[gmx-users] Error regarding missing hydrogen atoms

[Vishal Pandya]

Hello Gromacs Users,

I have been trying to run a simulation of PTM residues which has NAG, BMA,
MAN, etc glycosylated residues in my protein. First, I would like to ask
does anyone has .hdb file for such molecules for charmm22* or charmm36 ff
as I am having following error:

*WARNING: atom H1 is missing in residue NAG 2345 in the pdb file*
* You might need to add atom H1 to the hydrogen database of
building block NAG*
* in the file merged.hdb (see the manual)*

*WARNING: atom O1 is missing in residue NAG 2345 in the pdb file*

*WARNING: atom HO1 is missing in residue NAG 2345 in the pdb file*
* You might need to add atom HO1 to the hydrogen database of
building block NAG*
* in the file merged.hdb (see the manual)*

*WARNING: atom H5 is missing in residue NAG 2345 in the pdb file*
* You might need to add atom H5 to the hydrogen database of
building block NAG*
* in the file merged.hdb (see the manual)*


*WARNING: atom H2 is missing in residue NAG 2345 in the pdb file*
* You might need to add atom H2 to the hydrogen database of
building block NAG*
* in the file merged.hdb (see the manual)*

*WARNING: atom HN is missing in residue NAG 2345 in the pdb file*
* You might need to add atom HN to the hydrogen database of
building block NAG*
* in the file merged.hdb (see the manual)*

I do have a .rtp pertaining to its bonds, impropers, atoms but just to make
it future-proof to use pdb2gmx, I would like to have it.

Cheers,
Vishal
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Re: [gmx-users] Bug?! Lost particles while sorting

[Mark Abraham]

Hi,

That particular output indicates that the code is not working as intended.
Please open an issue on the GROMACS redmine and attach the tpr, the log
file from your run, and and instructions on how to reproduce.

Thanks,

Mark

On Wed, 30 Aug 2017 19:34 Mohsen Ramezanpour 
wrote:

> Dear Gromacs users,
>
> I am running simulations using Gromacs version 2016.3 while using GPU.
>
> I get an error in my simulations as follows:
>
> Program: gmx mdrun, version 2016.3
> Source file: src/gromacs/mdlib/nbnxn_grid.cpp (line 404)
> MPI rank:15 (out of 16)
>
> Software inconsistency error:
> Lost particles while sorting
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
> Googling the error I found that there were relevant bugs before (discussed
> by Dr. Berk Hess):
>
> https://redmine.gromacs.org/issues/1379
>
> https://redmine.gromacs.org/issues/1153
>
> However, they should have been fixed in the newer versions as mentioned in
> the above links.
>
> Can someone please let me know what the problem could be in this case?
>
> Many thanks in advance,
>
> Cheers,
> Mohsen
> --
> *Rewards work better than punishment ...*
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Re: [gmx-users] possible bug in posre

[Sergio Manzetti]

That means intercalation is affected directly by this, and the results will 
have no meaningful physical sense. Has anyone succssfully simulated 
intercalation in the DNA by some molecules without a method that disrupts the 
physicochemical energies of the DNA and the intercalator? 


Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
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 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 



From: "Justin Lemkul"  
To: "gmx-users"  
Sent: Wednesday, August 30, 2017 4:50:55 PM 
Subject: Re: [gmx-users] possible bug in posre 

On 8/30/17 10:39 AM, Sergio Manzetti wrote: 
> Its only the constraints in DPOSRE that I am concerned about. They do keep 
> the antisense and the sense strands together, however, do they keep this 
> together so that also intercalation between the bases is not any longer 
> physically related? 

Constraints and restraints are different; -DPOSRES has nothing to do 
with constraints. 

Position restraints bias the positions of the affected atoms towards 
their reference coordinates. They are absolute in space, so they don't 
"keep strands together" in the literal sense, but they simply 
prevent/disfavor anything from moving. 

