Re: [gmx-users] How to write pull code in umbrella sampling

[Qing Lv]

Thank you, Justin.


My goal is to investigate the conformation transition of a 30aa loop between an 
unstructured loop and an alpha-helix. I found a transition pathway on free 
energy landscape and selected a number of frames along the pathway for umbrella 
sampling. So, should I define C-alpha of this 30aa loop as pull-group1 and 
C-alpha of the remaining part as pull-group2 ? Would the pull geometry still be 
"distance"? But this will just restrain the distance between COM of the 2 
groups to the initial distance, but cannot restrain the conformation of the 
loop.
Or need I divide the loop into many small segments (pull-groups) and define the 
pull coordinates separately? This seems horrible...


Thanks,
Qing


At 2017-04-08 09:06:46, "Justin Lemkul"  wrote:
>
>
>On 4/7/17 8:56 PM, Qing Lv wrote:
>> Dear Colleagues,
>>
>>
>> I am trying to do an umbrella sampling using a series of conformations 
>> extracted from several unbiased MD trajectories. But I am not sure about the 
>> pull code in .mdp file.
>> Below is the pull code from the tutorial of Dr. Justin Lemkul :
>> define  = -DPOSRES_B ; (Why ??)
>
>Did you read the paper I linked from the tutorial, which explains why this is 
>done for this very specific case?
>
>> ; Pull code
>> pull= yes
>> pull_ngroups= 2
>> pull_ncoords= 1
>> pull_group1_name= Chain_B
>> pull_group2_name= Chain_A
>> pull_coord1_type= umbrella  ; harmonic biasing force
>> pull_coord1_geometry= distance  ; simple distance increase
>> pull_coord1_groups  = 1 2
>> pull_coord1_dim = N N Y
>> pull_coord1_rate= 0.0
>> pull_coord1_k   = 1000  ; kJ mol^-1 nm^-2
>> pull_coord1_start   = yes   ; define initial COM distance > 0
>>
>>
>>
>> Conformations in Justin's tutorial are from steered MD. However, my 
>> conformations are not from SMD, and I have not done SMD on this system. So, 
>> how to define pull_group1 and pull_group2? And pull_coord1_geometry still 
>> set to "distance" ?
>
>The pull groups don't depend on where the configurations came from.  They 
>define 
>the reaction coordinate.  You can use whatever pull geometry makes sense; in 
>the 
>tutorial it is a simple linear reaction coordinate directly along the z-axis. 
>Other applications may require different definitions.
>
>> Also, need I fix any part of protein in umbrella sampling (with " -DPOSRES 
>> ") ? Why?
>
>Generally, no, but you haven't given any useful detail about what your 
>simulation system is.
>
>-Justin
>
>-- 
>==
>
>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
>
>jalem...@outerbanks.umaryland.edu | (410) 706-7441
>http://mackerell.umaryland.edu/~jalemkul
>
>==
>-- 
>Gromacs Users mailing list
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[gmx-users] Regarding gmx sorient

[Dilip H N]

Hello,
I have done md simulation of amino acid in solvent mixture, How can i
calculate the gmx sorient..??
I am not able to understand anything in the link
http://manual.gromacs.org/programs/gmx-sorient.html

Is it like for calculating the RDF,(in which we have to first index the
files and thn in gmx rdf  command give -ref and -sel  in end) ..??

How can i calculate it.. what are the steps i need to follow in brief .. is
there anything tht i need to index, etc..,,??

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



   Sent with Mailtrack

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[gmx-users] failed to restart the REMD

[YanhuaOuyang]

Hi,
I have run REMD for 80ns. But I can't restart the REMD. The errors are as 
following:

Fatal error in MPI_Allreduce: Message truncated, error stack:
MPI_Allreduce(1339)...: MPI_Allreduce(sbuf=0x7fff4ac3fa90, 
rbuf=0x29af530, count=4, MPI_FLOAT, MPI_SUM, comm=0x8400) fai
led
MPIR_Allreduce_impl(1180).:
MPIR_Allreduce_intra(410).:
MPIR_Bcast_intra(1524): Failure during collective
MPIR_Bcast_intra(1499):
MPIR_Bcast_binomial(147)..:
MPIDI_CH3U_Receive_data_found(129): Message from rank 0 and tag 2 truncated; 
260 bytes received but buffer size is 16

I tried to restart the REMD many times and both use remd0.cpt and 
remd0_prev.cpt. But they all failed and appear error as above.
I don't know how to fix such problem.


Best regards,
Ouyang

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[gmx-users] How to write pull code in umbrella sampling

[Qing Lv]

Dear Colleagues,


I am trying to do an umbrella sampling using a series of conformations 
extracted from several unbiased MD trajectories. But I am not sure about the 
pull code in .mdp file.
Below is the pull code from the tutorial of Dr. Justin Lemkul :
define  = -DPOSRES_B ; (Why ??)
; Pull code 
pull= yes   
pull_ngroups= 2
pull_ncoords= 1
pull_group1_name= Chain_B
pull_group2_name= Chain_A
pull_coord1_type= umbrella  ; harmonic biasing force
pull_coord1_geometry= distance  ; simple distance increase
pull_coord1_groups  = 1 2
pull_coord1_dim = N N Y
pull_coord1_rate= 0.0
pull_coord1_k   = 1000  ; kJ mol^-1 nm^-2
pull_coord1_start   = yes   ; define initial COM distance > 0



Conformations in Justin's tutorial are from steered MD. However, my 
conformations are not from SMD, and I have not done SMD on this system. So, how 
to define pull_group1 and pull_group2? And pull_coord1_geometry still set to 
"distance" ?
Also, need I fix any part of protein in umbrella sampling (with " -DPOSRES ") ? 
Why?
Any one can provide a template of pull code for such simulations?


Thanks a lot
Qing Lv


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Re: [gmx-users] Extending simulation

[RAHUL SURESH]

Thank you
On Fri, 7 Apr 2017 at 5:33 PM, Justin Lemkul  wrote:

>
>
> On 4/7/17 5:07 AM, João Henriques wrote:
> > Dear Rahul,
> >
> > I've never worked with gmx-2016, but the error message is extremely
> clear.
> > Therefore I will skip the explanation and just give you the solution.
> > Rename the old tpr as md_old.tpr (or something or the sort) and the new
> > extended one as md.tpr. Then it shouldn't complain because all run files
> > have the same name (md.*) and appending will raise no problems.
> >
>
> Alternatively, do not try to append when changing file names (mdrun
> -noappend)
> and avoid having to rename your files at all.
>
> -Justin
>
> > Best regards,
> > /J
> >
> > On Fri, Apr 7, 2017 at 10:54 AM, RAHUL SURESH 
> > wrote:
> >
> >> I want to extend my simulation for another 15ns. Previously generated
> files
> >> are md.log, md.xtc, md.edr and md.tpr.
> >>
> >> I used the following commands
> >>
> >>
> >>
> >> *gmx convert-tpr -s md.tpr -extend 15000 -o 25nsmd.tpr*
> >>
> >>
> >> *gmx mdrun -s 25nsmd.tpr -cpi md.cpt*
> >> I get the following error
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> *Fatal error:File appending requested, but 2 of the 3 output files are
> not
> >> present or arenamed differently. For safety reasons, GROMACS-2016 and
> later
> >> only allows fileappending to be used when all files have the same names
> as
> >> they had in theoriginal run. Checkpointing is merely intended for plain
> >> continuation of runs.For safety reasons you must specify all file names
> >> (e.g. with -deffnm), andall these files must match the names used in the
> >> run prior to checkpointingsince we will append to them by default. If
> the
> >> files are not available, youcan add the -noappend flag to mdrun and
> write
> >> separate new parts. For mereconcatenation of files, you should use the
> gmx
> >> trjcat tool instead.*
> >> The 2 file missing are
> >> md.edr
> >> md.xtc
> >>
> >> Here I haven't changed any file name then why do i get this error?
> >> --
> >> 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.
> >>
>
> --
> ==
>
> 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
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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Re: [gmx-users] Md simulation by Gromacs

[Erik Marklund]

Dear Maria,

Let’s keep this to the user list. I am first of all not a private tutor. 
Secondly, the answers you get (below) might be relevant for others.

> On 6 Apr 2017, at 16:04, maria khan  wrote:
> 
> Good evening Dear sir Erik Marklund..
> 
> I am very Thankful for your attention ..Actually i even dont know the basics 
> and one of the NAMD expert user told me so that gromacs use united atom ff 
> thats why gromacs is fast and NAMD use all atom thats why it is slow.
> 

That is incorrect. Gromacs can do both all-atom and united-atom. Gromacs can 
also make use of virtual sites, which allows for a longer time step, hence more 
simulated ns per hour. You can also choose not to. And then there are on top of 
that a number of reasons why gromacs is really fast without cutting (important) 
corners.

> Now my problems are : is there any option for considering hydrogen atom  to 
> process its calculation in MD run as last time when i did simulation i 
> applied the command of ignoring hydrogen atom ,,secondly what is the 
> difference Between ignoring h- atoms and considering it in MD running.I mean 
> would it effect the result of calculation after MD run..and if there is 
> option for taking h- atom as part of amino acid then why there is an option 
> for ignoring it..
> 

Please be specific. Are you referring to pdb2gmx -ignh? That just tells pdb2gmx 
to derive hydrogen positions and occupancies based on hydrogen bonding patterns 
and force-field-related information. It doesn’t normally produce topologies 
without hydrogens, and the hydrogens are thus part of the subsequent 
simulations. See the user-list archives. I know this has been discussed before. 
And you can also inspect the output files to see what they contain.

> Furthermore i dont know about forming parameters for my ligand thats is 
> alkaloid so im confuse how to form its parameter and if some one has 
> published its parameters then how i can find..i just need a stepwise protocol 
> for MD simulation,,most of the manuals are not understandable my majors are 
> pure biochemistry and mostly the explanations there are mathematica basedl.
> 

Well, parametrisation is not really for beginners. I also think others are more 
experienced in that area than I am.

> And yes i have studied the old version of manuals not updated one.
> 
> IF u have simplist form of manuals or any other stuff, kindly send me that i 
> very thankful. Last time u shared a paper of ur self but it was not my 
> research related.
> 

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Re: [gmx-users] gromacs Query

[Aman Deep]

thank you sir I have applied nstxout, nstvout, nstfout as zero and it is
now working

Thankyou




On Fri, Apr 7, 2017 at 6:04 PM, Mark Abraham 
wrote:

> Hi,
>
> On Fri, 7 Apr 2017 11:18 Aman Deep  wrote:
>
> > sir, I didn't understand what is E here ???
> >
>
> As Justin suggested, that was a typo for "maybe".
>
> and after removing  nstxout  still, it is not helping..
> >
>
> I did not suggest doing that. I did ask what your GROMACS version was.
>
> Don't use both nstxtcout and nstxout-compressed (which is its successor,
> but maybe not understood by old versions of GROMACS, but I can't help you
> if you won't share that information :-)).
>
> Mark
>
> On Fri, Apr 7, 2017 at 1:25 PM, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > Which version of GROMACS is this? The only problem I can see is that
> you
> > > are using both nstxtcout and its successor (don't), and may E that is
> > > confusing the parser.
> > >
> > > Mark
> > >
> > > On Fri, 7 Apr 2017 07:41 Aman Deep  wrote:
> > >
> > > > sir, i am using this output control but still, it is generating same
> > > space
> > > > data
> > > >
> > > >
> > > > ; Run parameters
> > > > integrator = md; leap-frog integrator
> > > > nsteps  = 2500 ; 2 * 50 = 5 ps (50 ns)
> > > > dt  = 0.002 ; 2 fs
> > > >
> > > > ; Output control
> > > > nstxout = 0 ; save coordinates every 10.0 ps
> > > > nstxtcout   =250; save velocities
> every
> > > > 50.0 ps
> > > > nstenergy   = 250   ; save energies every
> > > 50.0
> > > > ps
> > > > nstlog  = 250 ; update log file every 50.0 ps
> > > > nstxout-compressed = 250  ; save compressed coordinates every
> > > 10.0
> > > > ps; nstxout-compressed replaces
> > nstxtcout
> > > > xtc-grps= Protein ; replaces xtc-grps
> > > >
> > > >
> > > > On Mon, Apr 3, 2017 at 3:15 PM, Mark Abraham <
> mark.j.abra...@gmail.com
> > >
> > > > wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > If you ask for .trr output, you get it. Stop using non-zero nst*out
> > mdp
> > > > > settings that you don't want.
> > > > >
> > > > > Mark
> > > > >
> > > > > On Mon, Apr 3, 2017 at 11:31 AM Aman Deep <
> r.amandeep2...@gmail.com>
> > > > > wrote:
> > > > >
> > > > > > sir,
> > > > > >
> > > > > > I have tried *nstxctout  *but it still making trr file ... is
> there
> > > any
> > > > > > option to  make only xtc file ???
> > > > > >
> > > > > > On Mon, Apr 3, 2017 at 1:14 PM, Mark Abraham <
> > > mark.j.abra...@gmail.com
> > > > >
> > > > > > wrote:
> > > > > >
> > > > > > > Hi,
> > > > > > >
> > > > > > > See
> > > > > > >
> > > > > > http://www.gromacs.org/Documentation/How-tos/
> > > > > Reducing_Trajectory_Storage_
> > > > > > > Volume
> > > > > > >
> > > > > > > Mark
> > > > > > >
> > > > > > > On Mon, Apr 3, 2017 at 9:27 AM Aman Deep <
> > r.amandeep2...@gmail.com
> > > >
> > > > > > wrote:
> > > > > > >
> > > > > > > > sir is there any way to create only XTC file from mdrun only.
> > the
> > > > > > server
> > > > > > > on
> > > > > > > > which I am working is not providing enough space and my trr
> > file
> > > is
> > > > > too
> > > > > > > > much large.
> > > > > > > >
> > > > > > > > thank you
> > > > > > > >
> > > > > > > > --
> > > > > > > > Aman Deep
> > > > > > > > MSc Bioinformatics
> > > > > > > > Jamia Millia Islamia
> > > > > > > > New Delhi - 110025
> > > > > > > > --
> > > > > > > > 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.
> > > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > --
> > > > > > Aman Deep
> > > > > > MSc Bioinformatics
> > > > > > Jamia Millia Islamia
> > > > > > New Delhi - 110025
> > > > > > --
> > > > > > Gromacs Users mailing list
> > > > > >
> > > > > > * Please search the 

Re: [gmx-users] gromacs Query

[Mark Abraham]

Hi,

On Fri, 7 Apr 2017 11:18 Aman Deep  wrote:

> sir, I didn't understand what is E here ???
>

As Justin suggested, that was a typo for "maybe".

and after removing  nstxout  still, it is not helping..
>

I did not suggest doing that. I did ask what your GROMACS version was.

Don't use both nstxtcout and nstxout-compressed (which is its successor,
but maybe not understood by old versions of GROMACS, but I can't help you
if you won't share that information :-)).

Mark

On Fri, Apr 7, 2017 at 1:25 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Which version of GROMACS is this? The only problem I can see is that you
> > are using both nstxtcout and its successor (don't), and may E that is
> > confusing the parser.
> >
> > Mark
> >
> > On Fri, 7 Apr 2017 07:41 Aman Deep  wrote:
> >
> > > sir, i am using this output control but still, it is generating same
> > space
> > > data
> > >
> > >
> > > ; Run parameters
> > > integrator = md; leap-frog integrator
> > > nsteps  = 2500 ; 2 * 50 = 5 ps (50 ns)
> > > dt  = 0.002 ; 2 fs
> > >
> > > ; Output control
> > > nstxout = 0 ; save coordinates every 10.0 ps
> > > nstxtcout   =250; save velocities every
> > > 50.0 ps
> > > nstenergy   = 250   ; save energies every
> > 50.0
> > > ps
> > > nstlog  = 250 ; update log file every 50.0 ps
> > > nstxout-compressed = 250  ; save compressed coordinates every
> > 10.0
> > > ps; nstxout-compressed replaces
> nstxtcout
> > > xtc-grps= Protein ; replaces xtc-grps
> > >
> > >
> > > On Mon, Apr 3, 2017 at 3:15 PM, Mark Abraham  >
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > If you ask for .trr output, you get it. Stop using non-zero nst*out
> mdp
> > > > settings that you don't want.
> > > >
> > > > Mark
> > > >
> > > > On Mon, Apr 3, 2017 at 11:31 AM Aman Deep 
> > > > wrote:
> > > >
> > > > > sir,
> > > > >
> > > > > I have tried *nstxctout  *but it still making trr file ... is there
> > any
> > > > > option to  make only xtc file ???
> > > > >
> > > > > On Mon, Apr 3, 2017 at 1:14 PM, Mark Abraham <
> > mark.j.abra...@gmail.com
> > > >
> > > > > wrote:
> > > > >
> > > > > > Hi,
> > > > > >
> > > > > > See
> > > > > >
> > > > > http://www.gromacs.org/Documentation/How-tos/
> > > > Reducing_Trajectory_Storage_
> > > > > > Volume
> > > > > >
> > > > > > Mark
> > > > > >
> > > > > > On Mon, Apr 3, 2017 at 9:27 AM Aman Deep <
> r.amandeep2...@gmail.com
> > >
> > > > > wrote:
> > > > > >
> > > > > > > sir is there any way to create only XTC file from mdrun only.
> the
> > > > > server
> > > > > > on
> > > > > > > which I am working is not providing enough space and my trr
> file
> > is
> > > > too
> > > > > > > much large.
> > > > > > >
> > > > > > > thank you
> > > > > > >
> > > > > > > --
> > > > > > > Aman Deep
> > > > > > > MSc Bioinformatics
> > > > > > > Jamia Millia Islamia
> > > > > > > New Delhi - 110025
> > > > > > > --
> > > > > > > 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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Re: [gmx-users] Extending simulation

[Justin Lemkul]

On 4/7/17 5:07 AM, João Henriques wrote:

Dear Rahul,

I've never worked with gmx-2016, but the error message is extremely clear.
Therefore I will skip the explanation and just give you the solution.
Rename the old tpr as md_old.tpr (or something or the sort) and the new
extended one as md.tpr. Then it shouldn't complain because all run files
have the same name (md.*) and appending will raise no problems.



Alternatively, do not try to append when changing file names (mdrun -noappend) 
and avoid having to rename your files at all.


-Justin


Best regards,
/J

On Fri, Apr 7, 2017 at 10:54 AM, RAHUL SURESH 
wrote:


I want to extend my simulation for another 15ns. Previously generated files
are md.log, md.xtc, md.edr and md.tpr.

I used the following commands



*gmx convert-tpr -s md.tpr -extend 15000 -o 25nsmd.tpr*


*gmx mdrun -s 25nsmd.tpr -cpi md.cpt*
I get the following error












*Fatal error:File appending requested, but 2 of the 3 output files are not
present or arenamed differently. For safety reasons, GROMACS-2016 and later
only allows fileappending to be used when all files have the same names as
they had in theoriginal run. Checkpointing is merely intended for plain
continuation of runs.For safety reasons you must specify all file names
(e.g. with -deffnm), andall these files must match the names used in the
run prior to checkpointingsince we will append to them by default. If the
files are not available, youcan add the -noappend flag to mdrun and write
separate new parts. For mereconcatenation of files, you should use the gmx
trjcat tool instead.*
The 2 file missing are
md.edr
md.xtc

Here I haven't changed any file name then why do i get this error?
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Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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Re: [gmx-users] gromacs Query

[Justin Lemkul]

On 4/7/17 6:17 AM, Aman Deep wrote:

sir, I didn't understand what is E here ???



I think Mark made a typo in writing the word "maybe" here.

The point he was making is that you're trying to specify nstxtcout and 
nstxout-compressed, which is a mixture of syntax from different GROMACS 
versions.  You can't/shouldn't do that.



and after removing  nstxout  still, it is not helping..



All of the .trr options (nstxout, nstvout, nstfout) default to zero, so a .trr 
file is only written if you ask for it by setting any one of those to a non-zero 
value.


-Justin


On Fri, Apr 7, 2017 at 1:25 PM, Mark Abraham 
wrote:


Hi,

Which version of GROMACS is this? The only problem I can see is that you
are using both nstxtcout and its successor (don't), and may E that is
confusing the parser.

Mark

On Fri, 7 Apr 2017 07:41 Aman Deep  wrote:


sir, i am using this output control but still, it is generating same

space

data


; Run parameters
integrator = md; leap-frog integrator
nsteps  = 2500 ; 2 * 50 = 5 ps (50 ns)
dt  = 0.002 ; 2 fs

; Output control
nstxout = 0 ; save coordinates every 10.0 ps
nstxtcout   =250; save velocities every
50.0 ps
nstenergy   = 250   ; save energies every

50.0

ps
nstlog  = 250 ; update log file every 50.0 ps
nstxout-compressed = 250  ; save compressed coordinates every

10.0

ps; nstxout-compressed replaces nstxtcout
xtc-grps= Protein ; replaces xtc-grps


On Mon, Apr 3, 2017 at 3:15 PM, Mark Abraham 
wrote:


Hi,

If you ask for .trr output, you get it. Stop using non-zero nst*out mdp
settings that you don't want.

Mark

On Mon, Apr 3, 2017 at 11:31 AM Aman Deep 
wrote:


sir,

I have tried *nstxctout  *but it still making trr file ... is there

any

option to  make only xtc file ???

On Mon, Apr 3, 2017 at 1:14 PM, Mark Abraham <

mark.j.abra...@gmail.com



wrote:


Hi,

See


http://www.gromacs.org/Documentation/How-tos/

Reducing_Trajectory_Storage_

Volume

Mark

On Mon, Apr 3, 2017 at 9:27 AM Aman Deep 

Re: [gmx-users] determining restraints for pulling

[Justin Lemkul]

On 4/7/17 1:43 AM, abhisek Mondal wrote:

Is it possible to pull (distance pull) along negative of Z axis (for
example, I'm saying Z) ? Do I need to mention -Z in pull code or the
program improvises if I say Z axis distance pull in .mdp ?



Yes, you can define a pull vector in the negative Z dimension (pull-coordN-vec = 
0 0 -1 or whatever is appropriate).


-Justin


On Wed, Apr 5, 2017 at 5:40 PM, Justin Lemkul  wrote:



Please keep the discussion on the mailing list.

On 4/5/17 8:04 AM, abhisek Mondal wrote:


Hello Justin,

Can you provide some direction to this approach I'm using for performing
umbrella sampling of a protein-ligand complex ?

I had restrained it during the equilibration of the molecule. As advised
in the
Protein-ligand simulation tutorial. But I'm unsure regarding what kind of
treatment I'm supposed to give the complex while targeting for umbrella
sampling. Do I need to restrain the ligand during equilibration ?

I have solved the crystal structure of the complex and want to determine
if I
pull out the ligand then how the side chains reorient according to the
ligand
withdrawal. That's the goal.

Some suggestions regarding the issue will be highly appreciated.



What does your examination of the literature for similar systems suggest
as an appropriate protocol?

-Justin

Thank you


On Wed, Apr 5, 2017 at 3:51 PM, abhisek Mondal > wrote:

I had restrained it during the equilibration of the molecule. As
advised in
the Protein-ligand simulation tutorial. But I'm unsure regarding what
kind
of treatment I'm supposed to give the complex while targeting for
umbrella
sampling. Do I need to restrain the ligand during equilibration ?

I have solved the crystal structure of the complex and want to
determine if
I pull out the ligand then how the side chains reorient according to
the
ligand withdrawal. That's the goal.

On Wed, Apr 5, 2017 at 3:09 PM, Mark Abraham <
mark.j.abra...@gmail.com
> wrote:

Hi,

Why are you trying to keep the ligand in place (by restraining
it) and pull
it out?

Mark

On Wed, 5 Apr 2017 09:51 abhisek Mondal > wrote:

> Hi,
>
> I'm trying to pull a ligand from a protein-ligand complex. As
per the
> ligand-protein tutorial, I have restrained the ligand in
topology file and
> it looks like:
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Include ligand topology
> #include "drg.itp"
>
> ; Include position restraints
> #ifdef POSRES_LIG
> #include "posre_ACO.itp"
> #endif
>
> ; Include water topology
> #include "gromos43a1.ff/spc.itp"
>
> In the md_pull.mdp, I'm using:
>
> title   = Umbrella pulling simulation
> define  = -DPOSRES
> ; Run parameters
> integrator  = md;applying leap frog algorithm
>
> So, is it proper for pulling ligand (ACO) from the protein or
I'm doing
> something wrong ? I'm really lost here, please help me out.
>
> 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
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before
> posting!
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-users
 or
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-users

Re: [gmx-users] Position restraint on DPPC lipid bilayer

[Justin Lemkul]

On 4/7/17 1:20 AM, Sithara Perera wrote:

Hi!,

 I' making a 512 DPPC bi-layer out of 128 bilayer available in
http://www.cgmartini.nl. The force field used is martini.

 But once the energy minimization is done, the bi-layer crashes and
accumulates to  globules.

 So I made an position.itp file using the command


gmx genrestr -f dppc221.gro -n test.ndx -o lipid_posre.itp -fc 1000 1000
1000

And included in the topology file.

Topology file also include

include "martini_v2.0.itp"
#include "martini_v2.0_lipids.itp"  from martini as well.



 But then when the command

gmx grompp -f minim.mdp -c dppc221.gro -p dppc_bilayer.top -o em2.tpr

is given , following error occurs.

Fatal error:
[ file posre.itp, line 29 ]:
Atom index (25) in position_restraints out of bounds (1-24).
This probably means that you have inserted topology section
"position_restraints"
in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right molecule.


How can I fix this?



http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds

As a rule of thumb, if you're ever passing a coordinate file containing multiple 
molecules to genrestr, you're probably going to get an incorrect restraint 
topology (note the warnings in the help text).


-Justin

--
==

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] GTX Titan XP performance for gromacs

[Kumar Meena, Santosh]

Dear all,


is anybody planing test GTX Titan XP, the consumer version of Quadro P6000 for 
gromacs. How do you expecting the performance with respect to GTX 1080 TI.


Thanks in advance.


Regards

Dr. Santosh Kumar

Postdoctoral Researcher
Department of Chemistry and Biochemistry
University of California, San Diego
9500 Gilman Drive
Urey Hall 4205
La Jolla, CA 92093
E-mail:
san.i...@gmail.com
sme...@ucsd.edu
Mobile: +18582609293
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Re: [gmx-users] gromacs Query

[Aman Deep]

sir, I didn't understand what is E here ???

and after removing  nstxout  still, it is not helping..

On Fri, Apr 7, 2017 at 1:25 PM, Mark Abraham 
wrote:

> Hi,
>
> Which version of GROMACS is this? The only problem I can see is that you
> are using both nstxtcout and its successor (don't), and may E that is
> confusing the parser.
>
> Mark
>
> On Fri, 7 Apr 2017 07:41 Aman Deep  wrote:
>
> > sir, i am using this output control but still, it is generating same
> space
> > data
> >
> >
> > ; Run parameters
> > integrator = md; leap-frog integrator
> > nsteps  = 2500 ; 2 * 50 = 5 ps (50 ns)
> > dt  = 0.002 ; 2 fs
> >
> > ; Output control
> > nstxout = 0 ; save coordinates every 10.0 ps
> > nstxtcout   =250; save velocities every
> > 50.0 ps
> > nstenergy   = 250   ; save energies every
> 50.0
> > ps
> > nstlog  = 250 ; update log file every 50.0 ps
> > nstxout-compressed = 250  ; save compressed coordinates every
> 10.0
> > ps; nstxout-compressed replaces nstxtcout
> > xtc-grps= Protein ; replaces xtc-grps
> >
> >
> > On Mon, Apr 3, 2017 at 3:15 PM, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > If you ask for .trr output, you get it. Stop using non-zero nst*out mdp
> > > settings that you don't want.
> > >
> > > Mark
> > >
> > > On Mon, Apr 3, 2017 at 11:31 AM Aman Deep 
> > > wrote:
> > >
> > > > sir,
> > > >
> > > > I have tried *nstxctout  *but it still making trr file ... is there
> any
> > > > option to  make only xtc file ???
> > > >
> > > > On Mon, Apr 3, 2017 at 1:14 PM, Mark Abraham <
> mark.j.abra...@gmail.com
> > >
> > > > wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > See
> > > > >
> > > > http://www.gromacs.org/Documentation/How-tos/
> > > Reducing_Trajectory_Storage_
> > > > > Volume
> > > > >
> > > > > Mark
> > > > >
> > > > > On Mon, Apr 3, 2017 at 9:27 AM Aman Deep  >
> > > > wrote:
> > > > >
> > > > > > sir is there any way to create only XTC file from mdrun only. the
> > > > server
> > > > > on
> > > > > > which I am working is not providing enough space and my trr file
> is
> > > too
> > > > > > much large.
> > > > > >
> > > > > > thank you
> > > > > >
> > > > > > --
> > > > > > Aman Deep
> > > > > > MSc Bioinformatics
> > > > > > Jamia Millia Islamia
> > > > > > New Delhi - 110025
> > > > > > --
> > > > > > 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
> > > > >
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> > > > > Support/Mailing_Lists/GMX-Users_List before posting!
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> > or
> > > > > send a mail to gmx-users-requ...@gromacs.org.
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Aman Deep
> > > > MSc Bioinformatics
> > > > Jamia Millia Islamia
> > > > New Delhi - 110025
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
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> > > > posting!
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> or
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> > > >
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> > >
> >
> >
> >
> > --
> > Aman Deep
> > MSc Bioinformatics
> > Jamia Millia Islamia
> > New Delhi - 110025
> > --
> > Gromacs Users mailing list
> >
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> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> >
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> > 

Re: [gmx-users] Extending simulation

[João Henriques]

I forgot a small detail, you need to include "-deffnm md" to your mdrun
command, as the error message clearly states.

/J

On Fri, Apr 7, 2017 at 11:07 AM, João Henriques <
joao.m.a.henriq...@gmail.com> wrote:

> Dear Rahul,
>
> I've never worked with gmx-2016, but the error message is extremely clear.
> Therefore I will skip the explanation and just give you the solution.
> Rename the old tpr as md_old.tpr (or something or the sort) and the new
> extended one as md.tpr. Then it shouldn't complain because all run files
> have the same name (md.*) and appending will raise no problems.
>
> Best regards,
> /J
>
> On Fri, Apr 7, 2017 at 10:54 AM, RAHUL SURESH 
> wrote:
>
>> I want to extend my simulation for another 15ns. Previously generated
>> files
>> are md.log, md.xtc, md.edr and md.tpr.
>>
>> I used the following commands
>>
>>
>>
>> *gmx convert-tpr -s md.tpr -extend 15000 -o 25nsmd.tpr*
>>
>>
>> *gmx mdrun -s 25nsmd.tpr -cpi md.cpt*
>> I get the following error
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> *Fatal error:File appending requested, but 2 of the 3 output files are not
>> present or arenamed differently. For safety reasons, GROMACS-2016 and
>> later
>> only allows fileappending to be used when all files have the same names as
>> they had in theoriginal run. Checkpointing is merely intended for plain
>> continuation of runs.For safety reasons you must specify all file names
>> (e.g. with -deffnm), andall these files must match the names used in the
>> run prior to checkpointingsince we will append to them by default. If the
>> files are not available, youcan add the -noappend flag to mdrun and write
>> separate new parts. For mereconcatenation of files, you should use the gmx
>> trjcat tool instead.*
>> The 2 file missing are
>> md.edr
>> md.xtc
>>
>> Here I haven't changed any file name then why do i get this error?
>> --
>> 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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Re: [gmx-users] Extending simulation

[João Henriques]

Dear Rahul,

I've never worked with gmx-2016, but the error message is extremely clear.
Therefore I will skip the explanation and just give you the solution.
Rename the old tpr as md_old.tpr (or something or the sort) and the new
extended one as md.tpr. Then it shouldn't complain because all run files
have the same name (md.*) and appending will raise no problems.

Best regards,
/J

On Fri, Apr 7, 2017 at 10:54 AM, RAHUL SURESH 
wrote:

> I want to extend my simulation for another 15ns. Previously generated files
> are md.log, md.xtc, md.edr and md.tpr.
>
> I used the following commands
>
>
>
> *gmx convert-tpr -s md.tpr -extend 15000 -o 25nsmd.tpr*
>
>
> *gmx mdrun -s 25nsmd.tpr -cpi md.cpt*
> I get the following error
>
>
>
>
>
>
>
>
>
>
>
>
> *Fatal error:File appending requested, but 2 of the 3 output files are not
> present or arenamed differently. For safety reasons, GROMACS-2016 and later
> only allows fileappending to be used when all files have the same names as
> they had in theoriginal run. Checkpointing is merely intended for plain
> continuation of runs.For safety reasons you must specify all file names
> (e.g. with -deffnm), andall these files must match the names used in the
> run prior to checkpointingsince we will append to them by default. If the
> files are not available, youcan add the -noappend flag to mdrun and write
> separate new parts. For mereconcatenation of files, you should use the gmx
> trjcat tool instead.*
> The 2 file missing are
> md.edr
> md.xtc
>
> Here I haven't changed any file name then why do i get this error?
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Re: [gmx-users] gromacs Query

[Mark Abraham]

Hi,

Which version of GROMACS is this? The only problem I can see is that you
are using both nstxtcout and its successor (don't), and may E that is
confusing the parser.

Mark

On Fri, 7 Apr 2017 07:41 Aman Deep  wrote:

> sir, i am using this output control but still, it is generating same space
> data
>
>
> ; Run parameters
> integrator = md; leap-frog integrator
> nsteps  = 2500 ; 2 * 50 = 5 ps (50 ns)
> dt  = 0.002 ; 2 fs
>
> ; Output control
> nstxout = 0 ; save coordinates every 10.0 ps
> nstxtcout   =250; save velocities every
> 50.0 ps
> nstenergy   = 250   ; save energies every 50.0
> ps
> nstlog  = 250 ; update log file every 50.0 ps
> nstxout-compressed = 250  ; save compressed coordinates every 10.0
> ps; nstxout-compressed replaces nstxtcout
> xtc-grps= Protein ; replaces xtc-grps
>
>
> On Mon, Apr 3, 2017 at 3:15 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > If you ask for .trr output, you get it. Stop using non-zero nst*out mdp
> > settings that you don't want.
> >
> > Mark
> >
> > On Mon, Apr 3, 2017 at 11:31 AM Aman Deep 
> > wrote:
> >
> > > sir,
> > >
> > > I have tried *nstxctout  *but it still making trr file ... is there any
> > > option to  make only xtc file ???
> > >
> > > On Mon, Apr 3, 2017 at 1:14 PM, Mark Abraham  >
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > See
> > > >
> > > http://www.gromacs.org/Documentation/How-tos/
> > Reducing_Trajectory_Storage_
> > > > Volume
> > > >
> > > > Mark
> > > >
> > > > On Mon, Apr 3, 2017 at 9:27 AM Aman Deep 
> > > wrote:
> > > >
> > > > > sir is there any way to create only XTC file from mdrun only. the
> > > server
> > > > on
> > > > > which I am working is not providing enough space and my trr file is
> > too
> > > > > much large.
> > > > >
> > > > > thank you
> > > > >
> > > > > --
> > > > > Aman Deep
> > > > > MSc Bioinformatics
> > > > > Jamia Millia Islamia
> > > > > New Delhi - 110025
> > > > > --
> > > > > 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
> > > >
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> > > > Support/Mailing_Lists/GMX-Users_List before posting!
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> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > >
> > >
> > >
> > > --
> > > Aman Deep
> > > MSc Bioinformatics
> > > Jamia Millia Islamia
> > > New Delhi - 110025
> > > --
> > > 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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> >
>
>
>
> --
> Aman Deep
> MSc Bioinformatics
> Jamia Millia Islamia
> New Delhi - 110025
> --
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Re: [gmx-users] gromacs Query

[Aman Deep]

sir, i am using this output control but still, it is generating same space
data


; Run parameters
integrator = md; leap-frog integrator
nsteps  = 2500 ; 2 * 50 = 5 ps (50 ns)
dt  = 0.002 ; 2 fs

; Output control
nstxout = 0 ; save coordinates every 10.0 ps
nstxtcout   =250; save velocities every
50.0 ps
nstenergy   = 250   ; save energies every 50.0
ps
nstlog  = 250 ; update log file every 50.0 ps
nstxout-compressed = 250  ; save compressed coordinates every 10.0
ps; nstxout-compressed replaces nstxtcout
xtc-grps= Protein ; replaces xtc-grps


On Mon, Apr 3, 2017 at 3:15 PM, Mark Abraham 
wrote:

> Hi,
>
> If you ask for .trr output, you get it. Stop using non-zero nst*out mdp
> settings that you don't want.
>
> Mark
>
> On Mon, Apr 3, 2017 at 11:31 AM Aman Deep 
> wrote:
>
> > sir,
> >
> > I have tried *nstxctout  *but it still making trr file ... is there any
> > option to  make only xtc file ???
> >
> > On Mon, Apr 3, 2017 at 1:14 PM, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > See
> > >
> > http://www.gromacs.org/Documentation/How-tos/
> Reducing_Trajectory_Storage_
> > > Volume
> > >
> > > Mark
> > >
> > > On Mon, Apr 3, 2017 at 9:27 AM Aman Deep 
> > wrote:
> > >
> > > > sir is there any way to create only XTC file from mdrun only. the
> > server
> > > on
> > > > which I am working is not providing enough space and my trr file is
> too
> > > > much large.
> > > >
> > > > thank you
> > > >
> > > > --
> > > > Aman Deep
> > > > MSc Bioinformatics
> > > > Jamia Millia Islamia
> > > > New Delhi - 110025
> > > > --
> > > > 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
> > >
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> > > 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.
> > >
> >
> >
> >
> > --
> > Aman Deep
> > MSc Bioinformatics
> > Jamia Millia Islamia
> > New Delhi - 110025
> > --
> > 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.
> >
> --
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>



-- 
Aman Deep
MSc Bioinformatics
Jamia Millia Islamia
New Delhi - 110025
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