Any update on the post-processing of forces?
Should be going through the developer's list instead?
> On Nov 9, 2018, at 1:35 PM, SARAH JEANNE LEFAVE <s.lefave.utah.edu> wrote:
>
> ah, ok! well at least we know what the issue it!
>
> Thank you and looking forward to getting it worked out!
>
>> On Nov 9, 2018, at 1:22 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>
>> Yikes - just scanning through the code in sander it seems like a call
>> to write forces was never actually implemented during imin=5
>> post-processing. I'll have to look into doing this when I have time,
>> but I'll be traveling next week so I may not be able to get to it
>> until I'm back. I'll CC the developer's list in case another developer
>> wants to take a crack at it...
>>
>> Thanks for the report!
>>
>> -Dan
>> On Fri, Nov 9, 2018 at 3:17 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>>
>>> Hi,
>>>
>>> I do see that the forces output from imin=5 are in fact zero - let me
>>> dig into this a little deeper...
>>>
>>> -Dan
>>> On Thu, Nov 8, 2018 at 4:31 PM SARAH JEANNE LEFAVE <s.lefave.utah.edu> wrote:
>>>>
>>>> Ah ok! Thank you!
>>>>
>>>> Are there other force functionalities that weren’t implemented until later? Specifically with imin=5 to post-process and calculate forces? I’ve been trying with amber 16 and have gotten 0 for all the forces after trying many variations of input specification. Using ntwf =-1 with a normal production does output the forces but I’d like to do a post process calculation where solvent charges are 0.
>>>>
>>>> Thanks Dan!
>>>>
>>>>> On Nov 8, 2018, at 2:07 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>>>>
>>>>> That explains it - usefrcascoords wasn't added until version 17. I
>>>>> recommend upgrading to at least AmberTools 18 or the current GitHub
>>>>> version (https://github.com/Amber-MD/cpptraj).
>>>>>
>>>>> -Dan
>>>>>> On Thu, Nov 8, 2018 at 3:50 PM SARAH JEANNE LEFAVE <s.lefave.utah.edu> wrote:
>>>>>>
>>>>>> V16.16
>>>>>>
>>>>>>> On Nov 8, 2018, at 1:46 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>>>>>>
>>>>>>> Which version of cpptraj are you using?
>>>>>>>
>>>>>>> -Dan
>>>>>>>> On Thu, Nov 8, 2018 at 3:34 PM SARAH JEANNE LEFAVE <s.lefave.utah.edu> wrote:
>>>>>>>>
>>>>>>>> Hi all,
>>>>>>>>
>>>>>>>> We have been outputting both force and velocity data into a combined NetCDF file. In cpptraj when we do the following with ‘usefrcascoords’ the coordinates that are being output are still the positional coordinates. We get the same values regardless of ‘usefrcascoords’ being present.
>>>>>>>>
>>>>>>>> parm parameter.parm7
>>>>>>>> trajin combinedtraj.nc usefrcascoords
>>>>>>>> trajout forces.pdb pdb
>>>>>>>> run
>>>>>>>>
>>>>>>>> We have also used the “mdfrc” flag with trajout to generate a new NetCDF file then used ncdump to get a readable file. This file does contain both positional coordinates and force data but it would be preferable to have separate be able to generate a separate coordinate and force file.
>>>>>>>>
>>>>>>>> parm parameter.parm7
>>>>>>>> trajin combinedtraj.nc
>>>>>>>> trajout forces.nc mdfrc
>>>>>>>> run
>>>>>>>>
>>>>>>>> Is there something we are missing with cpptraj?
>>>>>>>> Thank you!
>>>>>>>> Sarah
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Received on Mon Nov 26 2018 - 10:00:03 PST
