[gmx-users] cant load trajectory, low memory
Justin Lemkul
jalemkul at vt.edu
Mon Apr 24 18:58:25 CEST 2017
On 4/24/17 12:56 PM, abhisek Mondal wrote:
> Hello,
>
> I'm using the configurations generated by pulling run to re-box > resolvate
>> ion addition > EM > npt_umbrella(10ns) and forward.
>
> So, please clarify me something. Am I following correct path ? Should I
> have given a npt equilibration step prior to npt_umbrella step ?
>
Yes, as Mark said, you're essentially building all new simulation systems.
Since this is part of an umbrella sampling series, be sure you're getting the
same (or at least, very similar) number of water molecules in each box.
-Justin
> Thank you.
>
> On Mon, Apr 24, 2017 at 4:26 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
>> Hi,
>>
>> I already answered that. You're effectively starting again, so do that.
>>
>> Mark
>>
>> On Mon, Apr 24, 2017 at 12:28 PM abhisek Mondal <abhisek.mndl at gmail.com>
>> wrote:
>>
>>> Ok, I got it this time.
>>> But what kind of equilibration I'm to perform on these stripped
>> structures.
>>> Should I perform normal NPT equilibration as done before generating
>>> configurations ? or I'm to run gmx grompp -f npt_umbrella.mdp -c
>> conf0.gro
>>> -p topol.top -n index.ndx -o npt0.tpr (using standard mdp from tutorial
>>> page) and followed by mdrun step ?
>>>
>>>
>>>
>>>
>>> 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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>>>>>>>>>>>
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>>>>>>>>>>>
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>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> 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*
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>
>
>
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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