toby10222...@sina.com wrote:
Hi
The first option(genbox -cp -cs spc216.gro -maxsol 328) is not
suitable for my system, because according to Gromacs, the tube is not
large enough for 328 water molecules. This option can only insert 257
molecules into the tube. The tube is a (8,8) carbon nanotube with its
radius 1.08 nm and length 24.6 nm.
When I take the second option(genbox -cp -ci water.gro -nmol 328), it
occupies huge memory which causes an following error.
Well, if the first option failed, consider whether or not there actually is
sufficient room to place that many water molecules. If you want to keep trying,
you could add a fraction of the total amount each time, sequentially using -ci
-nmol, until all 328 are placed, but again I'm skeptical if that can be done.
-Justin
Program genbox, VERSION 4.0.5
Source code file: smalloc.c, line: 179
Fatal error:
Not enough memory. Failed to realloc 115408 bytes for nlist->jjnr,
nlist->jjnr=0xbff58158
(called from file ns.c, line 499)
-------------------------------------------------------
"Rub It Right Accross Your Eyes" (F. Zappa)
: Cannot allocate memory
Besides using larger memory computers, are there any other methods to
do this in Gromacs, such as decreasing the distance between water
molecules?
----- 原始邮件 -----
发件人：Justin A. Lemkul <jalem...@vt.edu>
收件人：Discussion list for GROMACS users <gmx-users@gromacs.org>
主题：Re: [gmx-users] Insert a certain number of water molecules into
ananotube
日期：2009-7-19 19:47:45
toby10222...@sina.com wrote:
> Dear all:
>
>
>
> I am trying to insert a certain number of water molecules into a
> nanotube with Gromacs-4.0.5.
>
> When I input the command "genbox -cp tube.gro -ci spc216.gro -nmol 328
> -try 20 -o",
>
> I get the following error.
>
>
>
> Program genbox, VERSION 4.0.5
> Source code file: gmx_genbox.c, line: 318
>
> Fatal error:
> more then one residue in insert molecules
> program terminated
>
>
>
> Should the insert molecules be no more than one residue?
>
You are using a file (spc216.gro) that contains 216 residues, not one, so
Gromacs is crashing.
> If it should be, how can I insert 328 water molecules into the tube?
>
> Are there any other commands in Gromacs that can be used for the same
thing?
>
Two options:
genbox -cp -cs spc216.gro -maxsol 328
or obtain a water.gro that contains 1 water molecule and
genbox -cp -ci water.gro -nmol 328
-Justin
>
>
> Thank you in advance!
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> 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
--
========================================
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
