On 9/22/14 1:23 AM, RINU KHATTRI wrote:
hello justin
yes i did minimization and equilibrium
i have one confusion when i am going for extension of simulation by
tpbconv -s md_0_1.tpr -extend 9000 -o nextr.tpr
for mdrun i have to use which checkpoint file md_0_1.cpt after 1 ns or
state.cpt i am always confused with it i am usin 4.5.5 so append is
default still the outputfile of 1st run is not appended
just backoff traj,trr to #traj.trr.1#
mdrun -s nextr.tpr -cpi state.cpt
or mdrun -s nextr -cpi md_0_1.cpt
kindly help
I have no idea. How did you name your files? Do state.cpt and md_0_1.cpt
co-exist? What is in them? If you ran a 1-ns simulation with mdrun -deffnm
md_0_1, then you extend using md_0_1.cpt. This is why I always name my files
descriptively or organize different parts of a simulation (equilibration,
production intervals, etc) in different directories.
-Justin
On Thu, Sep 18, 2014 at 5:58 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 9/18/14 6:38 AM, RINU KHATTRI wrote:
hello
i am also facing the same problem i worked on the protein complex
(popc ) but once again i am using same procedure its gives error even
i changed .mdp file parameters
Changed to what? From what?
after running it gives 61%
mdrun
grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -n index.ndx -o
npt.tpr
mdrun -nt 4 -deffnm npt
Did previous minimization and/or equilibration runs succeed?
-Justin
kindly help
On Thu, Sep 18, 2014 at 2:23 PM, Ujwala Patil <ujwalanpa...@gmail.com>
wrote:
Hello I am doing simulation of dioxane+ water system
during energy minimization i got error
Too many LINCS warnings (1337)
If you know what you are doing you can adjust the lincs warning threshold
in your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem
my em.mdp file is
integrator = steep ;
emtol = 500.0
emstep = 0.01
nsteps = 500
nstlist = 1.4
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
rvdw = 1.4
constraints = none
pbc = xyz
i have seen some similar type of error
but not able to fix
please help me to solve the problem
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
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==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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