On 11/10/12 10:10 AM, vidhya sankar wrote:
Dear Justin Thank you For your Previous reply,
For My
system After First Shrinking Using Cut-off Value DPPC 18
perl inflategro.pl system.gro 4 DPPC 18 system_inflated.gro 5 area.dat
Then I do the EM.During EM I need to use -maxwarn 1 option Otherwise I have
got Error as follows in grompp If i use -maxwarn 1 then it runs Successfully
May i use this -maxwan option in first Shrinking ?
There are very few reasons to use -maxwarn; this is not one of them, as far as I
can see.
./grompp_d -f emdppc.mdp -c system_inflated.gro -p 2KDQ.top -o 2KDQDPPCem.tpr
Number of degrees of freedom in T-Coupling group rest is 19557.00
Largest charge group radii for Van der Waals: 1.201, 1.144 nm
Largest charge group radii for Coulomb: 1.201, 1.144 nm
WARNING 1 [file emdppc.mdp]:
The sum of the two largest charge group radii (2.345197) is larger than
rlist (1.200000)
The magnitude of the charge group radii suggests you have broken molecules or
otherwise unacceptable geometry produced by some previous instability. This
warning is discussed in greater detail at
http://www.gromacs.org/Documentation/Errors#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [email protected]
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 [email protected].
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
