[gmx-users] Distance Restraints on Protein - possible at all?
NG HUI WEN
HuiWen.Ng at nottingham.edu.my
Wed Feb 22 01:17:59 CET 2012
From: NG HUI WEN
Sent: Sunday, February 19, 2012 1:19 PM
To: gmx-users at gromacs.org
Subject: Distance Restraints on Protein - possible at all?
Dear gmxusers,
I have been trying to apply distance restraints on my protein but have been unsuccessful thus far.
I have consulted the user forum previously and with some much-appreciated help I have managed to get my simulation (with distance restraints applied) to run. However, the joy did not last long as the simulation crashed very quickly (after ~40-50ps).
Below is an account of the attempts I made. Please bear with me as it is quite lenghty. I have tried to resolve the problem (but all to no avail) by :
a)changing the distance restraint group from CA to backbone - in case the protein is too floppy
b)fc from 10000 to 1000 (default) to 0 - in order to check if the problem comes from the strenght of restraints
Below sum up what I had done:
1) prepare disre.itp file
genrestr -f posre_NVT_rep1.gro -o ca_disre.itp -disre
2) mdp looks:
title = NPT
define = -DDISRES
integrator = md
nsteps = 500000
dt = 0.002
nstxout = 50000
nstvout = 50000
nstenergy = 2500
nstlog = 500
nstxtcout = 50000
continuation = yes
constraint_algorithm = lincs
constraints = all-bonds
lincs_iter = 1
lincs_order = 4
ns_type = grid
nstlist = 10
rlist = 1.2
rcoulomb = 1.2
rvdw = 1.2
coulombtype = PME
pme_order = 4
fourierspacing = 0.12
tcoupl = v-rescale
tc-grps = Protein POPC WATER_SOL_CL
tau_t = 0.1 0.1 0.1
ref_t = 310 310 310
pcoupl = Parrinello-Rahman
pcoupltype = semiisotropic
tau_p = 1.0
ref_p = 1.0 1.0
compressibility = 4.5e-5 4.5e-5
pbc = xyz
DispCorr = EnerPres
gen_vel = no
nstcomm = 10
comm-mode = Linear
comm-grps = Protein_POPC WATER_SOL_CL
energygrps = Protein POPC WATER_SOL_CL
; DISRE parameters
disre = simple
disre-fc = (i)10000/ (ii)1000 / (iii) 0
3) top file looks like this:
; Include forcefield parameters
#include "gromos53a6_lipid.ff/forcefield.itp"
;Include Protein Topology
#include "A2a.itp"
; Include Position restraint file
#ifdef DISRES
#include "ca_disre.itp"
#endif
;
#ifdef POSRES
#include "posre.itp"
#endif
;
;Include POPC topology
#include "popc.itp"
#ifdef LIPID_POSRES
#include "lipid_posre.itp"
#endif
;Include water topology
#include "gromos53a6_lipid.ff/spc.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include topology for ions
#include "gromos53a6_lipid.ff/ions.itp"
[ system ]
; Name
POPC and protein in water
[ molecules ]
; Compound #mols
Protein_chain_X 1
POPC 327
SOL 24767
CL 11
4) prepare .tpr file
grompp -f NPT_disres.mdp -c posre_NPT_rep1.gro -n index.ndx -p merged.top -t posre_NPT_rep1.cpt -o disre.tpr
5) mdrun
mdrun-mpi -v -s disre.tpr -deffnm disre -pd
The following are snippets of the output and log file before the simulations blew up:
i)fc= 10000
step 21300, will finish Wed Feb 15 11:07:18 2012
step 21400, will finish Wed Feb 15 11:08:38 2012
Step 21481, time 42.962 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.007728, max 0.339710 (between atoms 9 and 11)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 21482, time 42.964 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.022906, max 0.865028 (between atoms 12 and 16)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
16 17 31.6 0.1212 0.1447 0.1230
12 16 104.7 0.1266 0.0207 0.1530
9 11 110.7 0.0878 0.0397 0.1330
Wrote pdb files with previous and current coordinates
Step 21483, time 42.966 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.009368, max 0.641094 (between atoms 9 and 11)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1 2 33.3 0.0928 0.0961 0.1000
18 20 34.2 0.1474 0.1635 0.1470
16 18 60.0 0.1842 0.1310 0.1330
16 17 64.8 0.1447 0.1264 0.1230
14 15 30.4 0.0979 0.1525 0.1530
11 15 77.5 0.2435 0.1147 0.1470
11 12 34.5 0.2609 0.1633 0.1470
9 11 95.3 0.0397 0.2183 0.1330
Wrote pdb files with previous and current coordinates
Step 21484, time 42.968 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.013088, max 0.518530 (between atoms 12 and 16)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1 2 40.0 0.0961 0.0952 0.1000
18 19 59.6 0.0996 0.0782 0.1000
....
ii) fc= 1000 (default)
step 21200, will finish Thu Feb 16 02:22:10 2012
step 21300, will finish Thu Feb 16 02:22:09 2012
step 21400, will finish Thu Feb 16 02:22:07 2012
Step 21481, time 42.962 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.007728, max 0.339710 (between atoms 9 and 11)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 21482, time 42.964 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.022906, max 0.865028 (between atoms 12 and 16)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
16 17 31.6 0.1212 0.1447 0.1230
12 16 104.7 0.1266 0.0207 0.1530
9 11 110.7 0.0878 0.0397 0.1330
Wrote pdb files with previous and current coordinates
Step 21483, time 42.966 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.009368, max 0.641094 (between atoms 9 and 11)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1 2 33.3 0.0928 0.0961 0.1000
18 20 34.2 0.1474 0.1635 0.1470
16 18 60.0 0.1842 0.1310 0.1330
16 17 64.8 0.1447 0.1264 0.1230
14 15 30.4 0.0979 0.1525 0.1530
11 15 77.5 0.2435 0.1147 0.1470
11 12 34.5 0.2609 0.1633 0.1470
9 11 95.3 0.0397 0.2183 0.1330
Wrote pdb files with previous and current coordinates
... ... ...
log file at the start and just before the simulation blew up:
Started mdrun on node 0 Wed Feb 15 14:46:26 2012
Step Time Lambda
0 0.00000 0.00000
Grid: 15 x 15 x 16 cells
Energies (kJ/mol)
Angle G96Angle Proper Dih. Ryckaert-Bell. Improper Dih.
