AMBER Archive (2004)

Subject: Re: AMBER: Increase lastrst in the &cntrl namelist

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Wed Sep 01 2004 - 12:54:37 CDT

the major difference is that the format is completely different.
also amber8 prmtop files contain some information not in
amber7 prmtops. you can use amber8 leap to generate a new
prmtop using the old leap input, it should work fine.

===================================================================
Carlos L. Simmerling, Ph.D.
Assistant Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
===================================================================

Sichun Yang wrote:

>Just follow up, I found it seems that sander in amber8 doesn't like the
>parm file since I am using the old format of prmtop.
>What is the major difference between the 'old' and 'new' prmtop?
>
>Thanks,
>-Sichun
>
>On Wed, 1 Sep 2004, Osman Gani wrote:
>
>
>
>>Dear Dave & Sichum,
>>Just to take a chance to be corrected if needed-
>>I had the same problem and I increased "lastist" and "lastrst" untill SANDER stopped complaining. In my case, I creased it to:
>>lastist = 2500000,
>>lastrst = 10000000,
>>My system was of 57000 atoms in periodic boundary MD in SANDER8.
>>
>>Regards,
>>Osman
>>-----Original Message-----
>>From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu]On Behalf
>>Of Sichun Yang
>>Sent: 1. september 2004 08:29
>>To: amber_at_scripps.edu
>>Subject: Re: AMBER: Increase lastrst in the &cntrl namelist
>>
>>
>>
>>Dear David,
>>
>>Thank you for your response.
>>
>>I'm using Amber8 and sander is built with -DHAS_10_12.
>>
>>After I insert one line into the namelist like:
>> &cntrl
>> ....
>> lastrst = 800000,
>> /
>>
>>I have the error as follows:
>> Exceeding lastrst in get_stack
>> lastrst = 6504
>> top_stk= 0
>> isize = 22133
>> request= 22133
>> Increase lastrst in the &cntrl namelist
>>
>>I have the same error message without the "lastrst = 800000,"
>>
>>Thanks,
>>-Sichun
>>
>>On Tue, 31 Aug 2004, David A. Case wrote:
>>
>>
>>
>>>On Tue, Aug 31, 2004, Sichun Yang wrote:
>>>
>>>
>>>>I have the error message and then increase the namelist by inserting
>>>>an extra line: lastrst = 2500000.
>>>>However, I check the output and it seems sander didn't take this input.
>>>>Any suggstion? Thanks,
>>>>
>>>>
>>>We need more information: what is the *exact* error message, both before
>>>you added the extra line, and after you added it? What sort of calcualtion
>>>are you running? Which version of amber?
>>>
>>>...dac
>>>
>>>
>>>
>>-----------------------------------------------------------------------
>>The AMBER Mail Reflector
>>To post, send mail to amber_at_scripps.edu
>>To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>>
>>
>>
>
>-----------------------------------------------------------------------
>The AMBER Mail Reflector
>To post, send mail to amber_at_scripps.edu
>To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu