回复：Re: [gmx-users] Insert a certain number of water molecules into ananotube

[Justin A. Lemkul]

toby10222224 at 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 <jalemkul at vt.edu>
> 收件人：Discussion list for GROMACS users <gmx-users at gromacs.org>
> 主题：Re: [gmx-users] Insert a certain number of water molecules into 
> ananotube
> 日期：2009-7-19 19:47:45
> 
> 
> 
> toby10222224 at 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!
>  >
>  >
>  > ------------------------------------------------------------------------
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> -- 
> ========================================
> 
> 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
> 
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-- 
========================================

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

========================================