Paymon Pirzadeh wrote:
Thanks for the tips!
But I still have problem with my added ion. Justin had told me that ion
names are force-field specific! Since I am using OPLSaa, I checked the
itp file for Na ion name, and it was Na+. I used this name with the
No, it's not. It's NA+. From ions.itp in the #ifdef _FF_OPLS section:
[ moleculetype ]
; molname nrexcl
NA+ 1
[ atoms ]
; id at type res nr residu name at name cg nr charge mass
1 opls_407 1 NA+ NA 1 1 22.98977
-pname switch, but again during the grompp I ran into the following
error:
Warning: atom name 65870 in AFP_I.top and
AFP_I_solvated_54_62_102_null.gro does not match (NA - Na)
WARNING 1 [file AFP_I.top, line 4151]:
1 non-matching atom name
atom names from AFP_I.top will be used
atom names from AFP_I_solvated_54_62_102_null.gro will be ignored
I really do not know what I am doing wrong here! Also regarding past
discussions, adding this single ion has lead into the following note:
NOTE 1 [file AFP_I.top, line 4151]:
System has non-zero total charge: 1.000000e-02
I am not sure if that much charge will cause me troubles or not!
I am somewhat troubled by the magnitude of charge discrepancy. Look in the .top
to see where things start going wrong (i.e., not an integer). I would think
your system would have to be quite large to accumulate such a difference in charge.
-Justin
Payman
On Wed, 2009-08-26 at 07:53 +1000, Mark Abraham wrote:
Paymon Pirzadeh wrote:
Can I change the charge of Na ion added from +1 to +0.99 to cancel the
negative charge exactly? Does that hurt science or simulation?
It's probably irrelevant. The representation of "decimal" numbers on
computers can be inexact, such that things like 0.02 added to itself 100
times does not pass a test for equality with 2. You may be observing
this kind of thing here. Your protein's [atoms] directive has a running
count of the total charge on the molecule - go and read it and see that
each residue has an integral charge. Hopefully you can observe where the
rounding error might be occurring and you can make a judgement about
whether this might be true.
Mark
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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 gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
