Thanks for giving me insight to resolve the problem regarding grompp.
Now i came across new problem regarding energy minimization
MDRUN(mdrun)step while giving this command to command prompt.
{mdrun -v -s em.tpr -o em.trr -e em.edr -c after_em.gro -g emlog.log }
I came across this problem which i am mentioning below.
Reading file em.tpr, VERSION 3.3.1 (single precision)
Loaded with Money
Back Off! I just backed up em.edr to ./#em.edr.2#
Steepest Descents:
Tolerance (Fmax) = 1.00000e+02
Number of steps = 4000
-------------------------------------------------------1.31850e+12, atom=
1924
Program mdrun, VERSION 3.3.1
Source code file: nsgrid.c, line: 226
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value -2147483648. It should have been within [ 0 .. 216 ]
Please report this to the mailing list ([email protected])
-------------------------------------------------------
What should be problem? I am attaching emergy minimization em.mdp file.
For getting insight about i will be thankful to you.
KINSHUK
> [EMAIL PROTECTED] wrote:
>> Hi all,
>> I have been trying to simulate peptide (octa alanine). In genbox i have
>> inserted 40 molecule of guanidium ion & 800 water molecule (by -ci &
>> maxsol option in gromacs 3.3.3)then again with genbox i added 40
>> molecules of thiocynate ion & 80 water molecules as above mentioned way.
>> When i tried to do grompp for energy minimization i was encountered with
>> many warning listed below though i have included the *.itp files of both
>> ions in the topology *.top file of peptide.I need some insight about
>> this
>> so that i can resolve this problem.
>>
>> I have attached the em.mdp file along with this mail.
>
> This is not the problem, but your T-coupling groups aren't useful. See
> http://wiki.gromacs.org/index.php/thermostats
>
>> If i will be getting help i'll be thankful for you.
>
> The order of molecules in your .top files [ molecules ] section probably
> doesn't match the order of molecules in your structure file. See chapter
> 5 of the GROMACS manual if you don't understand this.
>
> Mark
> _______________________________________________
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;
; Input file
;
title = Octamer ; a string
cpp = /lib/cpp ; c-preprocessor
define = -DFLEX_SPC
dt = 0.002 ; time step
integrator = steep
nsteps = 4000 ; number of steps
nstcomm = 1 ; reset c.o.m. motion
nstxout = 2000 ; write coords
nstvout = 50 ; write velocities
nstlog = 50 ; print to logfile
nstenergy = 50 ; print energies
energygrps = System
nstlist = 10 ; update pairlist
ns_type = grid
constraint_algorithm = shake
shake_tol = 0.0001
coulombtype = PME
vdwtype = shift
rlist = 1.4 ; cut-off for ns
rvdw = 1.4
rvdw_switch = 0.8
rcoulomb = 1.4
rcoulomb_switch = 0.8
tcoupl = berendsen ; temperature bath (yes,no)
ref_t = 298
tc_grps = Protein
tau_t = 0.1
Pcoupl = no
tau_p = 0.5
ref_p = 1.0
gen_vel = yes ; generate initial velocities
gen_temp = 298 ; initial temperature
gen_seed = 173529 ; random seed
emtol = 100
emstep = 0.01
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