On 11/11/2011 5:13 PM, LindaSong wrote:
Thank you very much for your reply, Mark
It is the topology problem. It seems I did it in a wrong way. Now the
topology goes like this:
[ molecules ]
; Compound #mols
Protein_chain_A 1
Protein_chain_A2 1
POPC 256
This problem solved.
But then comes a new one. When I did the g_membed, the system blowed
up after one iteration!
I think I really shouldn't ignore the warning from the grompp.
However, as an inexper ienced user, I don't know how to improve the
mdp file. Can you give me any hint?
Use a text editor that writes plain text. Junk " " throughout
cannot help things. As before, reporting the actual text of the warning
is critical to working out what might be wrong.
Mark
The mdp file for the g_membed is like this:
cpp = /lib/cpp
; Run parameters
integrator = md
nsteps = 1000
dt = 0.002
; Output control
nstxout = 10&n bsp;
nstvout = 10
nstenergy = 10
nstlog = 10
; Bond parameters
continuation = no
constraint_algorithm = lincs
constraints = all-bonds
lincs_iter = 1
lincs_order = 4
; Neighborsearching
ns_type = grid
nstlist = 1
rlist = 1.4
rcoulomb = 1.4
rvdw &nb sp; = 1.4
; Electrostatics
coulombtype = PME
pme_order = 4
fourierspacing = 0.16
; Temperature coupling is on
tcoupl = V-rescale
tc-grps = Protein Non-Protein
tau_t = 0.1 0.1 & nbsp;
ref_t = 300 300
; Pressure coupling is on
Pcoupl = Berendsen
pcoupltype = semiisotropic
tau_p = 1.0
compressibility = 4.5e-5 4.5e-5
ref_p ; = 1.0 1.0
; Velocity generation
gen_vel = yes
gen_temp = 300
gen_seed = 173529
; Energy monitoring
energygrps = Protein
; Non-equilibrium MD
freezegrps = Protein
freezedim &nb sp; = Y Y Y
; Energy group exclusions
energygrp_excl = Protein Protein
Thanks a lot!
Linda
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