-Justin 

-- 
== 

Justin A. Lemkul, Ph.D. 
Assistant Professor 
Virginia Tech Department of Biochemistry 

303 Engel Hall 
340 West Campus Dr. 
Blacksburg, VA 24061 

jalem...@vt.edu | (540) 231-3129 
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Re: [gmx-users] possible bug in posre

[Justin Lemkul]

On 8/30/17 10:39 AM, Sergio Manzetti wrote:

Its only the constraints in DPOSRE that I am concerned about. They do keep the 
antisense and the sense strands together, however, do they keep this together 
so that also intercalation between the bases is not any longer physically 
related?


Constraints and restraints are different; -DPOSRES has nothing to do 
with constraints.


Position restraints bias the positions of the affected atoms towards 
their reference coordinates.  They are absolute in space, so they don't 
"keep strands together" in the literal sense, but they simply 
prevent/disfavor anything from moving.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] possible bug in posre

[Sergio Manzetti]

Its only the constraints in DPOSRE that I am concerned about. They do keep the 
antisense and the sense strands together, however, do they keep this together 
so that also intercalation between the bases is not any longer physically 
related? 


Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 



From: "Justin Lemkul"  
To: "gmx-users"  
Sent: Wednesday, August 30, 2017 3:43:09 PM 
Subject: Re: [gmx-users] possible bug in posre 

On 8/30/17 9:33 AM, Sergio Manzetti wrote: 
> Weird stuff, because the 1 simulation turned out well, even without POSRE. 
> 
> Can this POSRE be reliable, in terms of intercalation of molecules? In other 
> words, does the energy that is imposed by POSRE really reflect the energy 
> landscape of the bonds simulated in the remaining of the molecules in the 
> box, by lincs? If the dposre is an aiddtional energy to the h-bonds of the 
> DNA, then any intercalation study is really futile! 

You're talking about both constraints and restraints here, and typically 
restraints are applied to non-H atoms and constraints involve bonds to H 
atoms. Restraints are biasing potentials to prevent motion. You'll 
have to explain what you're studying and why you think you need 
restraints (which are typically only used during equilibration). 
Restraints are artificial, so anything that comes out of a restrained 
simulation should be interpreted with care, because you could be 
completely preventing relevant dynamics. Binding of a molecule to a 
restrained target may be completely unphysical. 

-Justin 

-- 
== 

Justin A. Lemkul, Ph.D. 
Assistant Professor 
Virginia Tech Department of Biochemistry 

303 Engel Hall 
340 West Campus Dr. 
Blacksburg, VA 24061 

jalem...@vt.edu | (540) 231-3129 
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html 

== 

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Re: [gmx-users] triclinic box

[Hermann, Johannes]

Hi Nikko,

what do you insert for X Y Z in your editconf command? With which 
program do you "open" the gro file? If I remember it correctly, VMD has 
a problem displaying anything else than a rectangular box (If you just 
want to display the edges of your box). Try to display the water 
molecules and see if you get a different shape.


All the best

Johannes


On 30.08.2017 15:50, Niko Ukkonen wrote:

Dear All,

I'm trying to define a triclinic box. I used this command : gmx editconf -f
x.pdb -o box.gro -bt triclinic -box X Y Z -angles 90 90 120.

Then, I use gmx solvate to fill the box: gmx solvate -cp box.gro -cs tip4p
-p topol.top -o solve.gro
But, when I open it. it's like a cubic box. Would you please help me?

Thank you in advance,
Nikko


--
__
*Technische Universität München*
*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverfahrenstechnik
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Fax: +49 8928915714

Email: j.herm...@lrz.tum.de
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[gmx-users] triclinic box

[Niko Ukkonen]

Dear All,

I'm trying to define a triclinic box. I used this command : gmx editconf -f
x.pdb -o box.gro -bt triclinic -box X Y Z -angles 90 90 120.

Then, I use gmx solvate to fill the box: gmx solvate -cp box.gro -cs tip4p
-p topol.top -o solve.gro
But, when I open it. it's like a cubic box. Would you please help me?

Thank you in advance,
Nikko
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Re: [gmx-users] Surface tension for water

[André Farias de Moura]

I cannot understand the point of performing NPT coupling to compute surface
tension, the usual approach relies on NVT simulations instead. You might
want to take a look at this very nice investigation of the surface tension
of many water models (all done using GROMACS at constant NVT conditions):

http://rabida.uhu.es/dspace/bitstream/handle/10272/9574/Surface_tension.pdf?sequence=2

In principle, you could couple the lateral pressure to an external bath
with the exact surface tension of your model, then mechanical equilibrium
should be attained, but pressure varies wildly during MD simulations, so
actual mechanical equilibrium might not happen so easily (it seems to be
your case)

besides, your are coupling to the experimental surface tension of water,
whereas any water model has a different surface tension (usually smaller
than the experimental value). If you couple your system to a lateral
surface tension much different from what should be its equilibrium surface
tension during an MD simulation, then you are in fact applying a net
lateral pressure different from zero and again I guess this is why you are
getting your simulations crashing with high T and P values.

So unless you have a very clear idea of why you might want to perform that
simulation with a surface tension coupling, I would strongly suggest you to
use NVT instead.

IMNSHO surface tension coupling only makes sense if the liquid (whether
water or any other subphase you might be interested in) can support a
insoluble (or at least poorly soluble) film on each interface (film meaning
either monolayers, bilayers, multilayers or just another immiscible
liquid, maybe a solid state too, depending on P and T range).

I hope it helps

Andre

On Wed, Aug 30, 2017 at 2:26 AM, Iman Ahmadabadi  wrote:

> Dear Dan,
>
> As you can see in the images I sent to you, there is no error massage in
> output files. The properties of the system such as pressure or temperature
> is so high, that's why I've concluded that the system is crashed.
>
> Sincerely,
> Iman
>
> On Wed, Aug 30, 2017 at 12:44 AM, Iman Ahmadabadi <
> imanahmadabad...@gmail.com> wrote:
>
> > Hi Dan,
> >
> > There is no error massage, It's just a crashing and stopping the
> > simulation. The version is 4.6.0.
> >
> > Iman
> >
> > On Tue, Aug 29, 2017 at 9:57 PM, Iman Ahmadabadi <
> > imanahmadabad...@gmail.com> wrote:
> >
> >> Dear Dan,
> >>
> >> I have attached the NPT.mdp file in the following:
> >>
> >> title =  NPT equilibration
> >> ; Run parameters
> >> integrator = md
> >> nsteps = 2000
> >> dt= 0.001
> >>
> >> ; Output control
> >> nstxout = 500
> >> nstvout = 500
> >> nstenergy = 500
> >> nstlog = 500
> >>
> >> ; Bond parameters
> >> continuation= no
> >> constraint_algorithm= lincs
> >> constraints= all-bonds
> >> lincs_iter= 1
> >> lincs_order= 4
> >>
> >> ; Neighborsearching
> >> cutoff-scheme   = Verlet
> >> ns_type= grid
> >> nstlist= 20
> >> rlist   = 2.0
> >> rcoulomb= 2.0
> >> rvdw= 2.0
> >>
> >> ; Electrostatics
> >> coulombtype= PME
> >> pme_order= 4
> >> fourierspacing = 0.12
> >>
> >> ; Temperature coupling is on
> >> tcoupl = V-rescale
> >> tc-grps = system
> >> tau_t = 0.1
> >> ref_t = 298.15
> >>
> >> ; Pressure coupling is on
> >> pcoupl= berendsen
> >> pcoupltype= surface-tension
> >> tau_p= 2.0  2.0
> >> ref_p= 1440  1.0
> >> compressibility = 4.46e-5  0
> >> refcoord_scaling= com
> >>
> >> ; Periodic boundary conditions
> >> pbc = xyz
> >>
> >> ; Dispersion correction
> >> DispCorr = EnerPres
> >>
> >> ; Velocity generation
> >> gen_vel = yes
> >> lincs_warnangle = 90
> >>
> >>
> >> Now I'm gonna using semiisotropic instead of surface tension like in the
> >> following:
> >> pcoupltyp   = semiisotropic
> >> tau_p = 0.5
> >> ref_p  = 1.0  1.0
> >> compressibility = 4.46e-5  0
> >>
> >> Thank you for your help.
> >> Sincerely,
> >> Iman
> >>
> >> On Tue, Aug 29, 2017 at 6:04 PM, Iman Ahmadabadi <
> >> imanahmadabad...@gmail.com> wrote:
> >>
> >>> Dear All Users,
> >>>
> >>> I'm calculating the surface tension of the water, my box contains
> almost
> >>> 5000 water molecule in the middle of that. Through NVT equilibration,
> I got
> >>> reasonable results for surface tension but when I use NPT for my
> system,
> >>> the system crashes every time. The pressure coupling options are in the
> >>> following:
> >>>
> >>> pcoupltyp = surface-tension
> >>> tau_p= 0.5  0.5  &  1.0  1.0  &  2.0  2.0  (Crashing with all
> >>> three values)
> >>> ref_p  = 1440  1.0
> >>> compressibility = 4.46e-5  0
> >>>
> >>> first ref-p value is 720*2 = 1440. 720 is the surface tension of water
> >>> in 298.15.
> >>>
> >>> Now, I'm going to use semiisotropic for P-coupling:
> >>>
> >>> pcoupltyp   = semiisotropic
> >>> tau_p = 

Re: [gmx-users] possible bug in posre

[Justin Lemkul]

On 8/30/17 9:33 AM, Sergio Manzetti wrote:

Weird stuff, because the 1 simulation turned out well, even without POSRE.

Can this POSRE be reliable, in terms of intercalation of molecules? In other 
words, does the energy that is imposed by POSRE really reflect the energy 
landscape of the bonds simulated in the remaining of the molecules in the box, 
by lincs? If the dposre is an aiddtional energy to the h-bonds of the DNA, then 
any intercalation study is really futile!


You're talking about both constraints and restraints here, and typically 
restraints are applied to non-H atoms and constraints involve bonds to H 
atoms.  Restraints are biasing potentials to prevent motion.  You'll 
have to explain what you're studying and why you think you need 
restraints (which are typically only used during equilibration).  
Restraints are artificial, so anything that comes out of a restrained 
simulation should be interpreted with care, because you could be 
completely preventing relevant dynamics. Binding of a molecule to a 
restrained target may be completely unphysical.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] possible bug in posre

[Sergio Manzetti]

Weird stuff, because the 1 simulation turned out well, even without POSRE. 

Can this POSRE be reliable, in terms of intercalation of molecules? In other 
words, does the energy that is imposed by POSRE really reflect the energy 
landscape of the bonds simulated in the remaining of the molecules in the box, 
by lincs? If the dposre is an aiddtional energy to the h-bonds of the DNA, then 
any intercalation study is really futile! 


Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 



From: "Justin Lemkul"  
To: "gmx-users"  
Sent: Wednesday, August 30, 2017 3:35:48 PM 
Subject: Re: [gmx-users] possible bug in posre 

On 8/30/17 9:21 AM, Sergio Manzetti wrote: 
> Hi, I have made 5 copies of a simulation, using the following mdp , with 
> gen-seed = 17529, 17528, 17527, 17526 and 17525. In this simulation, thre is 
> a piece of DNA; with posre etc. In simulation one, after 20 ns, the DNA is 
> bound to some other molecule and everything looks OK. In simulation 2, 3, 4 
> and 5 the DNA strands fly everywhere in the box, outside the box and even 
> double up in longitude direction. All the directories are identical in their 
> files, and the grompp has been used respectively. Does this sound familiar to 
> some, or is it most likely a grompp error? This is the second time I try 
> this. 
> 
> 
> title = DNA in water stabilization 
> cpp = /lib/cpp 
> include = -I../top 
> define = 

The fact that there's no -DPOSRES here suggests you're probably not 
actually using restraints. Therefore, what you're seeing is your DNA 
diffusing across the box and experiencing the normal PBC imaging 
effects. If restraints are on, you'll see a corresponding energy term 
in the .log and .edr files. If it's not there, there are no restraints. 

