Re: [gmx-users] Regarding getting trajectories in gromacs..

[spss4]

 - Message from Dilip H N  -
    Date: Tue, 4 Apr 2017 10:18:23 +0530
    From: Dilip H N 
Reply-To: gmx-us...@gromacs.org
Subject: [gmx-users] Regarding getting trajectories in gromacs..
      To: gromacs.org_gmx-users@maillist.sys.kth.se


Hello,
I have ran a md simulation for
nsteps = 500 ; 2 * 500 = 1 ps (10 ns)
dt = 0.002 ; 1e+07 fs
nstxout    = 5000 ; save coordinates every 20.0 ps
nstvout    = 5000 ; save velocities every 20.0 ps
nstenergy    = 5000 ; save energies every 20.0 ps
nstlog    = 5000 ; update log file every 20.0 ps
nstxout-compressed  = 5000      ; save compressed coordinates every

20.0

ps

ie., for 10 ns.. and when i view the trr file in vmd , the bonds are
stretched/compressed.. so i tried with the command
gmx trjconv -f md.trr/xtc[1] -s md.tpr -pbc mol -o md-mol.xtc
this above command is for the whole 0 - 10 ns trajectory i got and all

the

bonds are intact now..
My question is that if i want to get the trajectories for 0-2ns,
2-4ns,4-6ns,6-8ns, 8-10ns, ie for every 2ns ..how to get it..??
gmx trjconv -f md.trr -s md.tpr -o  new.gro -b 0 -e 200
with this command i got the gro file... but how to view the trajectory of
this file...

1] What are the commands that i need to give to view individual
trajectories of 2 ns intervals
2] and how to view those obtained trajectories of 2ns in vmd without
getting bonds stretched/elongated..

--
With Best Regards,

DILIP.H.N
Ph.D Student

 Sent with Mailtrack




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- End message from Dilip H N  -

Hi,
You can generate a .trr file using -b 0 -e 2000. Your command should be
gmx trjconv -s md.tpr -f md.trr -b 0 -e 2000 -o traj_0-2ns.trr -pbc mol
Then you just load it to VMD. You can see the 2 ns trajectory without bond
stretching. :)

Links:
--
[1] http://md.trr/xtc
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[gmx-users] XYZ file and obgmx

[Lamm Gro]

Dear Gromacs users ,

I have a xyz file and I used OBGMX ( topology generator ) for that .
Now I have itp and top file , but the problem is I want to change UFF
forcefield ( that used by obgmx )  to gromacs forcefields like Amber03 .
Can you please let me know how can i do that ?

I am new in Gromacs and i hope you can help me .

Regards,
Saeed.
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[gmx-users] Regarding getting trajectories in gromacs..

[Dilip H N]

Hello,
I have ran a md simulation for
nsteps = 500 ; 2 * 500 = 1 ps (10 ns)
dt = 0.002 ; 1e+07 fs
nstxout= 5000 ; save coordinates every 20.0 ps
nstvout= 5000 ; save velocities every 20.0 ps
nstenergy= 5000 ; save energies every 20.0 ps
nstlog= 5000 ; update log file every 20.0 ps
nstxout-compressed  = 5000  ; save compressed coordinates every 20.0 ps

ie., for 10 ns.. and when i view the trr file in vmd , the bonds are
stretched/compressed.. so i tried with the command
gmx trjconv -f md.trr/xtc -s md.tpr -pbc mol -o md-mol.xtc
this above command is for the whole 0 - 10 ns trajectory i got and all the
bonds are intact now..
My question is that if i want to get the trajectories for 0-2ns,
2-4ns,4-6ns,6-8ns, 8-10ns, ie for every 2ns ..how to get it..??
gmx trjconv -f md.trr -s md.tpr -o  new.gro -b 0 -e 200
with this command i got the gro file... but how to view the trajectory of
this file...

1] What are the commands that i need to give to view individual
trajectories of 2 ns intervals
2] and how to view those obtained trajectories of 2ns in vmd without
getting bonds stretched/elongated..

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



   Sent with Mailtrack

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[gmx-users] continuation with different dt values

[Dayhoff, Guy]

Hi,

   I’m continuing a run and setting init-step as the total steps completed in 
the run i’m continuing from,
if I change the dt for the continuation do I need to scale the steps previously 
taken? i.e going from dt = 1
to dt =2, completing 100 steps in the first sim, does init-step take the value 
100 regardless of the change in dt?

My Best,
   Guy Dayhoff
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Re: [gmx-users] System almost blowing up

[Dayhoff, Guy]

>> Hi,
>> 
>>   I?m receiving a couple (~15) EM did not converge warnings as well as a few 
>> (~3) 1,4 interaction
>> warnings during my run. It looks like it starts down the path to blowing up 
>> but recovers. Is this ?recovery?
>> system dependent? Should I take these messages (even without the subsequent 
>> crash) to indicate an
>> underlying issue with my system/topology or equilibration? I?m not ignoring 
>> or circumventing any warning
>> during pdb2gmx, or any other commands.
>> 
>> For more context: I?m running the Drude-2013 forcefield, with a dt of .5fs 
>> emtol of 1.0 and niter of 150
>> using the V-rescale thermostat and Berendsen pressure coupling while my 
>> systems cell shape relaxes
>> as a continuation from position restrained NVT then NPT ensembles. The 
>> starting structures were minimized
>> in vacuum, then solvated and minimized once again prior to the posres 
>> equilibration.
>> 
> 
> Such a short dt and strict niter should not be necessary in practice.  The 
> failure of SCF to converge/LINCS warnings is what we typically refer to as 
> polarization catastrophe, so your system is on the brink of instability.  
> This 
> is one of the inherent problems of SCF in polarizable systems; it often fails 
> to 
> converge and leaves the system potentially unstable.  The reflective hardwall 
> is 
> much more reliable (and faster).  If the instability is happening in your 
> equilibration, that may be OK but it is something you should try to 
> troubleshoot 
> to make sure there's nothing else going wrong.
> 
> -Justin
> 
> -- 
> 

Got it. I have been spending some time investigating the issue i’m having and
after reading shellfc.cpp I was pretty confident the issue was with SCF not 
converging,
and so my niter and dt were an attempt at looking into that. 

The workflow i’ve been trying to use is…
EM -> Solvate -> EM -> posres NVT V-rescale -> posres berendsen NPT isotropic 
1bar w/ V-rescale tcoupl ->
berendsen NPT semi-isotropic various pressures w/ V-rescale tcoupl

then once my cell shape has reached an equilibrium I finally switch to NH 
thermostat and PR barostat for
the production run. 

If I switch to employing the hardwall (and the lagrangian dynamics for drudes) 
then I understand it is not
compatible yet with NPT ensembles. So, if I change my work flow as follows 
would it be appropriate still?

EM->Solvate->EM->posre NPT isotropic 1 bar w/ V-rescale tcoupl->NPT 
semi-isotropic varying pressures
w V-rescale tcoupl until cell shape is equilibrated using PR barostat, then 
switch to NVT without pcoupl
to use the hardwall during my production run?

For some reason, i’ve got this idea that I need to be tcoupling and pcoupling 
during my production runs
so i’ve been apprehensive to do this. 

My Best,
  Guy Dayhoff
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 156, Issue 13

[Dayhoff, Guy]

> Such a short dt and strict niter should not be necessary in practice.  The 
> failure of SCF to converge/LINCS warnings is what we typically refer to as 
> polarization catastrophe, so your system is on the brink of instability.  
> This 
> is one of the inherent problems of SCF in polarizable systems; it often fails 
> to 
> converge and leaves the system potentially unstable.  The reflective hardwall 
> is 
> much more reliable (and faster).  If the instability is happening in your 
> equilibration, that may be OK but it is something you should try to 
> troubleshoot 
> to make sure there's nothing else going wrong.
> 
> -Justin
> 

Got it. I have been spending some time investigating the issue i’m having and
after reading shellfc.cpp I was pretty confident the issue was with SCF not 
converging,
and so my niter and dt were an attempt at looking into that. 

The workflow i’ve been trying to use is…
EM -> Solvate -> EM -> posres NVT V-rescale -> posres berendsen NPT isotropic 
1bar w/ V-rescale tcoupl ->
berendsen NPT semi-isotropic various pressures w/ V-rescale tcoupl

then once my cell shape has reached an equilibrium I finally switch to NH 
thermostat and PR barostat for
the production run. 

If I switch to employing the hardwall (and the lagrangian dynamics for drudes) 
then I understand it is not
compatible yet with NPT ensembles. So, if I change my work flow as follows 
would it be appropriate still?

EM->Solvate->EM->posre NPT isotropic 1 bar w/ V-rescale tcoupl->NPT 
semi-isotropic varying pressures
w V-rescale tcoupl until cell shape is equilibrated using PR barostat, then 
switch to NVT without pcoupl
to use the hardwall during my production run?

For some reason, i’ve got this idea that I need to be tcoupling and pcoupling 
during my production runs
so i’ve been apprehensive to do this. 

My Best,
   Guy Dayhoff






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Re: [gmx-users] How to extend simulation?

[ZHANG Cheng]

Thank you. So if the below is correct, and it will run for 100 ns?


convert-tpr -s previous.tpr -extend 10 -o next.tpr
gmx mdrun -deffnm next -cpi previous.cpt





-- Original --
From:  "Justin Lemkul";;
Date:  Tue, Apr 4, 2017 02:12 AM
To:  "gmx-users"; 

Subject:  Re: [gmx-users] How to extend simulation?





On 4/3/17 2:07 PM, ZHANG Cheng wrote:
> (Following Justin's suggestion)
>
>
> Dear Gromacs Researchers,
> My old.mdp only sets 10 ns of simulation. Now it has finished, and I want to 
> extend it to 100 ns.
>
>
> As shown on
> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
>
>
> Should I use the following two lines of code for the files in the same folder?
> If the "deffnm" is set correctly?
> But in this case, will the new simulation still only have 10 ns?
>

No.

>
> convert-tpr -s previous.tpr -extend timetoextendby -o next.tpr

If you replace "timetoextendby" with some sensible value of time (ps), then 
this 
means "next.tpr" will specify some longer amount of time to run.

> gmx mdrun -deffnm next -cpi previous.cpt

...which is then passed to mdrun here.  This says "run the longer simulation 
specified in next.tpr, but start from the point specified in previous.cpt 
rather 
than starting over from time zero."

-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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Re: [gmx-users] How to extend simulation?

[Justin Lemkul]

On 4/3/17 2:07 PM, ZHANG Cheng wrote:

(Following Justin's suggestion)


Dear Gromacs Researchers,
My old.mdp only sets 10 ns of simulation. Now it has finished, and I want to 
extend it to 100 ns.


As shown on
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations


Should I use the following two lines of code for the files in the same folder?
If the "deffnm" is set correctly?
But in this case, will the new simulation still only have 10 ns?



No.



convert-tpr -s previous.tpr -extend timetoextendby -o next.tpr


If you replace "timetoextendby" with some sensible value of time (ps), then this 
means "next.tpr" will specify some longer amount of time to run.



gmx mdrun -deffnm next -cpi previous.cpt


...which is then passed to mdrun here.  This says "run the longer simulation 
specified in next.tpr, but start from the point specified in previous.cpt rather 
than starting over from time zero."


-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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Re: [gmx-users] How to extend simulation?

[Mark Abraham]

Hi,

Back up your files and try it :-) You will see that mdrun refuses to append
if you change -deffnm. So either don't append or don't change the name.

Mark

On Mon, Apr 3, 2017 at 8:09 PM ZHANG Cheng <272699...@qq.com> wrote:

> (Following Justin's suggestion)
>
>
> Dear Gromacs Researchers,
> My old.mdp only sets 10 ns of simulation. Now it has finished, and I want
> to extend it to 100 ns.
>
>
> As shown on
> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
>
>
> Should I use the following two lines of code for the files in the same
> folder?
> If the "deffnm" is set correctly?
> But in this case, will the new simulation still only have 10 ns?
>
>
> convert-tpr -s previous.tpr -extend timetoextendby -o next.tpr
> gmx mdrun -deffnm next -cpi previous.cpt
>
>
>
> Thank you.
>
>
> Yours sincerely
> Cheng
> --
> Gromacs Users mailing list
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[gmx-users] How to extend simulation?

[ZHANG Cheng]

(Following Justin's suggestion)


Dear Gromacs Researchers,
My old.mdp only sets 10 ns of simulation. Now it has finished, and I want to 
extend it to 100 ns.


As shown on 
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations


Should I use the following two lines of code for the files in the same folder? 
If the "deffnm" is set correctly? 
But in this case, will the new simulation still only have 10 ns?


convert-tpr -s previous.tpr -extend timetoextendby -o next.tpr
gmx mdrun -deffnm next -cpi previous.cpt



Thank you.


Yours sincerely
Cheng
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Re: [gmx-users] Using the md integrator for calculating free energy of solvation

[Justin Lemkul]

On 4/3/17 2:01 PM, Dan Gil wrote:

Thank you Dr. Lemkul,

I am trying to run grompp with the md integrator, but I am getting this
error:
"For proper sampling of the (nearly) decoupled state, stochastic dynamics
should be used"

Should I ignore this warning with the -maxwarn option and try running it? I
will see if I obtain comparable values for ethanol.



People have already done such a comparison and that's why grompp is telling you 
this - it's better to use the Langevin integrator.  You'll get better sampling, 
particularly towards the end states.  Using -maxwarn tells grompp "you're trying 
to prevent me from making a mistake, but I want to do it anyway" :)  You'd 
better have a really, really good reason to try to override it.


-Justin


Best Regards,

Dan


On Mon, Mar 27, 2017 at 12:51 PM, Justin Lemkul  wrote:




On 3/26/17 9:40 PM, Dan Gil wrote:


Hi,

I am following Dr. Sander Pronk's and Dr. Justin Lemkul's tutorial on
calculating free energy of solvation. Is it possible and theoretically
sound to use the md integrator instead of the sd integrator for these
calculations?



Langevin dynamics gives better sampling so it is frequently used for free
energy calculations.  You may get comparable results with the leap-frog
integrator, but I haven never done a side-by-side comparison.

-Justin

I have already done a considerable amount of work using md integration, and

I want to make sure that the free energy values I calculate are consistent
with my previous work.

If using the md integrator is not sound, is there an alternative way of
calculating solvation energy that will be consistent?

Best Regards,

Dan



--
==

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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--
==

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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Re: [gmx-users] Using the md integrator for calculating free energy of solvation

[Dan Gil]

Thank you Dr. Lemkul,

I am trying to run grompp with the md integrator, but I am getting this
error:
"For proper sampling of the (nearly) decoupled state, stochastic dynamics
should be used"

Should I ignore this warning with the -maxwarn option and try running it? I
will see if I obtain comparable values for ethanol.

Best Regards,

Dan


On Mon, Mar 27, 2017 at 12:51 PM, Justin Lemkul  wrote:

>
>
> On 3/26/17 9:40 PM, Dan Gil wrote:
>
>> Hi,
>>
>> I am following Dr. Sander Pronk's and Dr. Justin Lemkul's tutorial on
>> calculating free energy of solvation. Is it possible and theoretically
>> sound to use the md integrator instead of the sd integrator for these
>> calculations?
>>
>>
> Langevin dynamics gives better sampling so it is frequently used for free
> energy calculations.  You may get comparable results with the leap-frog
> integrator, but I haven never done a side-by-side comparison.
>
> -Justin
>
> I have already done a considerable amount of work using md integration, and
>> I want to make sure that the free energy values I calculate are consistent
>> with my previous work.
>>
>> If using the md integrator is not sound, is there an alternative way of
>> calculating solvation energy that will be consistent?
>>
>> Best Regards,
>>
>> Dan
>>
>>
> --
> ==
>
> 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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Re: [gmx-users] System almost blowing up

[Justin Lemkul]

On 4/3/17 1:42 PM, Dayhoff, Guy wrote:

Hi,

   I’m receiving a couple (~15) EM did not converge warnings as well as a few 
(~3) 1,4 interaction
warnings during my run. It looks like it starts down the path to blowing up but 
recovers. Is this “recovery”
system dependent? Should I take these messages (even without the subsequent 
crash) to indicate an
underlying issue with my system/topology or equilibration? I’m not ignoring or 
circumventing any warning
during pdb2gmx, or any other commands.

For more context: I’m running the Drude-2013 forcefield, with a dt of .5fs 
emtol of 1.0 and niter of 150
using the V-rescale thermostat and Berendsen pressure coupling while my systems 
cell shape relaxes
as a continuation from position restrained NVT then NPT ensembles. The starting 
structures were minimized
in vacuum, then solvated and minimized once again prior to the posres 
equilibration.



Such a short dt and strict niter should not be necessary in practice.  The 
failure of SCF to converge/LINCS warnings is what we typically refer to as 
polarization catastrophe, so your system is on the brink of instability.  This 
is one of the inherent problems of SCF in polarizable systems; it often fails to 
converge and leaves the system potentially unstable.  The reflective hardwall is 
much more reliable (and faster).  If the instability is happening in your 
equilibration, that may be OK but it is something you should try to troubleshoot 
to make sure there's nothing else going wrong.


-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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Re: [gmx-users] How to extend simulation by changing the mdp file?

[Justin Lemkul]

On 4/3/17 1:41 PM, ZHANG Cheng wrote:

Dear Gromacs Researchers,
My old.mdp only sets 10 ns of simulation. Now it has finished, and I want to 
extend it to 100 ns.


As shown on
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations


Should I use the following two lines of code for the files in the same folder?


grompp -f new.mdp -c old.tpr -o new.tpr -t old.cpt
gmx mdrun -deffnm new -cpi -append




You only need to invoke grompp if you're changing output settings and starting a 
new run, in which case you would not be using -cpi -append in your mdrun command.


The use of convert-tpr followed by mdrun is cleaner and easier.

-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] System almost blowing up

[Dayhoff, Guy]

Hi,

   I’m receiving a couple (~15) EM did not converge warnings as well as a few 
(~3) 1,4 interaction
warnings during my run. It looks like it starts down the path to blowing up but 
recovers. Is this “recovery” 
system dependent? Should I take these messages (even without the subsequent 
crash) to indicate an
underlying issue with my system/topology or equilibration? I’m not ignoring or 
circumventing any warning
during pdb2gmx, or any other commands.  

For more context: I’m running the Drude-2013 forcefield, with a dt of .5fs 
emtol of 1.0 and niter of 150
using the V-rescale thermostat and Berendsen pressure coupling while my systems 
cell shape relaxes
as a continuation from position restrained NVT then NPT ensembles. The starting 
structures were minimized
in vacuum, then solvated and minimized once again prior to the posres 
equilibration. 

My Best,
Guy Dayhoff

  
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[gmx-users] How to extend simulation by changing the mdp file?

[ZHANG Cheng]

Dear Gromacs Researchers,
My old.mdp only sets 10 ns of simulation. Now it has finished, and I want to 
extend it to 100 ns.


As shown on 
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations


Should I use the following two lines of code for the files in the same folder?


grompp -f new.mdp -c old.tpr -o new.tpr -t old.cpt
gmx mdrun -deffnm new -cpi -append


Thank you.


Yours sincerely
Cheng
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Re: [gmx-users] wt% of the solvent

[Sam Dav]

ISHRAT
Thank you very much.

On Sun, Apr 2, 2017 at 11:50 PM, ISHRAT JAHAN  wrote:

> Hi,
> You have to calculate the number of alcohol and water molecules in the box
> and use genbox command with -nmol option.In -nmol put number of alcohol
> molecule and from the output of genbox command remove the extra number of
> water molecules with the calculated one.
>
>
> On Sun, Apr 2, 2017 at 12:34 AM, Sam Dav  wrote:
>
> > Hello GROMACS users.
> > I'm trying to solvate a polymer in (20 wt% alcohol +80 wt% water)
> > which command should I use to get the correct percentage? I'm using
> linux.
> > or should I calculate the number of molecules in the box.
> > Thanks in advance
> > --
> > Gromacs Users mailing list
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Re: [gmx-users] Order in which gromacs calculates non-bonded parameters

[Mark Abraham]

Hi,

Offhand, gen-pairs won't work without matching pairtypes, but
nonbond_params will override anything that might have been looked up from
pairtypes.

Mark

On Mon, Apr 3, 2017 at 2:39 PM Vries, de, H.W. <
h.w.de.vrie...@student.rug.nl> wrote:

> Dear all,
>
> I was wondering: what priority does GROMACS use for comparing
> [nonbond_params], [pairtypes], and gen-pairs-based cross-terms?
>
> I.e., are pairtypes additive to gen-pairs, with nonbond_params overwriting
> any cross-term defined through cross-terms?
>
> The reason I am asking is that I am currently using tabulated potentials
> with gen-pairs = no, but I noticed that adjusting cross-terms defined
> through [pairtypes] does very little to my simulated properties, whereas
> doing the exact same thing under [nonbond_params] does seem to
> significantly alter outcomes (i.e. the desired effect). I read the
> documentation, but am still slightly confused.
>
> thank you for reading! Would be great to hear from someone.
>
> best regards,
>
> Henry de Vries
>
> --
> Henry de Vries
> Student Topmaster Nanoscience
> Micromechanics of Materials Group
> tel: +31 (0)6-30520328 <+31%206%2030520328>
> office: X5113.0129
> Nijenborgh 4, 9747AG
> Groningen, Netherlands
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[gmx-users] Order in which gromacs calculates non-bonded parameters

[Vries, de, H.W.]

Dear all,

I was wondering: what priority does GROMACS use for comparing
[nonbond_params], [pairtypes], and gen-pairs-based cross-terms?

I.e., are pairtypes additive to gen-pairs, with nonbond_params overwriting
any cross-term defined through cross-terms?

The reason I am asking is that I am currently using tabulated potentials
with gen-pairs = no, but I noticed that adjusting cross-terms defined
through [pairtypes] does very little to my simulated properties, whereas
doing the exact same thing under [nonbond_params] does seem to
significantly alter outcomes (i.e. the desired effect). I read the
documentation, but am still slightly confused.

thank you for reading! Would be great to hear from someone.

best regards,

Henry de Vries

-- 
Henry de Vries
Student Topmaster Nanoscience
Micromechanics of Materials Group
tel: +31 (0)6-30520328
office: X5113.0129
Nijenborgh 4, 9747AG
Groningen, Netherlands
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Re: [gmx-users] Missing bond

[Sudip Das]

Dear Justin,

Thanks for your kind help!

Best regards,
Sudip




On Mon, Apr 3, 2017 at 5:20 PM, Justin Lemkul  wrote:

>
>
> On 4/1/17 1:18 AM, Sudip Das wrote:
>
>> Dear All,
>>
>> While I am preparing my system topology with pdb2gmx for a system
>> containing enzyme with 30 non-ionic surfactant molecules in water, I got
>> 36
>> number of bonds per surfactant molecules, but actually it has 37 bonds
>> (anyways, the number of angle, dihedral etc. are correct). From the
>> generated topology for this surfactant, I found out the missing bond. But
>> I
>> checked that I have incorporated that bond in aminoacids.rtp file and that
>> bond type is also present in the ffbonded.itp file.
>>
>> To figure out the reason, I used the pdb2gmx for a system with only 30
>> surfactant molecules in water (no enzyme). Again I encountered the same
>> problem.
>>
>> So, what could be the solution? Please assist me.
>>
>>
> Something does not add up.  Angles and dihedrals are built from the bonds,
> so if there's a bond missing, the angles and dihedrals shouldn't be right.
> Which bond is missing?  If it's in the .rtp there's no way it is somehow
> ignored while the others get processed correctly.
>
> -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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Re: [gmx-users] Protein ligand complex simulation

[Mark Abraham]

Hi,

Look at your docking result before you use it for something else. (Same
goes for any computed result from any software.)

Mark

On Mon, 3 Apr 2017 14:06 RAHUL SURESH  wrote:

> The ligand is out of protein in the very first frame of production run.
>  Then that should be my docking error.?
>
> On Mon, 3 Apr 2017 at 5:30 PM, Justin Lemkul  wrote:
>
> >
> >
> > On 4/3/17 7:56 AM, RAHUL SURESH wrote:
> > > Dear Justin
> > >
> > > First I apologise for the error I had made in my previous mail. It's
> > during
> > > production.
> > >
> > > I have recentered it. The ligand is out of the protein. The ligand is
> not
> > > in position where I docked.
> > >
> >
> > Then watch the recentered trajectory to see what happened.  Dissociation
> > should
> > be apparent, and smooth if the PBC effects have been correctly accounted
> > for.
> > If the dissociation is real, either the initial position was unfavorable
> > (docking is sometimes incorrect!) or the topology of the ligand was
> > inadequate
> > and thus you got a poor model of the interactions.
> >
> > -Justin
> >
> > >
> > > On Mon, 3 Apr 2017 at 5:21 PM, Justin Lemkul  wrote:
> > >
> > >>
> > >>
> > >> On 4/1/17 8:59 AM, RAHUL SURESH wrote:
> > >>> I followed the complex simulation tutorial. Minimisation for 2ns
> > >>>
> > >>
> > >> FYI there is no time during energy minimization, so you did not do "2
> > ns"
> > >> of
> > >> minimization.
> > >>
> > >>> I used auto dock to dock ligand with protein. During simulation I
> find
> > >> the
> > >>> ligand out of protein. Is that usual?
> > >>>
> > >>
> > >> This is probably a periodicity effect.  There's no way during the
> > course of
> > >> minimization that a ligand-protein complex can completely dissociate.
> > Use
> > >> trjconv to make sure you've properly re-imaged the system.  A simple
> > >> recentering
> > >> should do it.
> > >>
> > >> -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
> > >>
> > >> * 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.
> > >>
> >
> > --
> > ==
> >
> > 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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> > posting!
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
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Re: [gmx-users] Protein ligand complex simulation

[Justin Lemkul]

On 4/3/17 8:05 AM, RAHUL SURESH wrote:

The ligand is out of protein in the very first frame of production run.
 Then that should be my docking error.?



It sounds like your starting configuration was prepared incorrectly (however you 
manipulated it to prepare the system) or this is a PBC effect.


-Justin


On Mon, 3 Apr 2017 at 5:30 PM, Justin Lemkul  wrote:




On 4/3/17 7:56 AM, RAHUL SURESH wrote:

Dear Justin

First I apologise for the error I had made in my previous mail. It's

during

production.

I have recentered it. The ligand is out of the protein. The ligand is not
in position where I docked.



Then watch the recentered trajectory to see what happened.  Dissociation
should
be apparent, and smooth if the PBC effects have been correctly accounted
for.
If the dissociation is real, either the initial position was unfavorable
(docking is sometimes incorrect!) or the topology of the ligand was
inadequate
and thus you got a poor model of the interactions.

-Justin



On Mon, 3 Apr 2017 at 5:21 PM, Justin Lemkul  wrote:




On 4/1/17 8:59 AM, RAHUL SURESH wrote:

I followed the complex simulation tutorial. Minimisation for 2ns



FYI there is no time during energy minimization, so you did not do "2

ns"

of
minimization.


I used auto dock to dock ligand with protein. During simulation I find

the

ligand out of protein. Is that usual?



This is probably a periodicity effect.  There's no way during the

course of

minimization that a ligand-protein complex can completely dissociate.

Use

trjconv to make sure you've properly re-imaged the system.  A simple
recentering
should do it.

-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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--
==

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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--
==

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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Re: [gmx-users] Protein ligand complex simulation

[RAHUL SURESH]

The ligand is out of protein in the very first frame of production run.
 Then that should be my docking error.?

On Mon, 3 Apr 2017 at 5:30 PM, Justin Lemkul  wrote:

>
>
> On 4/3/17 7:56 AM, RAHUL SURESH wrote:
> > Dear Justin
> >
> > First I apologise for the error I had made in my previous mail. It's
> during
> > production.
> >
> > I have recentered it. The ligand is out of the protein. The ligand is not
> > in position where I docked.
> >
>
> Then watch the recentered trajectory to see what happened.  Dissociation
> should
> be apparent, and smooth if the PBC effects have been correctly accounted
> for.
> If the dissociation is real, either the initial position was unfavorable
> (docking is sometimes incorrect!) or the topology of the ligand was
> inadequate
> and thus you got a poor model of the interactions.
>
> -Justin
>
> >
> > On Mon, 3 Apr 2017 at 5:21 PM, Justin Lemkul  wrote:
> >
> >>
> >>
> >> On 4/1/17 8:59 AM, RAHUL SURESH wrote:
> >>> I followed the complex simulation tutorial. Minimisation for 2ns
> >>>
> >>
> >> FYI there is no time during energy minimization, so you did not do "2
> ns"
> >> of
> >> minimization.
> >>
> >>> I used auto dock to dock ligand with protein. During simulation I find
> >> the
> >>> ligand out of protein. Is that usual?
> >>>
> >>
> >> This is probably a periodicity effect.  There's no way during the
> course of
> >> minimization that a ligand-protein complex can completely dissociate.
> Use
> >> trjconv to make sure you've properly re-imaged the system.  A simple
> >> recentering
> >> should do it.
> >>
> >> -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
> >>
> >> * 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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>
> --
> ==
>
> 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
>
> * Please search the archive at
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*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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Re: [gmx-users] Protein ligand complex simulation

[Justin Lemkul]

On 4/3/17 7:56 AM, RAHUL SURESH wrote:

Dear Justin

First I apologise for the error I had made in my previous mail. It's during
production.

I have recentered it. The ligand is out of the protein. The ligand is not
in position where I docked.



Then watch the recentered trajectory to see what happened.  Dissociation should 
be apparent, and smooth if the PBC effects have been correctly accounted for. 
If the dissociation is real, either the initial position was unfavorable 
(docking is sometimes incorrect!) or the topology of the ligand was inadequate 
and thus you got a poor model of the interactions.


-Justin



On Mon, 3 Apr 2017 at 5:21 PM, Justin Lemkul  wrote:




On 4/1/17 8:59 AM, RAHUL SURESH wrote:

I followed the complex simulation tutorial. Minimisation for 2ns



FYI there is no time during energy minimization, so you did not do "2 ns"
of
minimization.


I used auto dock to dock ligand with protein. During simulation I find

the

ligand out of protein. Is that usual?



This is probably a periodicity effect.  There's no way during the course of
minimization that a ligand-protein complex can completely dissociate.  Use
trjconv to make sure you've properly re-imaged the system.  A simple
recentering
should do it.

-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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--
==

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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Re: [gmx-users] Protein ligand complex simulation

[RAHUL SURESH]

Dear Justin

First I apologise for the error I had made in my previous mail. It's during
production.

I have recentered it. The ligand is out of the protein. The ligand is not
in position where I docked.


On Mon, 3 Apr 2017 at 5:21 PM, Justin Lemkul  wrote:

>
>
> On 4/1/17 8:59 AM, RAHUL SURESH wrote:
> > I followed the complex simulation tutorial. Minimisation for 2ns
> >
>
> FYI there is no time during energy minimization, so you did not do "2 ns"
> of
> minimization.
>
> > I used auto dock to dock ligand with protein. During simulation I find
> the
> > ligand out of protein. Is that usual?
> >
>
> This is probably a periodicity effect.  There's no way during the course of
> minimization that a ligand-protein complex can completely dissociate.  Use
> trjconv to make sure you've properly re-imaged the system.  A simple
> recentering
> should do it.
>
> -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
>
> * Please search the archive at
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> posting!
>
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>
-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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Re: [gmx-users] Regarding structure conformation

[Justin Lemkul]

On 4/3/17 2:23 AM, Vytautas Rakeviius wrote:

MD can not simulate chemical reactions. What you can do prepare different forms 
with acpype and compare all in some way.



External tools aren't even necessary.  One just needs to select the proper 
termini with pdb2gmx.


-Justin



On Monday, April 3, 2017 6:51 AM, Dilip H N  
wrote:


 Hello,

I have a non zwitterionic glycine molecule, and have solvated it with
water, created topology and ran the simulation...and during EM, NVT, MD
runs the non zwitterionic form of glycine is still as it is, it hasn't got
converted into zwitterionic form (which is the most stable form of glycine
in water/solvent)...
So how can i convert non zwitterionic glycine form to its zwitterionic
form..??
Ideally it should get converted into its most stable form during solvation,
but why is it not getting converted..?? how can i solve this issue..?? Is
there anything wrong.??

Thank you



--
==

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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Re: [gmx-users] Protein ligand complex simulation

[Justin Lemkul]

On 4/1/17 8:59 AM, RAHUL SURESH wrote:

I followed the complex simulation tutorial. Minimisation for 2ns



FYI there is no time during energy minimization, so you did not do "2 ns" of 
minimization.



I used auto dock to dock ligand with protein. During simulation I find the
ligand out of protein. Is that usual?



This is probably a periodicity effect.  There's no way during the course of 
minimization that a ligand-protein complex can completely dissociate.  Use 
trjconv to make sure you've properly re-imaged the system.  A simple recentering 
should do it.


-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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Re: [gmx-users] Missing bond

[Justin Lemkul]

On 4/1/17 1:18 AM, Sudip Das wrote:

Dear All,

While I am preparing my system topology with pdb2gmx for a system
containing enzyme with 30 non-ionic surfactant molecules in water, I got 36
number of bonds per surfactant molecules, but actually it has 37 bonds
(anyways, the number of angle, dihedral etc. are correct). From the
generated topology for this surfactant, I found out the missing bond. But I
checked that I have incorporated that bond in aminoacids.rtp file and that
bond type is also present in the ffbonded.itp file.

To figure out the reason, I used the pdb2gmx for a system with only 30
surfactant molecules in water (no enzyme). Again I encountered the same
problem.

So, what could be the solution? Please assist me.



Something does not add up.  Angles and dihedrals are built from the bonds, so if 
there's a bond missing, the angles and dihedrals shouldn't be right.  Which bond 
is missing?  If it's in the .rtp there's no way it is somehow ignored while the 
others get processed correctly.


-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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Re: [gmx-users] Fwd: analysis of osmolyte at particular distance from backbone

[Mark Abraham]

Hi,

Some of those tools calculate distribution functions. Please start by
looking at them and seeing if they seem suitable.

Mark

On Mon, Apr 3, 2017 at 11:59 AM ISHRAT JAHAN  wrote:

> sorry i did not get what you said...
> actually i want to calculate distribution of water at various distance
> around backbone as done in paper "Regulation and aggregation of
> intrinsically disordered peptides" by Zachary A.Levine et.al.
>
>
>
> On Mon, Apr 3, 2017 at 1:54 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > So, you want to make a selection according to a geometric criterion,
> which
> > is what gmx select does.
> >
> > Mark
> >
> > On Mon, Apr 3, 2017 at 10:12 AM ISHRAT JAHAN 
> wrote:
> >
> > > i want to calculate number of water molecule within given distance from
> > > protein.
> > >
> > >
> > > On Mon, Apr 3, 2017 at 1:20 PM, Mark Abraham  >
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > It's not clear to me what you actually want, or why trjorder is even
> a
> > > > possible tool for the job. Look at
> > > > http://manual.gromacs.org/documentation/2016/user-guide/cmdline.html
> > and
> > > > find something useful.
> > > >
> > > > Mark
> > > >
> > > > On Mon, Apr 3, 2017 at 9:46 AM ISHRAT JAHAN 
> > wrote:
> > > >
> > > > > -- Forwarded message --
> > > > > From: ISHRAT JAHAN 
> > > > > Date: Fri, Mar 31, 2017 at 12:51 PM
> > > > > Subject: analysis of osmolyte at particular distance from backbone
> > > > > To: gmx-us...@gromacs.org
> > > > >
> > > > >
> > > > > Dear all,
> > > > >
> > > > > I want to calculate the number of osmolyte molecule at particular
> > > > distance
> > > > > from backbone with respect to residue.I have tried the command
> > trjorder
> > > > but
> > > > > it gives the number of osmolytes w.r.t time and i want it w.r.t
> > > residue.
> > > > > Can anyone help me how to calculate this.
> > > > > Thanks in advance
> > > > > --
> > > > > 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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> > 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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Re: [gmx-users] Fwd: analysis of osmolyte at particular distance from backbone

[ISHRAT JAHAN]

sorry i did not get what you said...
actually i want to calculate distribution of water at various distance
around backbone as done in paper "Regulation and aggregation of
intrinsically disordered peptides" by Zachary A.Levine et.al.



On Mon, Apr 3, 2017 at 1:54 PM, Mark Abraham 
wrote:

> Hi,
>
> So, you want to make a selection according to a geometric criterion, which
> is what gmx select does.
>
> Mark
>
> On Mon, Apr 3, 2017 at 10:12 AM ISHRAT JAHAN  wrote:
>
> > i want to calculate number of water molecule within given distance from
> > protein.
> >
> >
> > On Mon, Apr 3, 2017 at 1:20 PM, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > It's not clear to me what you actually want, or why trjorder is even a
> > > possible tool for the job. Look at
> > > http://manual.gromacs.org/documentation/2016/user-guide/cmdline.html
> and
> > > find something useful.
> > >
> > > Mark
> > >
> > > On Mon, Apr 3, 2017 at 9:46 AM ISHRAT JAHAN 
> wrote:
> > >
> > > > -- Forwarded message --
> > > > From: ISHRAT JAHAN 
> > > > Date: Fri, Mar 31, 2017 at 12:51 PM
> > > > Subject: analysis of osmolyte at particular distance from backbone
> > > > To: gmx-us...@gromacs.org
> > > >
> > > >
> > > > Dear all,
> > > >
> > > > I want to calculate the number of osmolyte molecule at particular
> > > distance
> > > > from backbone with respect to residue.I have tried the command
> trjorder
> > > but
> > > > it gives the number of osmolytes w.r.t time and i want it w.r.t
> > residue.
> > > > Can anyone help me how to calculate this.
> > > > Thanks in advance
> > > > --
> > > > 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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> > >
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> > > Support/Mailing_Lists/GMX-Users_List before posting!
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Re: [gmx-users] gromacs Query

[Mark Abraham]

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!
> > >
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> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
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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
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Re: [gmx-users] gromacs Query

[Aman Deep]

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!
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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MSc Bioinformatics
Jamia Millia Islamia
New Delhi - 110025
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Re: [gmx-users] Energy Miinimization question

[Vytautas Rakeviius]

As you set smaller emtol you do better and longer minimization. So with 1000 
you stop simulation way before polymer forms some rings. You can check video 
with VMD Chimera or something.
 

On Saturday, April 1, 2017 8:25 PM, Mishelle Oña  
wrote:
 

 Hello everybody,

I have a question about the final conformation after energy minimization. I am 
simulating a polymer in vacuo and I used steepest descent method for energy 
minimization. When I use an emtol=1000 the structure I get is linear. Then I 
tried an emtol=30 because another study about the same polymer used this value 
but the final structure has some rings, I am not sure why this happened.

Thanks for your help.

Mishelle
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Re: [gmx-users] Fwd: analysis of osmolyte at particular distance from backbone

[Mark Abraham]

Hi,

So, you want to make a selection according to a geometric criterion, which
is what gmx select does.

Mark

On Mon, Apr 3, 2017 at 10:12 AM ISHRAT JAHAN  wrote:

> i want to calculate number of water molecule within given distance from
> protein.
>
>
> On Mon, Apr 3, 2017 at 1:20 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > It's not clear to me what you actually want, or why trjorder is even a
> > possible tool for the job. Look at
> > http://manual.gromacs.org/documentation/2016/user-guide/cmdline.html and
> > find something useful.
> >
> > Mark
> >
> > On Mon, Apr 3, 2017 at 9:46 AM ISHRAT JAHAN  wrote:
> >
> > > -- Forwarded message --
> > > From: ISHRAT JAHAN 
> > > Date: Fri, Mar 31, 2017 at 12:51 PM
> > > Subject: analysis of osmolyte at particular distance from backbone
> > > To: gmx-us...@gromacs.org
> > >
> > >
> > > Dear all,
> > >
> > > I want to calculate the number of osmolyte molecule at particular
> > distance
> > > from backbone with respect to residue.I have tried the command trjorder
> > but
> > > it gives the number of osmolytes w.r.t time and i want it w.r.t
> residue.
> > > Can anyone help me how to calculate this.
> > > Thanks in advance
> > > --
> > > 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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Re: [gmx-users] Fwd: analysis of osmolyte at particular distance from backbone

[ISHRAT JAHAN]

i want to calculate number of water molecule within given distance from
protein.


On Mon, Apr 3, 2017 at 1:20 PM, Mark Abraham 
wrote:

> Hi,
>
> It's not clear to me what you actually want, or why trjorder is even a
> possible tool for the job. Look at
> http://manual.gromacs.org/documentation/2016/user-guide/cmdline.html and
> find something useful.
>
> Mark
>
> On Mon, Apr 3, 2017 at 9:46 AM ISHRAT JAHAN  wrote:
>
> > -- Forwarded message --
> > From: ISHRAT JAHAN 
> > Date: Fri, Mar 31, 2017 at 12:51 PM
> > Subject: analysis of osmolyte at particular distance from backbone
> > To: gmx-us...@gromacs.org
> >
> >
> > Dear all,
> >
> > I want to calculate the number of osmolyte molecule at particular
> distance
> > from backbone with respect to residue.I have tried the command trjorder
> but
> > it gives the number of osmolytes w.r.t time and i want it w.r.t residue.
> > Can anyone help me how to calculate this.
> > Thanks in advance
> > --
> > 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] Fwd: analysis of osmolyte at particular distance from backbone

[Mark Abraham]

Hi,

It's not clear to me what you actually want, or why trjorder is even a
possible tool for the job. Look at
http://manual.gromacs.org/documentation/2016/user-guide/cmdline.html and
find something useful.

Mark

On Mon, Apr 3, 2017 at 9:46 AM ISHRAT JAHAN  wrote:

> -- Forwarded message --
> From: ISHRAT JAHAN 
> Date: Fri, Mar 31, 2017 at 12:51 PM
> Subject: analysis of osmolyte at particular distance from backbone
> To: gmx-us...@gromacs.org
>
>
> Dear all,
>
> I want to calculate the number of osmolyte molecule at particular distance
> from backbone with respect to residue.I have tried the command trjorder but
> it gives the number of osmolytes w.r.t time and i want it w.r.t residue.
> Can anyone help me how to calculate this.
> Thanks in advance
> --
> 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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[gmx-users] Fwd: analysis of osmolyte at particular distance from backbone

[ISHRAT JAHAN]

-- Forwarded message --
From: ISHRAT JAHAN 
Date: Fri, Mar 31, 2017 at 12:51 PM
Subject: analysis of osmolyte at particular distance from backbone
To: gmx-us...@gromacs.org


Dear all,

I want to calculate the number of osmolyte molecule at particular distance
from backbone with respect to residue.I have tried the command trjorder but
it gives the number of osmolytes w.r.t time and i want it w.r.t residue.
Can anyone help me how to calculate this.
Thanks in advance
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Re: [gmx-users] Fwd: Dipole moment of water

[Mark Abraham]

Hi,

I imagine it does whatever is standard, e.g. from negative to positive.
What does it report for a single water molecule?

Mark

On Mon, Apr 3, 2017 at 8:24 AM Alex  wrote:

> No comment on below question, please?
>
> Regards,
> Alex
>
> -- Forwarded message --
> From: Alex 
> Date: Wed, Mar 29, 2017 at 2:27 PM
> Subject: Dipole moment of water
> To: gmx-us...@gromacs.org
>
>
> Dear gromacs user,
>
> What is the direction of the water's dipole moment generated by "gmx
> h2order "? if it has defined from negative to positive charge or vise
> versa.
>
> Thanks.
>
> Regards,
> Alex
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Re: [gmx-users] gromacs Query

[Mark Abraham]

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
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[gmx-users] gromacs Query

[Aman Deep]

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

-- 
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MSc Bioinformatics
Jamia Millia Islamia
New Delhi - 110025
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Re: [gmx-users] Regarding structure conformation

[Vytautas Rakeviius]

MD can not simulate chemical reactions. What you can do prepare different forms 
with acpype and compare all in some way.
 

On Monday, April 3, 2017 6:51 AM, Dilip H N  
wrote:
 

 Hello,

I have a non zwitterionic glycine molecule, and have solvated it with
water, created topology and ran the simulation...and during EM, NVT, MD
runs the non zwitterionic form of glycine is still as it is, it hasn't got
converted into zwitterionic form (which is the most stable form of glycine
in water/solvent)...
So how can i convert non zwitterionic glycine form to its zwitterionic
form..??
Ideally it should get converted into its most stable form during solvation,
but why is it not getting converted..?? how can i solve this issue..?? Is
there anything wrong.??

Thank you
-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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[gmx-users] Fwd: Dipole moment of water

[Alex]

No comment on below question, please?

Regards,
Alex

-- Forwarded message --
From: Alex 
Date: Wed, Mar 29, 2017 at 2:27 PM
Subject: Dipole moment of water
To: gmx-us...@gromacs.org


Dear gromacs user,

What is the direction of the water's dipole moment generated by "gmx
h2order "? if it has defined from negative to positive charge or vise versa.

Thanks.

Regards,
Alex
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