Re: [gmx-users] Neutralizing

[mohammad r]

Thank you Justin for your help. 

On Wednesday, March 9, 2016 6:38 PM, Justin Lemkul  wrote:
 

 

On 3/9/16 1:42 AM, mohammad r wrote:
> Thank you Parham and Justin, Excuse me I have another question, in simulation
> of a water-peptide system, is it necessary to use QM/MM simulation during the
> entire process? Because I didn't see it in the tutorials. By the way I
> generated the pdb file by using charmm-gui then import it in amber to get the
> topology and coordinate files, finally I converted the topology and
> coordinate files to gromacs format and did the rest of simulation by gromacs.
> but I didn't run QM/MM simulation. Does it make trouble in the results?

The technique(s) used depend on the scientific question(s) being posed before 
doing the simulations.  If you expect some reactions, etc. to be taking place, 
then you need QM/MM.  If you just want to simulate a peptide over time, then 
plain MD is fine.  Methodological details like this should be decided long 
before one approaches a keyboard :)

-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] Fwd: Trouble with mpirun gmx- 2/2 machines not sharing correctly

[Jacob Nowatzke]

I've recently installed OpenMPI 1.10.2 alongside GROMACS 5.1.2. I've read
all over the web about how to, but I'm having issues left and right. I've
finally gotten to a point where *gmx* works, but in an odd way. I'll try to
explain without too much detail.


Machine1=
CPU: 8-core AMD FX9590
GPU: AMD HD8990 (dual-core)
RAM: 32GB

Machine2=
CPU: 6-core AMD FX6120
GPU: AMD R9 Nano (single-core)
RAM: 8GB

Machines are networked by LAN, which cat I don't remember (may be reason
for slow mdrun described soon?). I have added so many $PATH variables on
and off- I'm tired of it. I do have to ask if I have to add
usr/local/gromacs/bin to the $PATH and $LD_PATH in .bashrc? When I did this
is when the machines started picking up on eachother, as they would not
when only OMPI was specified in .bashrc. What's going on here?

My issue- besides understanding it all, this is the point where I've got
things somewhat working- is that I run something like "mpirun --hosts
Machine1,Machine2 --path usr/local/gromacs/bin gmx mdrun -v -deffnm nvt"
from Machine2 over ssh from separate laptop, everything seems to be going
smoothly... except this is only being run on Machine1(8990 is also
detected), with Machine2 components not being detected. Essentially, I'm
running gmx mdrun on Machine1 as if I was using ssh from Machine2.
Obviously, this isn't what I want to do. I'd like to see each machine with
their respective GPUs being utilized for gmx mdrun and the such.

If Machine1 is actually being utilized, then why is it performing steps at
a much slower rate than if I had used the same machine from ssh?

To top off this issue, when I run gmx grompp (or genion) it freezes before
bringing me back to the command line.

Obviously, I'm new, so I want to say that I really appreciate any help
here. Learning GROMACS has been a pleasure so far and I'm hoping to get
details down to utilize for homology modeling. Thanks for your help

-Jacob
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[gmx-users] How can I control PME domain decomposition

[柯谱]

Hi everyone,
 I am working on PP/PME optimization.  But I 
found while PP ranks could be controlled by, say -dd  9 8 8, PME node 
decomposition CANNOT be tuned.
 For instance,  below is the basic information 
for optimization:


   - Using a fourier grid of 216x192x192, spacing 0.065 0.062 0.062
   - Estimate for the relative computational load of the PME mesh part:
   0.24


I would like to run this simulation by -dd 9 8 
8 and the PME nodes setting 24 * 8, in which PME grid_x (216) and grid_y 
(192) is divisible by #PME_ranks_x (24)
  and PME grid_y (192) and grid_z (192) is divisible by 
#PME_ranks_y (8).  However, when I used -npme=192, gromacs automatically 
set


   Domain decomposition grid *9 x 8 x 8*, separate PME ranks *192*
   PME domain decomposition: *192 x 1 x 1*

which significantly slowed down the simulation.  Then my question is 
what can I do to control PME node decomposition?  Thanks for your help!

Best wishes,
Pu,
**
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[gmx-users] Beginner Question -- Grab Info from Output

[ANAND AMITKUMAR DHARIA]

Hi,

I am running gmx msd and would like to import the value of the calculated
diffusion coefficient and error that is output in my linux terminal. I know
I can view the trajectory with grace or parse the file in a text editor for
its values, but I would just like end calculation. Is there a way I can do
this? I can't seem to find the gmx program either in my computer.

Thanks,
Anand
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Re: [gmx-users] .mtx file

[Joaquim Rui de Castro Rodrigues]

Hi,

I don't think the hessian calculation is parallelized. Try running in one core.

HTH,
Rui Rodrigues




De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Em Nome De Alexander 
Alexander [alexanderwie...@gmail.com]
Enviado: quarta-feira, 9 de Março de 2016 23:00
Para: gmx-us...@gromacs.org
Assunto: [gmx-users] .mtx file

Dear Gromacs user,

I was wondering why no .mtx file as hessian file was produced in my gmx
mdrun?
I used below command to submit my mdrun job:

gmx mdrun -deffnm md -s md.tpr -mtx hessian.mtx -ntomp 4 -ntmpi 4

neither md.mtx nor hessian.mtx!?

Cheers,
Alex
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Re: [gmx-users] .mtx file

[Justin Lemkul]

On 3/9/16 6:00 PM, Alexander Alexander wrote:

Dear Gromacs user,

I was wondering why no .mtx file as hessian file was produced in my gmx
mdrun?
I used below command to submit my mdrun job:

gmx mdrun -deffnm md -s md.tpr -mtx hessian.mtx -ntomp 4 -ntmpi 4

neither md.mtx nor hessian.mtx!?



It's only produced when running NMA.

-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] .mtx file

[Alexander Alexander]

Dear Gromacs user,

I was wondering why no .mtx file as hessian file was produced in my gmx
mdrun?
I used below command to submit my mdrun job:

gmx mdrun -deffnm md -s md.tpr -mtx hessian.mtx -ntomp 4 -ntmpi 4

neither md.mtx nor hessian.mtx!?

Cheers,
Alex
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[gmx-users] axial velocity autocorrelation

[Aranha, Michelle]

Hello,


I am working with a confined system with damped motion of molecules in the x 
and y directions. Is there a workaround that would allow to calculate just the  
axial velocity (vz) autocorrelation rather than the total velocity 
autocorrelation?


Best regards,

Michelle
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[gmx-users] adding windows to thermodynamic integration

[Yoav Atsmon-Raz]

Hi everyone, I'm doing a TI calculation for a molecule that's of interest to me 
and the results after gmx bar processed the dhdl.xvg files aren't so good at 
certain points so I want to add some lambda values around the problematic ones 
and I was wondering if this means I have to do the entire set all over again 
(cause I need to input a new lambda vector) or can I just add several mdps for 
the new lambda values and let gmx bar work them along with the rest of the 
output is ok?

Thanks in advance,
Yoav

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[gmx-users] Steered Molecular Dynamics for citrate channel

[Bruna Franciele]

Dear gromacs users

I want to force the citrate to cross the channel using SMD, but when I run
the tutorial Umbrella Sampling for my system adapting the entries mdp for
gromacs-5.0.5 my results are staying bad!!

I want see citrato crossing the channel, and in the "generating
configurations" the citrate is in left of channel and  then right side of
channel.
How I can run this SMD protocol?

I'm using the entry mdp file for pull code:

; COM PULLING
pull = umbrella
pull_geometry = direction
pull_dim = Y N N
pull_start = yes
pull-print-reference = no
pull_nstxout = 1000
pull_nstfout = 1000
pull_ngroups = 2
pull-ncoords = 1
; Group name, weight (default all 1), vector, init, rate (nm/ps),
kJ/(mol*nm^2)
pull-group1-name = Protein ; ref
pull-group2-name = CIT ; pulled
pull-coord1-groups = 1 2
pull-coord1-origin = 0 0 0
pull-coord1-vec = 1 0 0
pull-coord1-init = 0
pull-coord1-rate = 0.0
pull-coord1-k = 1000


Someone can help me, please??

Bruna.

Bruna Franciele Faria
-Laboratory of Molecular Dynamic and Simulation
UFSJ - Brazil
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Re: [gmx-users] semi-permeable wall in gromacs

[Justin Lemkul]

On 3/9/16 12:28 PM, gozde ergin wrote:

Dear all,

I would like to compute the osmotic pressure directly from all-atom MD 
simulations of concentrated aqueous solutions.

The basic idea is to introduce “virtual” walls to represent the effect of ideal 
semipermeable membranes, separating a high concentration region from a pure 
water region.

The walls keep the ions confined, but the water molecules are allowed to pass 
freely, permitting an equalization of their chemical potential throughout the 
entire system.

The mean force per unit area exerted on the ions by the virtual walls during 
the simulations can be directly related to the osmotic pressure.



My question is is there a way to introduce semi-permeable walls in GROMACS?



Use flat-bottom restraints on the ions.

-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] semi-permeable wall in gromacs

[gozde ergin]

Dear all,

I would like to compute the osmotic pressure directly from all-atom MD 
simulations of concentrated aqueous solutions. 

The basic idea is to introduce “virtual” walls to represent the effect of ideal 
semipermeable membranes, separating a high concentration region from a pure 
water region. 

The walls keep the ions confined, but the water molecules are allowed to pass 
freely, permitting an equalization of their chemical potential throughout the 
entire system. 

The mean force per unit area exerted on the ions by the virtual walls during 
the simulations can be directly related to the osmotic pressure. 



My question is is there a way to introduce semi-permeable walls in GROMACS?

bests
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Re: [gmx-users] How the angle/bond length changes during simulation.

[Justin Lemkul]

On 3/9/16 10:01 AM, Dawid das wrote:

Dear Gromacs Experts,

How can I get a plot of a bond length/ valence angle/ dihedral angle during
simulation
from *xtc and *.ndx files? I am pretty sure that it is possible, but with
g_angle
and g_bond I can get only the distribution.


Get the bond distance(s) with g_dist.


By the way, when I use

g_angle -f npt-md2-cent.xtc -n index.ndx -type dihedral -all

and choose group like this from my index.ndx file:

[ angles ]
969 966 964 960
966 964 960 959

I don't get separate plots for each of two dihedral angles.
How can I get it?



You are.  That's what -all is for:

"Plot all angles separately in the averages file, in the order of appearance in 
the index file."


Open up angaver.xvg and you will see the average, then the two individual time 
series.


-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] Neutralizing

[Justin Lemkul]

On 3/9/16 1:42 AM, mohammad r wrote:

Thank you Parham and Justin, Excuse me I have another question, in simulation
of a water-peptide system, is it necessary to use QM/MM simulation during the
entire process? Because I didn't see it in the tutorials. By the way I
generated the pdb file by using charmm-gui then import it in amber to get the
topology and coordinate files, finally I converted the topology and
coordinate files to gromacs format and did the rest of simulation by gromacs.
but I didn't run QM/MM simulation. Does it make trouble in the results?


The technique(s) used depend on the scientific question(s) being posed before 
doing the simulations.  If you expect some reactions, etc. to be taking place, 
then you need QM/MM.  If you just want to simulate a peptide over time, then 
plain MD is fine.  Methodological details like this should be decided long 
before one approaches a keyboard :)


-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 the angle/bond length changes during simulation.

[Dawid das]

O'right, I found my mistake.
Now it works fine.

Thank you!