-Justin 

-- 
== 

Justin A. Lemkul, Ph.D. 
Assistant Professor 
Virginia Tech Department of Biochemistry 

303 Engel Hall 
340 West Campus Dr. 
Blacksburg, VA 24061 

jalem...@vt.edu | (540) 231-3129 
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html 

== 

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Re: [gmx-users] possible bug in posre

[Justin Lemkul]

On 8/30/17 9:21 AM, Sergio Manzetti wrote:

Hi, I have made 5 copies of a simulation, using the following mdp , with 
gen-seed = 17529, 17528, 17527, 17526 and 17525. In this simulation, thre is a 
piece of DNA; with posre etc. In simulation one, after 20 ns, the DNA is bound 
to some other molecule and everything looks OK. In simulation 2, 3, 4 and 5 the 
DNA strands fly everywhere in the box, outside the box and even double up in 
longitude direction. All the directories are identical in their files, and the 
grompp has been used respectively. Does this sound familiar to some, or is it 
most likely a grompp error? This is the second time I try this.


title = DNA in water stabilization
cpp = /lib/cpp
include = -I../top
define =


The fact that there's no -DPOSRES here suggests you're probably not 
actually using restraints.  Therefore, what you're seeing is your DNA 
diffusing across the box and experiencing the normal PBC imaging 
effects.  If restraints are on, you'll see a corresponding energy term 
in the .log and .edr files.  If it's not there, there are no restraints.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] Setting different intial velocities

[Justin Lemkul]

On 8/30/17 6:33 AM, Apramita Chand wrote:

Dear All,
  While doing NVT equilbration, I'm setting gen_seed=-1,gen_vel=yes and
following it up with NPT equilibration(gen_vel=no) and MD (gen_vel=no).
So if I want to generate different starting conditions by giving initial
velociies differently, I should modify my NVT.mdp file and change the
gen_seed. Is this procedure correct?


By specifying -1 as the seed, you're telling grompp to use a different 
number every time (it's based on the process ID of the command in the 
shell).



Is there any standard values to pass on to gen_seed or any number will do?


There is no such thing as a standard value for a random seed.

-Justin

--
==

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Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
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Re: [gmx-users] gmxdump gmxcheck commands not found

[Justin Lemkul]

On 8/30/17 6:26 AM, Apramita Chand wrote:

Dear All,
I'm running 4.5.7 version of gromacs.
I'm unable to run gmxdump or gmxcheck in my command line and it says
command not found.
I've tried almost all combinations of commands that I could but in vain.
Same happens for 4.6 version.
What is the correct command?


Both gmxdump and gmxcheck are correct names for commands in those 
(extremely old) versions of GROMACS.  If your shell doesn't recognize 
them, your environment isn't properly configured (see installation 
instructions).


-Justin

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==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] difference in potential energy

[Justin Lemkul]

On 8/30/17 6:24 AM, Emran Heshmati wrote:

Thanks to mark for his explanations.
We performed MD simulation on a peptide fragment as well as its mutants
where, its residues have been systematically replaced by alanine residue.
We found that potential and kinetic energies of one mutant (T=>A) is
significantly different from other molecules. interestingly there are other
similar substitutions in different positions indicating that molecules with
similar masses and chemical formula are being compared. apparently, we are
facing with an special case in which the changing of the position of a
residue has profound effect on the kinetic and potential energies. our
question is related to the interpretation of this finding!!


You're taking a larger residue and making it smaller, also eliminating 
hydrogen bonding by making the residue nonpolar. Kinetic and potential 
energies are extrinsic properties, so all you're likely seeing is a 
reflection of the fact that you've changed the size of the residue.  
Neither quantity is a free energy, which is what is actually useful.  
Your results might be completely different if you use a different force 
field, for instance.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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[gmx-users] possible bug in posre

[Sergio Manzetti]

Hi, I have made 5 copies of a simulation, using the following mdp , with 
gen-seed = 17529, 17528, 17527, 17526 and 17525. In this simulation, thre is a 
piece of DNA; with posre etc. In simulation one, after 20 ns, the DNA is bound 
to some other molecule and everything looks OK. In simulation 2, 3, 4 and 5 the 
DNA strands fly everywhere in the box, outside the box and even double up in 
longitude direction. All the directories are identical in their files, and the 
grompp has been used respectively. Does this sound familiar to some, or is it 
most likely a grompp error? This is the second time I try this. 


title = DNA in water stabilization 
cpp = /lib/cpp 
include = -I../top 
define = 
integrator = md 
dt = 0.002 
nsteps = 1000 
nstxout = 5000 
nstvout = 5000 
nstlog = 5000 
nstenergy = 300 
nstxout-compressed = 300 
compressed-x-grps = PRB SOL NA CL DNA 
energygrps = PRB SOL NA CL DNA 
nstlist = 10 
ns-type = grid 
rlist = 0.8 
coulombtype = PME 
rcoulomb = 0.8 
rvdw = 0.8 
tcoupl = V-Rescale 
tc-grps = System 
tau-t = 0.1 
ref-t = 310 
Pcoupl = No 
tau-p = 1.0 
compressibility = 4.5e-5 
ref-p = 1.0 
gen-vel = yes 
gen-temp = 310 
gen-seed = 17529 
constraints = all-bonds 



Sergio Manzetti 

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[gmx-users] Setting different intial velocities

[Apramita Chand]

Dear All,
 While doing NVT equilbration, I'm setting gen_seed=-1,gen_vel=yes and
following it up with NPT equilibration(gen_vel=no) and MD (gen_vel=no).
So if I want to generate different starting conditions by giving initial
velociies differently, I should modify my NVT.mdp file and change the
gen_seed. Is this procedure correct?
Is there any standard values to pass on to gen_seed or any number will do?


Looking forward to your suggestions

Thanking you,
yours sincerely
Apramita Chand
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[gmx-users] gmxdump gmxcheck commands not found

[Apramita Chand]

Dear All,
I'm running 4.5.7 version of gromacs.
I'm unable to run gmxdump or gmxcheck in my command line and it says
command not found.
I've tried almost all combinations of commands that I could but in vain.
Same happens for 4.6 version.
What is the correct command?

Thanking you,
Yours sincerely,
Apramita Chand
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Re: [gmx-users] difference in potential energy

[Emran Heshmati]

Thanks to mark for his explanations.
We performed MD simulation on a peptide fragment as well as its mutants
where, its residues have been systematically replaced by alanine residue.
We found that potential and kinetic energies of one mutant (T=>A) is
significantly different from other molecules. interestingly there are other
similar substitutions in different positions indicating that molecules with
similar masses and chemical formula are being compared. apparently, we are
facing with an special case in which the changing of the position of a
residue has profound effect on the kinetic and potential energies. our
question is related to the interpretation of this finding!!
Regards
Emran

On Sun, Jun 25, 2017 at 2:45 AM, Emran Heshmati  wrote:

> Dear Gromacs users
> I performed alanine scaning mutagenesis using gromacs on a peptide
> fragment consisting 16 aa. In one of the mutations, the kinetic energy of
> the system was significantly different. How can I interpret this result?
> any comment is welcome
> regards
> Emran
>
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