memory allocate problem

[변진영]

Dear g_mmpbas users,

When I run g_mmpbsa with protein-ligand complex that is represented by charmm force field, I met the Cannot allocate memory error

So I extracted the trajectory file from 0 ~ 5ns(half timesize; md production: 10ns) by using the 'gmx trjconv' to reduce the trajectory file size.

And I didn't have problem when I issued the 'gmx rms' or 'gmx gyrate', which the other topic mentioned as a solution

But I still have the same problem. 

How can I solve this problem?

Thank you

[Nikhil Maroli]

go through the thread, its already discussed here several times.

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Regards,

Nikhil Maroli

[변진영]

Could you link the thread..? I can't find the satisfied answer.

2020년 5월 21일 (목) 오후 8:34, Nikhil Maroli <scin...@gmail.com>님이 작성:

To view this discussion on the web visit https://groups.google.com/d/msgid/g_mmpbsa/CAMEzy6S7z9n2VGh9Qg7SmwO7XGGMkKt22OExS7TssbRi1ujotQ%40mail.gmail.com.

[변진영]

2020년 5월 22일 금요일 오전 9시 34분 22초 UTC+9, 변진영 님의 말:

Could you link the thread..? I can't find the satisfied answer.

2020년 5월 21일 (목) 오후 8:34, Nikhil Maroli <scin...@gmail.com>님이 작성:

go through the thread, its already discussed here several times.

On Thu, May 21, 2020 at 5:02 PM 변진영 <byunj...@gmail.com> wrote:

Dear g_mmpbas users,

When I run g_mmpbsa with protein-ligand complex that is represented by charmm force field, I met the Cannot allocate memory error

So I extracted the trajectory file from 0 ~ 5ns(half timesize; md production: 10ns) by using the 'gmx trjconv' to reduce the trajectory file size.

And I didn't have problem when I issued the 'gmx rms' or 'gmx gyrate', which the other topic mentioned as a solution

But I still have the same problem. 

How can I solve this problem?

Thank you

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Regards,

Nikhil Maroli

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[g_mmpbsa Mailing List]

Hi,

You might need to check gmemceil (http://rashmikumari.github.io/g_mmpbsa/Polar-solvation-input-parameters.html#gmemceil) and gridspace (http://rashmikumari.github.io/g_mmpbsa/Polar-solvation-input-parameters.html#gridspace) parameters.

Finer the grid, larger memory (also time) is required for the calculation and decreasing gmemceil can be used to tell how much memory is available for calculation.

[g_mmpbsa Mailing List]

Also, please read this: http://redmine.gromacs.org/issues/2752.

You might be trying to read tpr file generated from different version of Gromacs.

On Thursday, May 21, 2020 at 12:32:02 PM UTC+1, 변진영 wrote: