Re: [gmx-users] LINCS WARNING relative constraint deviation

2012-10-01 Thread Justin Lemkul 



On 10/1/12 7:10 AM, Ali Alizadeh wrote:

Dear all users

1- I am trying to simulate a system that contains 1182 methane
molecules(5910 atoms) and   1830 water molecules(5490), I
keep getting these errors.


Something is wrong with the starting configuration, topology, or .mdp settings 
(see below for comments) such that energy minimization fails almost instantly.


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


2- Gromacs does not give me  a .xtc file, Why?


Perhaps there's some quirk of the code that won't produce an .xtc file with an 
EM algorithm.  EM is normally quick and takes up little disk space, so the 
benefit to having a compressed trajectory is minimal in most cases.



My command lines for grompp and mdrun in terminal window:

grompp -f npt.mdp -c wwfull.top.gro -p topol.top -o topol.tpr -n ww.ndx
mdrun -s topol.tpr -o wwfull.trr -x wwfull.xtc

These are errors and my .mdp file:

...
Steepest Descents:
Tolerance (Fmax)   =  1.0e-04
Number of steps= 1000

Step 50, time 0.01 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000589, max 0.014000 (between atoms 2636 and 2638)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
2636   2637   39.40.1090   0.1092  0.1090

Step 51, time 0.0102 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.001802, max 0.029832 (between atoms 2026 and 2029)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
2331   2334   43.10.1090   0.1093  0.1090
2026   2028   49.60.1090   0.1095  0.1090
5071   5074   41.70.1090   0.1093  0.1090
4806   4808   47.00.1090   0.1095  0.1090

Step 52, time 0.0104 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.003002, max 0.049492 (between atoms 156 and 159)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
 471474   51.70.1090   0.1096  0.1090
2331   2334   32.40.1093   0.1078  0.1090
5071   5074   31.30.1093   0.1081  0.1090
 156160   55.30.1090   0.1095  0.1090
 916919   41.00.1090   0.1093  0.1090
5886   5890   61.10.1090   0.1092  0.1090

Step 53, time 0.0106 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.034606, max 0.843079 (between atoms 5886 and 5890)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
 471475   31.50.1049   0.1325  0.1090
 471474   92.90.1096   0.1519  0.1090
 471473   38.60.1044   0.1402  0.1090
 471472   92.70.1048   0.1568  0.1090
2331   2335   48.80.1082   0.1083  0.1090
2331   2334   48.40.1078   0.1070  0.1090
2331   2333   88.80.1110   0.1564  0.1090
2331   2332   88.80.1110   0.1586  0.1090
2026   2030   89.40.1103   0.1177  0.1090
2026   2028   40.00.1091   0.1191  0.1090
2026   2027   38.20.1089   0.1207  0.1090
5071   5075   41.90.1084   0.1048  0.1090
5071   5074   41.60.1081   0.1043  0.1090
5071   5073   88.60.1109   0.1376  0.1090
5071   5072   88.70.1110   0.1392  0.1090
4806   4810   89.30.1104   0.1176  0.1090
4806   4809   32.70.1104   0.0927  0.1090
4806   4808   35.20.1089   0.1140  0.1090
4806   4807   35.00.1088   0.1153  0.1090
 156160   92.70.1095   0.1324  0.1090
 156159   80.80.1036   0.0523  0.1090
 156158   90.00.1036   0.1338  0.1090
 156157   90.40.1037   0.1489  0.1090
2276   2280   38.30.1091   0.1114  0.1090
2276   2277   33.00.1089   0.1134  0.1090
2286   2290   37.80.1090   0.1102  0.1090
 916920   90.10.1068   0.1704  0.1090
 916919   45.90.1093   0.1237  0.1090
 916917   65.00.1067   0.1285  0.1090
1296   1300   31.20.1090   0.1094  0.1090
5886   5890   90.90.1092   0.2009  0.1090
5886   5889   47.90.1043   0.1326  0.1090
5886   5888   85.90.1045   0.1282  0.1090
5886   5887   91.40.1046   0.1208  0.1090

Back Off! I just backed up step53b_n0.pdb to ./#step53b_n0.pdb.1#

Back Off! I just backed up step53c_n0.pdb to ./#step53c_n0.pdb.1#
Wrote pdb files with previous and current coordinates
..
..
..

This is my .mdp file:
title= Yo
cpp  = /usr/bin/cpp
include  =
define   =

; RUN CONTROL PARAMETERS
integrator   = steep
; Start time and timestep in ps
tinit= 0
dt   = 0.0002
nsteps   = 1000
;

[gmx-users] LINCS WARNING relative constraint deviation

2011-06-19 Thread E. Nihal Korkmaz 
Dear all,

I am trying to simulate a GB simulation of a 112 amino acid long protein. I
keep getting these errors,

Step 27718, time 55.436 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 33.319842, max 438.763717 (between atoms 79 and 81)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 27718, time 55.436 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.058237, max 1.390675 (between atoms 91 and 93)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
 91 92   50.20.1016   0.1065  0.1010
 91 93   90.00.1002   0.2415  0.1010
 91 94   70.20.1025   0.1066  0.1010
 79 80   90.00.1057   1.0667  0.1090
 79 81   90.01.3066  47.9342  0.1090
 85 86   90.00.1084   0.1758  0.1090
 85 87   90.01.0654   0.1668  0.1090
 88 89   90.00.1097   0.6994  0.1090
 88 90   90.00.1125   0.1097  0.1090
 91 92   50.20.1016   0.1065  0.1010
 91 93   90.00.1002   0.2415  0.1010
 91 94   70.20.1025   0.1066  0.1010


I am copying my mdp parameters below, I'd appreciate any suggestions to fix
that.

integrator   = sd
tinit= 0
dt   = 0.002
nsteps   = 250
simulation_part  = 1
init_step= 1

nstxout  = 5000
nstvout  = 5000
nstenergy= 500
nstxtcout= 500
nstlog   = 500

xtc_grps = System
energygrps   = System
comm_mode= Linear
; neighbor searching and vdw/pme setting up
nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 2.0

implicit_solvent = GBSA
gb_algorithm = OBC
gb_saltconc  = 0.15
rgbradii = 2.0

coulombtype  = Cut-off
fourierspacing   = 0.1
pme_order= 6
rcoulomb = 2.0

vdwtype  = Cut-off
rvdw_switch  = 1.0
rvdw = 2.0

; cpt control
tcoupl   = V-rescale
tc-grps  = System
tau_t= 0.1
ref_t= 300.0

Pcoupl   = Berendsen
pcoupltype   = isotropic
tau_p= 1.0
compressibility  = 4.5e-5
ref_p= 1.0

; velocity  temperature control
gen_vel  = yes
gen_temp = 300.0
annealing= no
constraints  = hbonds
constraint_algorithm = lincs
morse= no


Thanks,
-- 
Elif Nihal Korkmaz

Research Assistant
University of Wisconsin - Biophysics
Member of Qiang Cui  Thomas Record Labs
1101 University Ave, Rm. 8359
Madison, WI 53706
Phone:  608-265-3644
Email:   kork...@wisc.edu
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists