Hi,
I will try, thans very much!
2011/7/18, Daniel Roe <daniel.r.roe.gmail.com>:
> Hi,
>
>> Estimated memory usage for this hbond call: 25.35 GB
>
> Do you have this much memory available on the computer you are running
> the ptraj hbond analysis on? If not, this is the reason for your
> segfault. The estimate is based on the number of possible hbonds, as
> well as the total # of frames that will be read in, so break up your
> analysis into manageable chunks. E.g. if you have 8 GB of memory
> available then reading in 500 sets at a time should be OK.
>
> -Dan
>
> On Fri, Jul 15, 2011 at 11:21 PM, qiao xue <xueqiaoup.gmail.com> wrote:
>> Thanks very much, Roe.
>>
>> I am using the Amber 10 and Ambertool1.2. The bugfix is 10.0 bugfixes.
>> And the compilers is Inter 11.1. The OS is linux.
>>
>> My system is made up of 127 residues. I did 5ns. There are 2500 frames
>> in the md trajectory.
>>
>> the input and out file are attached.
>>
>> 2011/7/14, Daniel Roe <daniel.r.roe.gmail.com>:
>>> Hi,
>>>
>>> On Wed, Jul 13, 2011 at 7:54 PM, qiao xue <xueqiaoup.gmail.com> wrote:
>>>> When I am doing the Hbond analysis it often suffers the error
>>>> "segmentation fault".
>>>
>>> Can you please post more details about your system so we can try and
>>> reproduce the error?
>>> - What version of AmberTools are you using, what bugfixes have you
>>> applied, what compilers (and version) are you using and on what OS?
>>> - How large is your system (# atoms), how many frames is your
>>> trajectory, are box coords present? Ideally attach the topology file
>>> and 1 coordinate frame or restart file.
>>> - Post the exact ptraj input you are using, and optionally attach the
>>> output you are getting.
>>> Thanks!
>>>
>>> -Dan
>>>
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>>>
>>
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Received on Tue Jul 19 2011 - 19:30:02 PDT