2016-03-09 16:11 GMT+01:00 Justin Lemkul :

>
>
> On 3/9/16 10:11 AM, Dawid das wrote:
>
>> 2016-03-09 16:07 GMT+01:00 Justin Lemkul :
>>
>>
>>> You are.  That's what -all is for:
>>>
>>> "Plot all angles separately in the averages file, in the order of
>>> appearance in the index file."
>>>
>>> Open up angaver.xvg and you will see the average, then the two individual
>>> time series.
>>>
>>
>>
>>
>> Than something does not work for me, because what I get is:
>>-1800.027099
>>-1790.025099
>>-1780.023980
>>-1770.022160
>>-1760.019040
>>-1750.016480
>>-1740.016160
>>
>> and so on
>>
>>
> That must be angdist.xvg because that is a distribution, not a time series.
>
>
> -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 the angle/bond length changes during simulation.

[Justin Lemkul]

On 3/9/16 10:11 AM, Dawid das wrote:

2016-03-09 16:07 GMT+01:00 Justin Lemkul :



You are.  That's what -all is for:

"Plot all angles separately in the averages file, in the order of
appearance in the index file."

Open up angaver.xvg and you will see the average, then the two individual
time series.




Than something does not work for me, because what I get is:
   -1800.027099
   -1790.025099
   -1780.023980
   -1770.022160
   -1760.019040
   -1750.016480
   -1740.016160

and so on



That must be angdist.xvg because that is a distribution, not a time series.

-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 the angle/bond length changes during simulation.

[Dawid das]

2016-03-09 16:07 GMT+01:00 Justin Lemkul :

>
> You are.  That's what -all is for:
>
> "Plot all angles separately in the averages file, in the order of
> appearance in the index file."
>
> Open up angaver.xvg and you will see the average, then the two individual
> time series.



Than something does not work for me, because what I get is:
  -1800.027099
  -1790.025099
  -1780.023980
  -1770.022160
  -1760.019040
  -1750.016480
  -1740.016160

and so on

Best regards,
Dawid Grabarek
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[gmx-users] How the angle/bond length changes during simulation.

[Dawid das]

Dear Gromacs Experts,

How can I get a plot of a bond length/ valence angle/ dihedral angle during
simulation
from *xtc and *.ndx files? I am pretty sure that it is possible, but with
g_angle
and g_bond I can get only the distribution.
By the way, when I use

g_angle -f npt-md2-cent.xtc -n index.ndx -type dihedral -all

and choose group like this from my index.ndx file:

[ angles ]
969 966 964 960
966 964 960 959

I don't get separate plots for each of two dihedral angles.
How can I get it?

Best regards,
Dawid Grabarek
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Re: [gmx-users] Regarding using random seed

[Tsjerk Wassenaar]

Right!

