Re: [gmx-users] Insufficient memory (128 GB) for ensemble entropy calculation with gmx covar/gmx anaeig

On 21/06/16 13:56, Tsjerk Wassenaar wrote: Hi David, And why the number of frames? Whoopsydaises. You're absolutely right. Cheers, Tsjerk On Tue, Jun 21, 2016 at 9:52 AM, David van der Spoel wrote: On 21/06/16 09:40, Qasim Pars wrote: Dear David, Could you

Re: [gmx-users] Insufficient memory (128 GB) for ensemble entropy calculation with gmx covar/gmx anaeig

Hi David, And why the number of frames? Cheers, Tsjerk On Tue, Jun 21, 2016 at 9:52 AM, David van der Spoel wrote: > On 21/06/16 09:40, Qasim Pars wrote: > >> Dear David, >> >> Could you please more explain each term of the formula you said? >> >> Formula=The number of

Re: [gmx-users] Insufficient memory (128 GB) for ensemble entropy calculation with gmx covar/gmx anaeig

On 21/06/16 10:25, Billy Williams-Noonan wrote: A related problem, when I compute the entropy for: = - - I get a T of -8640 kJ/mol (or =-28.9 kJ/mol/K) Unit for S is J/mol K. This value seems inordinately high... If T was actually -28.9 kJ/mol that

Re: [gmx-users] Insufficient memory (128 GB) for ensemble entropy calculation with gmx covar/gmx anaeig

A related problem, when I compute the entropy for: = - - I get a T of -8640 kJ/mol (or =-28.9 kJ/mol/K) This value seems inordinately high... If T was actually -28.9 kJ/mol that would match well with experimental data given my enthalpy. I am selecting

Re: [gmx-users] Insufficient memory (128 GB) for ensemble entropy calculation with gmx covar/gmx anaeig

On 21/06/16 09:40, Qasim Pars wrote: Dear David, Could you please more explain each term of the formula you said? Formula=The number of atoms (N * 3)^2 times number of frames times 4 bytes Why square the number of atoms? Because we build a matrix of all degrees of freedom. Why 4 bytes? The

Re: [gmx-users] Insufficient memory (128 GB) for ensemble entropy calculation with gmx covar/gmx anaeig

Dear David, Could you please more explain each term of the formula you said? Formula=The number of atoms (N * 3)^2 times number of frames times 4 bytes Why square the number of atoms? Why 4 bytes? Thanks in advance > On 21 Jun 2016, at 09:39, David van der Spoel wrote:

Re: [gmx-users] Insufficient memory (128 GB) for ensemble entropy calculation with gmx covar/gmx anaeig

Thank you David! :) On 21 June 2016 at 17:24, David van der Spoel wrote: > On 21/06/16 08:54, Billy Williams-Noonan wrote: > >> Thanks for your reply, I think this is helping. >> >>Using your equation above I would need about 82TB for 1000 frames... >> I >> somehow

Re: [gmx-users] Insufficient memory (128 GB) for ensemble entropy calculation with gmx covar/gmx anaeig

On 21/06/16 08:54, Billy Williams-Noonan wrote: Thanks for your reply, I think this is helping. Using your equation above I would need about 82TB for 1000 frames... I somehow feel that this would be inaccessible for any calculation using just one node, which is a requirement for g_covar.

Re: [gmx-users] Insufficient memory (128 GB) for ensemble entropy calculation with gmx covar/gmx anaeig

Apologies... For the 50 frames (not 1000) I have been using, it would take 4.1 TB of RAM. This still seems a bit high. On 21 June 2016 at 16:54, Billy Williams-Noonan < billy.williams-noo...@monash.edu> wrote: > Thanks for your reply, I think this is helping. > >Using your equation above I

Re: [gmx-users] Insufficient memory (128 GB) for ensemble entropy calculation with gmx covar/gmx anaeig

Thanks for your reply, I think this is helping. Using your equation above I would need about 82TB for 1000 frames... I somehow feel that this would be inaccessible for any calculation using just one node, which is a requirement for g_covar. I could reduce the frames but I think I would wind

Re: [gmx-users] Insufficient memory (128 GB) for ensemble entropy calculation with gmx covar/gmx anaeig

On 21/06/16 08:11, Billy Williams-Noonan wrote: Sorry, the original post provides an example of the -dt flag with 100ps intervals. You can calculate how much space you need by number of atoms (N * 3)^2 times number of frames times 4 bytes. Do you select just your biomolecule? On 21 June

Re: [gmx-users] Insufficient memory (128 GB) for ensemble entropy calculation with gmx covar/gmx anaeig

Sorry, the original post provides an example of the -dt flag with 100ps intervals. On 21 June 2016 at 16:10, Billy Williams-Noonan < billy.williams-noo...@monash.edu> wrote: > Thank you for your reply. :) > >My main problem is with gmx covar which does not have a -skip flag. As > you can

Re: [gmx-users] Insufficient memory (128 GB) for ensemble entropy calculation with gmx covar/gmx anaeig

Thank you for your reply. :) My main problem is with gmx covar which does not have a -skip flag. As you can see from the OP I have tried the -dt flag with 250ps intervals. It still crashes due to insufficient memory. It also crasses with 5000ps intervals, giving me just 20ps of frames to

Re: [gmx-users] Insufficient memory (128 GB) for ensemble entropy calculation with gmx covar/gmx anaeig

On 21/06/16 07:34, Billy Williams-Noonan wrote: Hi Gromacs Users, I am running g_mmpbsa.py to calculate the binding enthalpy of a cyclic peptide in a drug target. At the same time I am trying to generate ensemble estimates for entropy for the protein, ligand and complex. By using these two

[gmx-users] Insufficient memory (128 GB) for ensemble entropy calculation with gmx covar/gmx anaeig

Hi Gromacs Users, I am running g_mmpbsa.py to calculate the binding enthalpy of a cyclic peptide in a drug target. At the same time I am trying to generate ensemble estimates for entropy for the protein, ligand and complex. By using these two variables I aim to get an idea of the Gibbs free