Re: [gmx-users] cant load trajectory, low memory

[abhisek Mondal]

Hi,

I'm facing a strange problem. I have equilibrated my protein-ligand  system
in NVT run of 20ns. The temperature curve get finely converged here. But
when I try to run NPT after that, it gives me an issue as "The sum of the
two largest charge group radii (13.169886) is larger than rlist (1.40)".
MDP used:
title   = NPT Equilibration
define  = -DPOSRES ; position restrain the protein
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 500   ; 2 * 500 = 10ns
dt  = 0.002 ; 2 fs
; Output control
nstxout = 1000  ; save coordinates every 2 ps
nstvout = 1000  ; save velocities every 2 ps
nstenergy   = 1000  ; save energies every 2 ps
nstlog  = 1000  ; update log file every 2 ps
; Bond parameters
continuation = no; Initial simulation
constraint_algorithm = lincs ; holonomic constraints
constraints  = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter   = 1 ; accuracy of LINCS
lincs_order  = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cels
nstlist = 5 ; 10 fs
rlist   = 1.4   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.4   ; short-range electrostatic cutoff (in nm)
rvdw= 1.4   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = V-rescale ; Berendsen is not suitable for
 free-energy calculations, so using this
tc-grps = Protein_ACO  Water_and_ions ; two coupling groups - more
accurate
tau_t   = 0.1 0.1 ; time constant, in ps
ref_t   = 310 310 ; reference temperature, one for each group,
in K
; Pressure coupling is on
pcoupl  = Berendsen ; Pressure coupling on in NPT, also
weak coupling
pcoupltype  = isotropic ; uniform scaling of x-y-z box vectors
tau_p   = 2.0   ; time constant, in ps
ref_p   = 1.0   ; reference pressure (in bar)
compressibility = 4.5e-5; isothermal compressibility, bar^-1
refcoord_scaling= com
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; Velocity generation is off, as continuing
from NVT
gen_temp= 310   ; temperature for velocity generation
gen_seed= -1; random seed
; COM motion removal
; These options remove COM motion of the system
nstcomm = 10
comm-mode   = Linear
comm-grps   = System


I don't understand why am i getting this error after successful completion
of 1st equilibration step.
Am I making any mistakes here ?
Please suggest.

Thank you

On Tue, Apr 25, 2017 at 3:50 PM, Mark Abraham 
wrote:

> Hi,
>
> Presumably that was discussed in the tutorial you were following. The Unix
> diff tool can help with physically inspecting what is different between
> those files. But really you should already know! A good rule of thumb is
> not run a big calculation on expensive hardware
> unless you know why you are doing it.
>
> Mark
>
> On Tue, 25 Apr 2017 12:13 abhisek Mondal  wrote:
>
> > Hi,
> >
> > I'm going with it.
> >
> > I still have a question. If I reconstruct the system (stripping the
> solvent
> > and thus making smaller box size) I need to go through NVT>NPT
> > equilibrations again. This part I got it.
> > The question is, do I need to run the npt_umbrella.mdp or simple npt.mdp
> > will do ?
> > What is the difference between running npt simulation with npt.mdp and
> > npt_umbrella.mdp ?
> >
> > Please help me to catch up here.
> >
> > Thank you.
> >
> > On Mon, Apr 24, 2017 at 10:28 PM, Justin Lemkul  wrote:
> >
> > >
> > >
> > > 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 

Re: [gmx-users] cant load trajectory, low memory

[Mark Abraham]

Hi,

Presumably that was discussed in the tutorial you were following. The Unix
diff tool can help with physically inspecting what is different between
those files. But really you should already know! A good rule of thumb is
not run a big calculation on expensive hardware
unless you know why you are doing it.

Mark

On Tue, 25 Apr 2017 12:13 abhisek Mondal  wrote:

> Hi,
>
> I'm going with it.
>
> I still have a question. If I reconstruct the system (stripping the solvent
> and thus making smaller box size) I need to go through NVT>NPT
> equilibrations again. This part I got it.
> The question is, do I need to run the npt_umbrella.mdp or simple npt.mdp
> will do ?
> What is the difference between running npt simulation with npt.mdp and
> npt_umbrella.mdp ?
>
> Please help me to catch up here.
>
> Thank you.
>
> On Mon, Apr 24, 2017 at 10:28 PM, Justin Lemkul  wrote:
>
> >
> >
> > 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  >
> >> 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.m...@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 ?
> 
> 
>  
> >>>
> >>>
> --
> 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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> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] cant load trajectory, low memory

[abhisek Mondal]

Hi,

I'm going with it.

I still have a question. If I reconstruct the system (stripping the solvent
and thus making smaller box size) I need to go through NVT>NPT
equilibrations again. This part I got it.
The question is, do I need to run the npt_umbrella.mdp or simple npt.mdp
will do ?
What is the difference between running npt simulation with npt.mdp and
npt_umbrella.mdp ?

Please help me to catch up here.

Thank you.

On Mon, Apr 24, 2017 at 10:28 PM, Justin Lemkul  wrote:

>
>
> 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 
>> 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 
>>> 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 ?


 
>>>
>>>
-- 
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

* For (un)subscribe requests visit
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] cant load trajectory, low memory

[Justin Lemkul]

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 
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 
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 <

tasneemkausa...@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.m...@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
Group10 (Prot-Masses) has  1588 elements
Group11 (non-Protein) has 27049675 elements
Group12 (  Other) has59 elements
Group13 (ACO) has59 elements
Group14 ( NA) has 16615 elements
Group15 ( CL) has 16615 elements
Group16 (  Water) has 27016386 elements
Group17 (SOL) has 27016386 elements
Group18 (  non-Water) has 34877 elements
Group19 (Ion) has 33230 elements
Group20 (ACO) has59 elements
Group21 ( NA) has 16615 elements
Group22 ( CL) has 16615 elements
Group23 ( Water_and_ions) has 27049616 elements
Group24 (

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.abra...@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.m...@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.abra...@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.m...@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.abra...@gmail.com



wrote:



Hi,

You can only load a trajectory with fewer frames. Either

don't

write

so

many, or filter 

Re: [gmx-users] cant load trajectory, low memory

[abhisek Mondal]

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 ?

Thank you.

On Mon, Apr 24, 2017 at 4:26 PM, Mark Abraham 
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 
> 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 <
> tasneemkausa...@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.m...@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
> > > > Group10 (Prot-Masses) has  1588 elements
> > > > Group11 (non-Protein) has 27049675 elements
> > > > Group12 (  Other) has59 elements
> > > > Group13 (ACO) has59 elements
> > > > Group14 ( NA) has 16615 elements
> > > > Group15 ( CL) has 16615 elements
> > > > Group16 (  Water) has 27016386 elements
> > > > Group17 (SOL) has 27016386 elements
> > > > Group18 (  non-Water) has 34877 elements
> > > > Group19 (Ion) has 33230 elements
> > > > Group20 (ACO) has59 elements
> > > > Group21 ( NA) has 16615 elements
> > > > Group22 ( CL) has 16615 elements
> > > > Group23 ( Water_and_ions) has 27049616 elements
> > > > Group24 (
> > > >
> > > > 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.abra...@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.m...@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.abra...@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 ;-)
> > > > > > >
> 

Re: [gmx-users] cant load trajectory, low memory

[Mark Abraham]

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 
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  >
> 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 
> > 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
> > > Group10 (Prot-Masses) has  1588 elements
> > > Group11 (non-Protein) has 27049675 elements
> > > Group12 (  Other) has59 elements
> > > Group13 (ACO) has59 elements
> > > Group14 ( NA) has 16615 elements
> > > Group15 ( CL) has 16615 elements
> > > Group16 (  Water) has 27016386 elements
> > > Group17 (SOL) has 27016386 elements
> > > Group18 (  non-Water) has 34877 elements
> > > Group19 (Ion) has 33230 elements
> > > Group20 (ACO) has59 elements
> > > Group21 ( NA) has 16615 elements
> > > Group22 ( CL) has 16615 elements
> > > Group23 ( Water_and_ions) has 27049616 elements
> > > Group24 (
> > >
> > > 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.abra...@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.m...@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"  >
> > > > 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  >
> > > > 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.
> > > > > > >
> > > > 

Re: [gmx-users] cant load trajectory, low memory

[abhisek Mondal]

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 
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 
> 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
> > Group10 (Prot-Masses) has  1588 elements
> > Group11 (non-Protein) has 27049675 elements
> > Group12 (  Other) has59 elements
> > Group13 (ACO) has59 elements
> > Group14 ( NA) has 16615 elements
> > Group15 ( CL) has 16615 elements
> > Group16 (  Water) has 27016386 elements
> > Group17 (SOL) has 27016386 elements
> > Group18 (  non-Water) has 34877 elements
> > Group19 (Ion) has 33230 elements
> > Group20 (ACO) has59 elements
> > Group21 ( NA) has 16615 elements
> > Group22 ( CL) has 16615 elements
> > Group23 ( Water_and_ions) has 27049616 elements
> > Group24 (
> >
> > 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 
> > 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  >
> > > 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" 
> > > 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 
> > > 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.abra...@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 

Re: [gmx-users] cant load trajectory, low memory

[Tasneem Kausar]

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 
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 
> 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
>> Group10 (Prot-Masses) has  1588 elements
>> Group11 (non-Protein) has 27049675 elements
>> Group12 (  Other) has59 elements
>> Group13 (ACO) has59 elements
>> Group14 ( NA) has 16615 elements
>> Group15 ( CL) has 16615 elements
>> Group16 (  Water) has 27016386 elements
>> Group17 (SOL) has 27016386 elements
>> Group18 (  non-Water) has 34877 elements
>> Group19 (Ion) has 33230 elements
>> Group20 (ACO) has59 elements
>> Group21 ( NA) has 16615 elements
>> Group22 ( CL) has 16615 elements
>> Group23 ( Water_and_ions) has 27049616 elements
>> Group24 (
>>
>> 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 
>> 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 
>> > 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" 
>> > 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 
>> > 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.abra...@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.m...@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.
>> > 

Re: [gmx-users] cant load trajectory, low memory

[Tasneem Kausar]

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 
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
> Group10 (Prot-Masses) has  1588 elements
> Group11 (non-Protein) has 27049675 elements
> Group12 (  Other) has59 elements
> Group13 (ACO) has59 elements
> Group14 ( NA) has 16615 elements
> Group15 ( CL) has 16615 elements
> Group16 (  Water) has 27016386 elements
> Group17 (SOL) has 27016386 elements
> Group18 (  non-Water) has 34877 elements
> Group19 (Ion) has 33230 elements
> Group20 (ACO) has59 elements
> Group21 ( NA) has 16615 elements
> Group22 ( CL) has 16615 elements
> Group23 ( Water_and_ions) has 27049616 elements
> Group24 (
>
> 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 
> 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 
> > 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" 
> > 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 
> > 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"  >
> > > > 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  >
> > > > 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*
> > > > > > >
> > > > 

Re: [gmx-users] cant load trajectory, low memory

[Mark Abraham]

Hi,

You need to make an index group (e.g. gmx select or gmx make_ndx) that has
the things you want (e.g. protein + ACO, or perhaps everything but
water+ions). See also
http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume.
I'd guess your system has at least a factor of 10 more water than you need.
More like a factor of 100 ;-)

Mark

On Mon, Apr 24, 2017 at 11:52 AM abhisek Mondal 
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
> Group10 (Prot-Masses) has  1588 elements
> Group11 (non-Protein) has 27049675 elements
> Group12 (  Other) has59 elements
> Group13 (ACO) has59 elements
> Group14 ( NA) has 16615 elements
> Group15 ( CL) has 16615 elements
> Group16 (  Water) has 27016386 elements
> Group17 (SOL) has 27016386 elements
> Group18 (  non-Water) has 34877 elements
> Group19 (Ion) has 33230 elements
> Group20 (ACO) has59 elements
> Group21 ( NA) has 16615 elements
> Group22 ( CL) has 16615 elements
> Group23 ( Water_and_ions) has 27049616 elements
> Group24 (
>
> 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 
> 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 
> > 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" 
> > 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 
> > 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"  >
> > > > 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  >
> > > > 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*
> > > > 

Re: [gmx-users] cant load trajectory, low memory

[abhisek Mondal]

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
Group10 (Prot-Masses) has  1588 elements
Group11 (non-Protein) has 27049675 elements
Group12 (  Other) has59 elements
Group13 (ACO) has59 elements
Group14 ( NA) has 16615 elements
Group15 ( CL) has 16615 elements
Group16 (  Water) has 27016386 elements
Group17 (SOL) has 27016386 elements
Group18 (  non-Water) has 34877 elements
Group19 (Ion) has 33230 elements
Group20 (ACO) has59 elements
Group21 ( NA) has 16615 elements
Group22 ( CL) has 16615 elements
Group23 ( Water_and_ions) has 27049616 elements
Group24 (

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 
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 
> 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" 
> 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 
> 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" 
> > > 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 
> > > 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*
> > > > > > --
> > > > > > 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
> > > > > >
> > > > > > * For (un)subscribe requests visit
> > > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_
> gmx-users
> > > or
> > > > > > send a mail to gmx-users-requ...@gromacs.org.
> > > > > 

Re: [gmx-users] cant load trajectory, low memory

[Mark Abraham]

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 
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"  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  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" 
> > 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 
> > 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*
> > > > > --
> > > > > 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
> > > > >
> > > > > * For (un)subscribe requests visit
> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > > > > send a mail to gmx-users-requ...@gromacs.org.
> > > > >
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at http://www.gromacs.org/
> > > > Support/Mailing_Lists/GMX-Users_List before posting!
> > > >
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> > > >
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> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
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> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
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> * Please search the archive at
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Re: [gmx-users] cant load trajectory, low memory

[abhisek Mondal]

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"  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  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" 
> 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 
> 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*
> > > > --
> > > > 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
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > > --
> > > 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
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> >
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
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>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
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Re: [gmx-users] cant load trajectory, low memory

[Mark Abraham]

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  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"  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  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*
> > > --
> > > 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
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
> > 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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> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
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>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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Re: [gmx-users] cant load trajectory, low memory

[abhisek Mondal]

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"  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  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*
> > --
> > 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
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
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>
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> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] cant load trajectory, low memory

[Mark Abraham]

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  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*
> --
> 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
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] cant load trajectory, low memory

[abhisek Mondal]

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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