T.
On Mar 9, 2016 12:24 PM, "neha chaudhary" 
wrote:

> Hi,
>
> So all I have to do is to extract different configurations from my already
> performed MD simulation. Then I have to prepare a new system using that
> configuration with the following parameters and rerun the simulations:
>
> continuation = no
> gen_vel = yes
> gen-seed = -1
>
> Right?
>
>
> Best Regards,
>
> *Neha*
>
> Research Scholar,
> Centre for Computational Biology and Bioinformatics,
> School of Life Sciences,
> Central University of Himachal Pradesh,
>
>
>
>
>
> On Wed, Mar 9, 2016 at 4:06 PM, Tsjerk Wassenaar 
> wrote:
>
> > Hi Neha,
> >
> > Set
> >
> > continuation = no
> > gen_vel = yes
> >
> > (check http://manual.gromacs.org/online/mdp_opt.html#vel)
> >
> > Best,
> >
> > Tsjerk
> >
> >
> > On Wed, Mar 9, 2016 at 11:16 AM, neha chaudhary <
> > nehachaudhary...@gmail.com>
> > wrote:
> >
> > > Thanks Tsjerk for replying,
> > >
> > > I want to ask one more question that to start with new velocities, what
> > > changes I have to make and in which .mdp file?
> > >
> > > Best Regards,
> > >
> > > *Neha*
> > >
> > > Research Scholar,
> > > Centre for Computational Biology and Bioinformatics,
> > > School of Life Sciences,
> > > Central University of Himachal Pradesh,
> > >
> > >
> > >
> > >
> > >
> > > On Wed, Mar 9, 2016 at 3:37 PM, Tsjerk Wassenaar 
> > > wrote:
> > >
> > > > Hi Neha,
> > > >
> > > > You can perform a simulation first, and then extract configurations,
> > > which
> > > > you simulate with new starting velocities. Alternatively, you can
> > > generate
> > > > a number of different starting structures using elastic-network
> > modeling,
> > > > like with the ElNemo server. Mind to first energy minimize the
> > resulting,
> > > > extrapolated structures, as they may be stretchedhere and there.
> > > >
> > > > Hope it helps,
> > > >
> > > > Tsjerk
> > > >
> > > > On Wed, Mar 9, 2016 at 10:54 AM, neha chaudhary <
> > > > nehachaudhary...@gmail.com>
> > > > wrote:
> > > >
> > > > > Hello there,
> > > > >
> > > > >
> > > > > Can anyone tell me how can I start my MD simulations with different
> > > > > starting structure (random seed) for my protein-ligand complex.
> Can I
> > > > start
> > > > > with different sets of coordinates and velocities? If yes, how?
> > > > >
> > > > >
> > > > > Thanks,
> > > > >
> > > > > *Neha*
> > > > > Research Scholar,
> > > > > Centre for Computational Biology and Bioinformatics,
> > > > > School of Life Sciences,
> > > > > Central University of Himachal Pradesh,
> > > > > --
> > > > > 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.
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Tsjerk A. Wassenaar, Ph.D.
> > > > --
> > > > 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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> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
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> > >
> >
> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > --
> > 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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Re: [gmx-users] Regarding using random seed

[neha chaudhary]

Hi,

So all I have to do is to extract different configurations from my already
performed MD simulation. Then I have to prepare a new system using that
configuration with the following parameters and rerun the simulations:

continuation = no
gen_vel = yes
gen-seed = -1

Right?


Best Regards,

*Neha*

Research Scholar,
Centre for Computational Biology and Bioinformatics,
School of Life Sciences,
Central University of Himachal Pradesh,





On Wed, Mar 9, 2016 at 4:06 PM, Tsjerk Wassenaar  wrote:

> Hi Neha,
>
> Set
>
> continuation = no
> gen_vel = yes
>
> (check http://manual.gromacs.org/online/mdp_opt.html#vel)
>
> Best,
>
> Tsjerk
>
>
> On Wed, Mar 9, 2016 at 11:16 AM, neha chaudhary <
> nehachaudhary...@gmail.com>
> wrote:
>
> > Thanks Tsjerk for replying,
> >
> > I want to ask one more question that to start with new velocities, what
> > changes I have to make and in which .mdp file?
> >
> > Best Regards,
> >
> > *Neha*
> >
> > Research Scholar,
> > Centre for Computational Biology and Bioinformatics,
> > School of Life Sciences,
> > Central University of Himachal Pradesh,
> >
> >
> >
> >
> >
> > On Wed, Mar 9, 2016 at 3:37 PM, Tsjerk Wassenaar 
> > wrote:
> >
> > > Hi Neha,
> > >
> > > You can perform a simulation first, and then extract configurations,
> > which
> > > you simulate with new starting velocities. Alternatively, you can
> > generate
> > > a number of different starting structures using elastic-network
> modeling,
> > > like with the ElNemo server. Mind to first energy minimize the
> resulting,
> > > extrapolated structures, as they may be stretchedhere and there.
> > >
> > > Hope it helps,
> > >
> > > Tsjerk
> > >
> > > On Wed, Mar 9, 2016 at 10:54 AM, neha chaudhary <
> > > nehachaudhary...@gmail.com>
> > > wrote:
> > >
> > > > Hello there,
> > > >
> > > >
> > > > Can anyone tell me how can I start my MD simulations with different
> > > > starting structure (random seed) for my protein-ligand complex. Can I
> > > start
> > > > with different sets of coordinates and velocities? If yes, how?
> > > >
> > > >
> > > > Thanks,
> > > >
> > > > *Neha*
> > > > Research Scholar,
> > > > Centre for Computational Biology and Bioinformatics,
> > > > School of Life Sciences,
> > > > Central University of Himachal Pradesh,
> > > > --
> > > > 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.
> > > >
> > >
> > >
> > >
> > > --
> > > Tsjerk A. Wassenaar, Ph.D.
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
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> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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[gmx-users] Query about a simple MD with constant electric field

