[gmx-users] About support for infinite systems in cvs version

[Wei Zhang]

Dear David,

I know what's the problem now. And I know what "pbc=full" means now. Thanks.
I found that when posre.itp is present in the working directory, with 
#ifdef POSRES         
#include "posre.itp"  
#endif                
in the topology file, even without "-r" in "grompp" command, there are constraints used all the same.  

======= 2003-09-19 20:06:00 您在来信中写道：=======

>On Fri, 2003-09-19 at 19:48, Wei Zhang wrote:
>> Dear David,
>> 
>> Oh, sorry, Maybe it's not problem on the pbc support.
>> 
>> I used bonds type 1, angles 1, dihedrals 1 for the interaction of carbon atoms in the nanotube.  pbc=xyz. When I ran Gromacs 3.1.2 in windows XP, the structure was steady. But when I changed it into the CVS version, and used pbc=full,the structure became unsteady and deformed.
>
>have you checked energies? are the bond energies ridiculously large?
>
>> 	
>> 
>> ======= 2003-09-20 01:17:00 您在来信中写道：=======
>> 
>> >Dear David,
>> >
>> >I don't see the support for infinite systems in the current CVS verion Gromacs works.
>> >
>> >I simulated a carbon nanotube. I used periodic boundary condition. When I use the windows version 3.1.2, it runs fine. But when I use the CVS version and let pbc=full, it gives bad result. 
>> >  
>> >
>> >　　　　　　　　Wei Zhang
>> >　　　　　　　　zhangw at sinr.ac.cn
>> >　　　　　　　　　　2003-09-20
>> >
>> >
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>> 			
>> 
>> 　　　　　　　　致
>> 礼！
>>  
>> 				 
>> 　　　　　　　　Wei Zhang
>> 　　　　　　　　zhangw at sinr.ac.cn
>> 　　　　　　　　　　2003-09-20
>> 
>> 
>> 
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>-- 
>Groeten, David.
>________________________________________________________________________
>Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
>Husargatan 3, Box 596,  	75124 Uppsala, Sweden
>phone:	46 18 471 4205		fax: 46 18 511 755
>spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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　　　　　　　　致
礼！
 
				 
　　　　　　　　Wei Zhang
　　　　　　　　zhangw at sinr.ac.cn
　　　　　　　　　　2003-09-21