3.62720e+04 5.42463e+03 1.35029e+04 1.73286e+04 3.49678e+03
LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR)
1.12718e+04 7.18682e+04 8.12244e+04 -7.18252e+03 -1.27427e+06
Coul. recip. Dis. Rest. D.R.Viol. (nm) Potential Kinetic En.
-3.89615e+05 0.00000e+00 0.00000e+00 -1.43068e+06 2.42524e+05
Total Energy Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
-1.18815e+06 3.08494e+02 -1.97177e+02 5.79670e+02 1.01684e-05
Step Time Lambda
500 1.00000 0.00000
Energies (kJ/mol)
Angle G96Angle Proper Dih. Ryckaert-Bell. Improper Dih.
3.59484e+04 5.33007e+03 1.32268e+04 1.70061e+04 3.50560e+03
LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR)
1.10240e+04 7.14613e+04 8.03669e+04 -7.03778e+03 -1.26659e+06
Coul. recip. Dis. Rest. D.R.Viol. (nm) Potential Kinetic En.
-3.88952e+05 5.48165e+01 9.39514e+00 -1.42466e+06 2.43342e+05
Total Energy Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
-1.18131e+06 3.09534e+02 -1.89310e+02 4.99800e+02 1.05856e-05
... ...
Step Time Lambda
21000 42.00000 0.00000
Energies (kJ/mol)
Angle G96Angle Proper Dih. Ryckaert-Bell. Improper Dih.
3.62118e+04 5.30282e+03 1.34838e+04 1.83737e+04 3.33814e+03
LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR)
1.12261e+04 6.97720e+04 8.28599e+04 -6.87470e+03 -1.25607e+06
Coul. recip. Dis. Rest. D.R.Viol. (nm) Potential Kinetic En.
-3.87420e+05 4.27582e+01 6.98584e+00 -1.40975e+06 2.44245e+05
Total Energy Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
-1.16551e+06 3.10684e+02 -1.80638e+02 -5.00713e+02 1.04526e-05
Large VCM(group Protein_POPC): 73.33204, 29.76558, -12.48454, Temp-cm: 2.95863e+05
Large VCM(group Water_SOL_CL): -46.46529, -18.86033, 7.91055, Temp-cm: 3.35241e+04
iii) fc = 0
The end of the log file looks:
Step Time Lambda
29000 58.00000 0.00000
Energies (kJ/mol)
Angle G96Angle Proper Dih. Ryckaert-Bell. Improper Dih.
3.65061e+04 5.60824e+03 1.42205e+04 1.80483e+04 3.37686e+03
LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR)
1.09448e+04 6.89125e+04 8.18947e+04 -6.41177e+03 -1.21650e+06
Coul. recip. Dis. Rest. D.R.Viol. (nm) Potential Kinetic En.
-3.85131e+05 0.00000e+00 4.54606e+05 -1.36853e+06 2.44457e+05
Total Energy Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
-1.12408e+06 3.10953e+02 -1.57129e+02 5.40099e+02 1.15690e-05
Step Time Lambda
29500 59.00000 0.00000
Energies (kJ/mol)
Angle G96Angle Proper Dih. Ryckaert-Bell. Improper Dih.
3.66857e+04 5.65841e+03 1.39441e+04 1.81639e+04 3.44242e+03
LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR)
1.11234e+04 6.94373e+04 8.36399e+04 -6.42711e+03 -1.21988e+06
Coul. recip. Dis. Rest. D.R.Viol. (nm) Potential Kinetic En.
-3.85140e+05 0.00000e+00 4.73981e+05 -1.36935e+06 2.43700e+05
Total Energy Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
-1.12565e+06 3.09991e+02 -1.57883e+02 3.05347e+02 1.18083e-05
-------------------------------------------------------
Program mpich_exe.10603, VERSION 4.5.5
Source code file: ns.c, line: 2549
Fatal error:
One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
The starting system has these dimensions 10.41535 10.32882 11.24541. Using g_energy to check the box size fluctuations, I got the following:
21
Last energy frame read 297 time 59.400
Statistics over 27501 steps [ 0.0000 through 55.0000 ps ], 1 data sets
All statistics are over 2751 points
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
Box-X 14.3931 1.2 2.47974 8.21254 (nm)
22
Last energy frame read 297 time 59.400
Statistics over 27501 steps [ 0.0000 through 55.0000 ps ], 1 data sets
All statistics are over 2751 points
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
Box-Y 14.2735 1.2 2.45914 8.14431 (nm)
23
Last energy frame read 297 time 59.400
Statistics over 27501 steps [ 0.0000 through 55.0000 ps ], 1 data sets
All statistics are over 2751 points
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
Box-Z 6.63204 1 2.01081 -6.84929 (nm)
The graphs of box sizes show that x and y were increasing while z was decreasing drastically before the system blew up.
Apologies for such a long post. I hope someone would have some clue as to why distance restraint can't be applied to my system. Your help is much appreciated.
Best wishes,
Huiwen
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