Bharath.K. Chakravarthi wrote:
HI....
I'm not sure about this kind of error but as per my knowledge the
problem might be with the parameter cpp in mdp file.
In my mdp file it is as follows
The problem is unrelated to cpp, since the error complained about the use of
"warnings" in the .mdp file. Further, if we are to assume Gromacs 4.0.x, the
cpp setting is ignored, as Gromacs has its own C pre-processor now.
title = ecoli_nusG
cpp = /usr/bin/cpp
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.001 ; ps !
nsteps = 100000 ; total 100 ps.
nstcomm = 1
..
..
and somewhere i read the nsteps should be between 50000-100000 for pr
dynamics.....
In general, yes, to obtain good equilibration you would certainly want to run
for more than 1.0 ps, but I would say there is no absolute setting that should
be applied.
-Justin
search gromacs tutorial for better clue...
On Sat, May 15, 2010 at 6:03 AM, manjula kasinathan <manju...@gmail.com
<mailto:manju...@gmail.com>> wrote:
hi snip
Thank u. as per ur suggestion i added sodium ions to my
protein. then i carried out mdrun for energy minimization nsteps
3000 but i runs only for 1108 steps. then i went to position
restrain steps the command i gave
grompp -f pr.mdp -c em.gro -p top.top -o pr.tpr
i got a fatal error
Too many warnings (1), grompp terminated.
If you are sure all warnings are harmless, use the
-maxwarn option
WARNING 1 [file pr.mdp, line unknown]:
Unknown or double left-hand 'warnings' in parameter file
y i'm getting this error.how can i correct this could any one help plz.
my pr.mdp file
title = FWS
warnings = 10
cpp = /usr/local/gromacs/share/gromacs/cpp
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 500 ; total 1.0 ps.
nstcomm = 1
nstxout = 250 ; collect data every 0.5 ps
nstvout = 1000
nstfout = 0
nstlog = 10
nstenergy = 10
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
; Berendsen temperature coupling is on
Tcoupl = v-rescale
tau_t = 0.1 0.1
tc-grps = protein non-protein
ref_t = 300 300
; Pressure coupling is on
Pcoupl = parrinello-rahman
Pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
with this warnings i proceeded with mdrun but i get the following
LINCS warnnings
starting mdrun 'Protein in water'
500 steps, 1.0 ps.
step 300, will finish Sat May 15 08:57:23 2010
Step 394, time 0.788 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000103, max 0.001028 (between atoms 4478 and 4480)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
4478 4480 33.4 0.1081 0.1091 0.1090
Step 423, time 0.846 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.442275, max 40.666431 (between atoms 8211 and 8212)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
8473 8476 88.6 0.1527 0.2741 0.1522
8473 8475 89.9 0.1094 3.6185 0.1090
8473 8474 89.5 0.1094 0.2778 0.1090
8471 8473 87.2 0.1455 0.2548 0.1449
8471 8472 33.2 0.1013 0.1241 0.1010
8215 8217 32.8 0.1090 0.1240 0.1090
8215 8216 39.2 0.1091 0.1282 0.1090
8211 8215 45.8 0.1536 0.1603 0.1529
8211 8213 44.0 0.1425 0.1645 0.1410
8211 8212 90.2 0.4225 4.5416 0.1090
8209 8211 45.6 0.1511 0.1348 0.1529
8209 8210 32.4 0.1098 0.1199 0.1090
8207 8209 33.3 0.1482 0.1823 0.1449
7224 7225 30.4 0.1013 0.1010 0.1010
5296 5297 30.5 0.1093 0.1092 0.1090
Warning: 1-4 interaction between 8208 and 8213 at distance 4.720
which is larger than the 1-4 table size 2.400 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
Step 424, time 0.848 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 171806.092017, max 19412182.000000 (between atoms 8235 and 8236)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
8507 8508 90.0 0.1011 0.2179 0.1010
8497 8499 39.8 0.1460 0.2065 0.1449
8497 8498 59.8 0.1009 0.1923 0.1010
8495 8497 44.0 0.1354 729.7847 0.1335
8495 8496 94.4 0.1235 729.7617 0.1229
8491 8493 89.7 0.1091 0.2077 0.1090
8487 8489 89.8 0.1091 0.5344 0.1090
8485 8491 32.7 0.1531 0.1890 0.1529
8485 8486 47.4 0.1091 0.1421 0.1090
8482 8485 50.7 0.1536 215.0330 0.1529
8482 8484 71.0 0.1094 214.9777 0.1090
8482 8483 92.6 0.1091 215.0566 0.1090
8480 8495 77.1 0.1633 417.3555 0.1522
8480 8482 84.2 0.1556 871.1644 0.1529
8480 8481 80.7 0.1078 911.5953 0.1090
8478 8480 43.4 0.1559 3067.7700 0.1449
8478 8479 92.3 0.1070 3786.8391 0.1010
t = 0.848 ps: Water molecule starting at atom 80338 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
could any one help me to overcome this problem. thanks in advance
hi justin as per ur suggestion i viewed my structure but there is no
clash in it.
y i'm getting this error?????
Cheers,
Manju
--
With Regards,
Manjulakasinathan
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--
Bharath.K.Chakravarthi
Post Graduate Student
Kuvempu University
Shimoga
Karnataka
Ph:9535629260
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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