Re: [AMBER] question about amber

From: Ross Walker <>
Date: Tue, 14 Jun 2011 01:33:08 -0700

Hi Sara,


I am cc'ing this to the AMBER mailing list since this is typically the best
place for such questions. You can signup here:


This seems like a VERY low density system for just 60,480 atoms. You should
check your box size to make sure it is correct.


I would also check that you are definitely using AMBER 10 and it has all the
latest patches.


Another thing is that this error message does not appear to be in Sander
(which has a limit of 2048), it is part of pmemd so I am assuming you are
using pmemd even though you do not mention it. In my version of AMBER 10,
from the original tar.bz2 release the maximum is 512 (gridhi) and NOT 256 so
are sure you are using a fully patched version of AMBER 10?


grep gridhi *

mdin_ewald_dat.fpp: integer, parameter :: gridhi = 512

mdin_ewald_dat.fpp: call int_legal_range('nfft1', nfft1, gridlo, gridhi,

mdin_ewald_dat.fpp: call int_legal_range('nfft2', nfft2, gridlo, gridhi,

mdin_ewald_dat.fpp: call int_legal_range('nfft3', nfft3, gridlo, gridhi,


So I am confused why you are seeing this error message. I would check your
simulation setup and environment carefully.


All the best



From: Sara Ahmadi []
Sent: Tuesday, June 14, 2011 1:12 AM
Subject: question about amber


Dear Prof. Ross Waalker

I am using amber 10 for simulation a hexagonal system. My system has 60480
atoms including water. I have used the periodic boundary condition and the
dimensions of the box is :
138.8290000 220.4190000 262.4840000, but I can not do the simulation. it
has the error " nfft3 must be in the range of 6 to 256! "

and now I don't know what should I do or which Item I have to change?

would you please help me

with best regards



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Received on Tue Jun 14 2011 - 02:00:03 PDT
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