[Ivan Gladich]

Dear Gromacs users

I am doing a very simple MD with a constant electric field of 1 V/nm 
along the positive z-direction in a system containing only one Na+ ion, 
starting from rest.
The ion is not coupled to the thermostat and it is placed in a box of 4 
nm* 4nm * 16 nm, in the X,Y,and Z direction respectively.


 I would expect my ion accelerating along the positive Z-direction with 
constant acceleration.
However my ion  starts to move in the positive  Z-direction but with 
constant velocity for all my 1 ns MD. Do I do something really wrong?


I am using gromacs 5.1.1 in double precision

Thanks for any possible help
Below my inputs
Ivan

###
conf.gro
###

Gyas ROwers Mature At Cryogenic Speed
 1
 2183Na  Na 6545   3.014   0.540   8.909
   4.0   4.0  16.0

##
topol.top
#

[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
1   2   yes 0.5 0.8333

[ atomtypes ]
;name  at.num   mass   charge   ptype   sigma   epsilon
Na11  79.901.  A0.385   0.0022

[ moleculetype ]
; molname   nrexcl
Na  1

[ atoms ]
; idat type res nr  residu name at name  cg nr  charge
1   Na  1   Na  Na   1  1.0

[ system ]
 THE-BEST

[ molecules ]
; Compoundnmols
 Na  1


#
grompp.mdp
#

title   = Na+Electric

; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 100   ;  = 1000ps
dt  = 0.001 ; 1 fs

; Output control
nstxout = 0   ; save coordinates every 1.0 ps
nstvout = 1000   ; save velocities every 1.0 ps
nstenergy   = 5000; save energies every 1 ps
nstlog  = 5000; update log file every 1 ps
nstxtcout   = 1000; xtc compressed trajectory output every 1 ps

; Neighborsearching
cutoff-scheme   = group ;Verlet
ns_type = grid  ; search neighboring grid cells
nstlist = 1; 20 fs, largely irrelevant with Verlet
rlist   = 0.9
rcoulomb= 0.9   ; short-range electrostatic cutoff (in nm)
rvdw= 0.9   ; short-range van der Waals cutoff (in nm)

; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range 
electrostatics

pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT

; Temperature coupling
tcoupl  = no ;

; Pressure coupling
pcoupl  = no;

; Periodic boundary conditions
pbc = xyz   ; 3-D PBC

; Dispersion correction
DispCorr= no ;

; Velocity generation
gen_vel = no

;Electric

E-x = 0 0 0
E-y = 0 0 0
E-z = 1 1 0 : 1 V nm-1

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Re: [gmx-users] Regarding using random seed

[Tsjerk Wassenaar]

Hi Neha,

Set

continuation = no
gen_vel = yes

(check http://manual.gromacs.org/online/mdp_opt.html#vel)

Best,

Tsjerk


On Wed, Mar 9, 2016 at 11:16 AM, neha chaudhary 
wrote:

> Thanks Tsjerk for replying,
>
> I want to ask one more question that to start with new velocities, what
> changes I have to make and in which .mdp file?
>
> Best Regards,
>
> *Neha*
>
> Research Scholar,
> Centre for Computational Biology and Bioinformatics,
> School of Life Sciences,
> Central University of Himachal Pradesh,
>
>
>
>
>
> On Wed, Mar 9, 2016 at 3:37 PM, Tsjerk Wassenaar 
> wrote:
>
> > Hi Neha,
> >
> > You can perform a simulation first, and then extract configurations,
> which
> > you simulate with new starting velocities. Alternatively, you can
> generate
> > a number of different starting structures using elastic-network modeling,
> > like with the ElNemo server. Mind to first energy minimize the resulting,
> > extrapolated structures, as they may be stretchedhere and there.
> >
> > Hope it helps,
> >
> > Tsjerk
> >
> > On Wed, Mar 9, 2016 at 10:54 AM, neha chaudhary <
> > nehachaudhary...@gmail.com>
> > wrote:
> >
> > > Hello there,
> > >
> > >
> > > Can anyone tell me how can I start my MD simulations with different
> > > starting structure (random seed) for my protein-ligand complex. Can I
> > start
> > > with different sets of coordinates and velocities? If yes, how?
> > >
> > >
> > > Thanks,
> > >
> > > *Neha*
> > > Research Scholar,
> > > Centre for Computational Biology and Bioinformatics,
> > > School of Life Sciences,
> > > Central University of Himachal Pradesh,
> > > --
> > > 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.
> > >
> >
> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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>



-- 
Tsjerk A. Wassenaar, Ph.D.
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Re: [gmx-users] Regarding using random seed

[neha chaudhary]

Thanks Tsjerk for replying,

I want to ask one more question that to start with new velocities, what
changes I have to make and in which .mdp file?

Best Regards,

*Neha*

Research Scholar,
Centre for Computational Biology and Bioinformatics,
School of Life Sciences,
Central University of Himachal Pradesh,





On Wed, Mar 9, 2016 at 3:37 PM, Tsjerk Wassenaar  wrote:

> Hi Neha,
>
> You can perform a simulation first, and then extract configurations, which
> you simulate with new starting velocities. Alternatively, you can generate
> a number of different starting structures using elastic-network modeling,
> like with the ElNemo server. Mind to first energy minimize the resulting,
> extrapolated structures, as they may be stretchedhere and there.
>
> Hope it helps,
>
> Tsjerk
>
> On Wed, Mar 9, 2016 at 10:54 AM, neha chaudhary <
> nehachaudhary...@gmail.com>
> wrote:
>
> > Hello there,
> >
> >
> > Can anyone tell me how can I start my MD simulations with different
> > starting structure (random seed) for my protein-ligand complex. Can I
> start
> > with different sets of coordinates and velocities? If yes, how?
> >
> >
> > Thanks,
> >
> > *Neha*
> > Research Scholar,
> > Centre for Computational Biology and Bioinformatics,
> > School of Life Sciences,
> > Central University of Himachal Pradesh,
> > --
> > 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.
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
> 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] Regarding using random seed

[Tsjerk Wassenaar]

Hi Neha,

You can perform a simulation first, and then extract configurations, which
you simulate with new starting velocities. Alternatively, you can generate
a number of different starting structures using elastic-network modeling,
like with the ElNemo server. Mind to first energy minimize the resulting,
extrapolated structures, as they may be stretchedhere and there.

Hope it helps,

Tsjerk

On Wed, Mar 9, 2016 at 10:54 AM, neha chaudhary 
wrote:

> Hello there,
>
>
> Can anyone tell me how can I start my MD simulations with different
> starting structure (random seed) for my protein-ligand complex. Can I start
> with different sets of coordinates and velocities? If yes, how?
>
>
> Thanks,
>
> *Neha*
> Research Scholar,
> Centre for Computational Biology and Bioinformatics,
> School of Life Sciences,
> Central University of Himachal Pradesh,
> --
> 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.
>



-- 
Tsjerk A. Wassenaar, Ph.D.
-- 
Gromacs Users mailing list

* Please search the archive at 
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[gmx-users] Regarding using random seed

[neha chaudhary]

Hello there,


Can anyone tell me how can I start my MD simulations with different
starting structure (random seed) for my protein-ligand complex. Can I start
with different sets of coordinates and velocities? If yes, how?


Thanks,

*Neha*
Research Scholar,
Centre for Computational Biology and Bioinformatics,
School of Life Sciences,
Central University of Himachal Pradesh,
-- 
Gromacs Users mailing list

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