+01, Fmax=2.873e+02 (atom 378)
Step 154, Epot=-1.199942e+04, Fnorm=3.681e+01, Fmax=6.652e+02 (atom 378)
Step 155, Epot=-1.200439e+04, Fnorm=7.122e+01, Fmax=1.091e+03 (atom 378)
.
.
.
.
.
Step 208, Epot=-1.231153e+04, Fnorm=2.409e+01, Fmax=2.882e+02 (atom 262)
Step 209, Epot=-1.231272e+04, Fnorm=2.635e+01, Fmax=3.012e+02 (atom 261)
Step 210, Epot=-1.231523e+04, Fnorm=3.957e+01, Fmax=7.031e+02 (atom 378)
Step 211, Epot=-1.232519e+04, Fnorm=6.187e+01, Fmax=1.273e+03 (atom 378)

Step -1, time -0.002 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000001, max 0.000005 (between atoms 775 and 776)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    262    263   30.3    0.1000   0.1000      0.1000
Step 212, Epot=-1.233691e+04, Fnorm=4.926e+01, Fmax=5.858e+02 (atom 378)
Step 213, Epot=-1.234682e+04, Fnorm=8.846e+01, Fmax=1.130e+03 (atom 261)
Step 214, Epot=-1.235149e+04, Fnorm=8.846e+01, Fmax=1.372e+03 (atom 262)

writing lowest energy coordinates.

Back Off! I just backed up em_cg_constrain_vacuum.gro to
./#em_cg_constrain_vacuum.gro.1#

Polak-Ribiere Conjugate Gradients converged to Fmax < 100 in 275 steps
Potential Energy  = -1.25808627767813e+04
Maximum force     =  9.11707505025239e+01 on atom 757
Norm of force     =  1.65933958355887e+01

I constraint h-bond in cg.mdp:
title               =  bovin
cpp                 =  /usr/bin/cpp
define              =  -DFLEXIBLE
constraints         =  h-bonds
integrator          =  cg
dt                  =  0.002    ; ps !
nsteps              =  2000
nstlist             =  10 
ns_type             =  grid
rlist               =  1.0
coulombtype         =  PME
rcoulomb            =  1.0
vdwtype             =  cut-off
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
emtol               =  100
emstep              =  0.001
; Highest order in the expansion of the constraint coupling matrix
lincs_order              = 8

; GENERATE VELOCITIES FOR STARTUP RUN
gen-vel                  = no
gen-temp                 = 293
gen-seed                 = 173529

in order to fix warning, I use distance_restraints as follows:

genrestr  -f em_xxx.gro  -o posre.itp -disre_dist 0.1 -disre_up2 1

acording to the posre.itp, revise xxx.top file,

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
[ distance_restraints ]
; ai aj type index type’ low up1 up2 fac
1 4 1 0 2 0.0 0.19 1.19 1.0
181 182 1 0 2 0.0 0.19 1.19 1.0
262 263 1 0 2 0.0 0.19 1.19 1.0
296 297 1 0 2 0.0 0.19 1.19 1.0
353 354 1 0 2 0.0 0.23 1.23 1.0
512 516 1 1 2 0.0 0.24 1.24 1.0
685 688 1 0 2 0.0 0.19 1.19 1.0
775 776 1 0 2 0.0 0.20 1.20 1.0
994 995 1 2 2 0.0 0.24 1.24 1.0
#endif

But things not changed, same warning

How should I do to fix it?

Thank you very much!

maggin




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