[gmx-users] cant load trajectory, low memory

Tasneem Kausar tasneemkausar12 at gmail.com
Mon Apr 24 12:11:18 CEST 2017 

If you are taking confout.gro as your starting input file, it will have all
water and ions of the previous simulation.

On Mon, Apr 24, 2017 at 3:35 PM, Tasneem Kausar <tasneemkausar12 at gmail.com>
wrote:

> Create index group that have both protein and ACO. gmx make_ndx will serve
> this task.
> Then create a pdb file file from gmx trjconv
> Or you can choose system as output and delete ions and solvent from any
> editor.
>
>
>
> On Mon, Apr 24, 2017 at 3:21 PM, abhisek Mondal <abhisek.mndl at gmail.com>
> wrote:
>
>> Hello,
>>
>> Alright. I have tried this but I'm stuck in the following scenario.
>> I'm using trjconv for getting pdb file of the protein-ligand complex (used
>> for umbrella sampling).
>> trjconv_mpi -f confout1.gro -o conf_1.pdb -n index.ndx -s npt.tpr
>>
>> This is giving me the following prompt:
>> Select group for output
>> Group     0 (         System) has 27051263 elements
>> Group     1 (        Protein) has  1588 elements
>> Group     2 (      Protein-H) has  1245 elements
>> Group     3 (        C-alpha) has   158 elements
>> Group     4 (       Backbone) has   474 elements
>> Group     5 (      MainChain) has   633 elements
>> Group     6 (   MainChain+Cb) has   784 elements
>> Group     7 (    MainChain+H) has   785 elements
>> Group     8 (      SideChain) has   803 elements
>> Group     9 (    SideChain-H) has   612 elements
>> Group    10 (    Prot-Masses) has  1588 elements
>> Group    11 (    non-Protein) has 27049675 elements
>> Group    12 (          Other) has    59 elements
>> Group    13 (            ACO) has    59 elements
>> Group    14 (             NA) has 16615 elements
>> Group    15 (             CL) has 16615 elements
>> Group    16 (          Water) has 27016386 elements
>> Group    17 (            SOL) has 27016386 elements
>> Group    18 (      non-Water) has 34877 elements
>> Group    19 (            Ion) has 33230 elements
>> Group    20 (            ACO) has    59 elements
>> Group    21 (             NA) has 16615 elements
>> Group    22 (             CL) has 16615 elements
>> Group    23 ( Water_and_ions) has 27049616 elements
>> Group    24 (
>>
>> Now how can I be able to get both Protein+ACO as a pdb file ?
>> If I could get Protein+ACO, then I could strip the box size for further
>> umbrella sampling procedure.
>>
>> However, is it possible to go with the following way:
>> editconf_mpi -f confout1.gro -o conf_1.gro -c -d 1.0 -bt cubic
>>
>> Please suggest me a way.
>>
>> Thank you.
>>
>> On Mon, Apr 24, 2017 at 1:38 AM, Mark Abraham <mark.j.abraham at gmail.com>
>> wrote:
>>
>> > Hi,
>> >
>> > Take a configuration of interest, strip the solvent, put it in a box you
>> > think is good, and re-equilibrate just like you did before you started.
>> >
>> > Mark
>> >
>> > On Sun, Apr 23, 2017 at 8:59 PM abhisek Mondal <abhisek.mndl at gmail.com>
>> > wrote:
>> >
>> > > Hi,
>> > >
>> > > Yes, I did when I started the simulation. The box size I used to start
>> > the
>> > > simulation was very big(I was dealing with an unknown sample). After
>> > > successfully generating the configurations I realized that further
>> work
>> > > could move faster if I could trim the box size little bit now.
>> > > So is there any way now to reduce the box size and proceed with
>> relevant
>> > > configurations towards PMF generation ?
>> > > Please suggest me a way here.
>> > >
>> > > Thank you.
>> > >
>> > > On Apr 24, 2017 12:22 AM, "Mark Abraham" <mark.j.abraham at gmail.com>
>> > wrote:
>> > >
>> > > > Hi,
>> > > >
>> > > > You get to choose the box size eg with editconf when you set up your
>> > > > simulation. It's not pre-defined ;-)
>> > > >
>> > > > Mark
>> > > >
>> > > > On Sun, 23 Apr 2017 20:28 abhisek Mondal <abhisek.mndl at gmail.com>
>> > wrote:
>> > > >
>> > > > > Hello,
>> > > > >
>> > > > > Another thing I wanted to ask.
>> > > > > After generating configurations I found out that the predefined
>> box
>> > > size
>> > > > > (used to reach so far) is excessively high.
>> > > > > Is it possible to trim the box size to perform further mdrun
>> during
>> > > > > umbrella sampling?
>> > > > >
>> > > > > Please suggest me a way, it is taking very long time with current
>> box
>> > > > size.
>> > > > >
>> > > > > Thank you.
>> > > > >
>> > > > >
>> > > > >
>> > > > > On Apr 23, 2017 10:02 PM, "Mark Abraham" <
>> mark.j.abraham at gmail.com>
>> > > > wrote:
>> > > > >
>> > > > > > Hi,
>> > > > > >
>> > > > > > You can only load a trajectory with fewer frames. Either don't
>> > write
>> > > so
>> > > > > > many, or filter it with trjconv first.
>> > > > > >
>> > > > > > Mark
>> > > > > >
>> > > > > > On Sun, 23 Apr 2017 17:20 abhisek Mondal <
>> abhisek.mndl at gmail.com>
>> > > > wrote:
>> > > > > >
>> > > > > > > Hi,
>> > > > > > > I'm having a problem loading trajectory file after umbrella
>> > > sampling.
>> > > > > The
>> > > > > > > file is so huge in size that the VMD finally runs out of
>> memory.
>> > > I'm
>> > > > > > > operating with 125gb of physical memory here though.
>> > > > > > >
>> > > > > > > Is there any way out of it ?
>> > > > > > >
>> > > > > > >
>> > > > > > > Thank you
>> > > > > > > --
>> > > > > > > Abhisek Mondal
>> > > > > > >
>> > > > > > > *Senior Research Fellow*
>> > > > > > >
>> > > > > > > *Structural Biology and Bioinformatics Division*
>> > > > > > > *CSIR-Indian Institute of Chemical Biology*
>> > > > > > >
>> > > > > > > *Kolkata 700032*
>> > > > > > >
>> > > > > > > *INDIA*
>> > > > > > > --
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>>
>>
>> --
>> Abhisek Mondal
>>
>> *Senior Research Fellow*
>>
>> *Structural Biology and Bioinformatics Division*
>> *CSIR-Indian Institute of Chemical Biology*
>>
>> *Kolkata 700032*
>>
>> *INDIA*
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
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>
>

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