AMBER Archive (2004)

Subject: Re: Re: AMBER: NB pairs exceeds?

From: Chen (csong_at_mail.sdu.edu.cn)
Date: Fri Jul 16 2004 - 03:40:42 CDT

Wulei,Thanks for your reply.But I think maybe there is something wrong with Leap,becaue after I solvate the DNA fragment,the density of the system is about 2.0g/cc when the buffer is 8.0;but it is about 1.0g/cc when the buffer is 5.0.
Further more,the pdb file of the solvated system looks very strange--only part of the fragment is solvated!

Maybe I made some mistakes when I used leap.I'll check it.
Thanks.

        

======= 2004-07-16 16:07:56 =======

>Maybe you should lower the cutoff value or modify the source file to relax the limitation of size of the non-bond list.
>
>good luck!
>wulei
>
>----- Original Message -----
>From: "Chen" <csong_at_mail.sdu.edu.cn>
>To: "amber" <amber_at_scripps.edu>
>Sent: Friday, July 16, 2004 3:35 PM
>Subject: AMBER: NB pairs exceeds?
>
>
>> Hi,amber users:
>> I met with a problem when I used sander(amber8) to do some simulations.It gave me some information like this:
>>
>>
>> * NB pairs 540 8952737 exceeds capacity ( 8952768) 0
>> SIZE OF NONBOND LIST = 8952768
>> SANDER BOMB in subroutine nonbond_list
>> Non bond list overflow!
>> check MAXPR in locmem.f
>>
>> What's the matter?Is it because that my system is too large? There are altogether 15543 atoms in my system.
>>
>> Thanks in advance.
>>
>> 　　　　　　　　
>>
>>
>> 　　　　　　　　Chen
>> 　　　　　　　　csong_at_mail.sdu.edu.cn
>> 　　　　　　　　　　2004-07-16
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= = = = = = = = = = = = = = = = = = = =
                        
 
                 
　　　　　　　　Chen
　　　　　　　　csong_at_mail.sdu.edu.cn
　　　　　　　　　　2004-07-16

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