Re: [gmx-users] Neutralizing

[mohammad r]

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?
Best, Mohammad. 

On Wednesday, March 9, 2016 4:26 AM, Justin Lemkul  wrote:
 

 

On 3/8/16 3:59 AM, mohammad r wrote:
> Thank you Parham
> You mean that it is not necessary to do QM/MM simulation?
>

The trivial task of adding ions to neutralize the net charge on the system 
certainly does not require anything like QM/MM.

-Justin

>      On Tuesday, March 8, 2016 11:13 AM, Parham Jabbarzadeh (Department of 
>Biomedical Science)  wrote:
>
>
>  Dear Sir
>
> Use this command:
>
> gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -neutral
>
> In this case, you don't need ​the number of ions​.
> Kind Regards
>
> Parham J. K.
> ​​==​==​=
> ​PhD candidate - Lecturer in drug discovery
> Faculty of Medicine and Health SciencesUniversity Putra MalaysiaMalaysia
> ​==​===Publication ::: Featured Publication ::: Website 
> ::: FaceBook
> On Tue, Mar 8, 2016 at 3:32 PM, mohammad r  wrote:
>
> Hi everybody, I’ve generated a water-peptide system, now I want to neutralize 
> it. Is adding adequate number of ions sufficient for neutralizing process or 
> I should do QM/MM simulation for the this process? Thank you, Mohammad.
> --
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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] distance restraints in mdp

[Justin Lemkul]

Please don't reply to the entire digest.  Copy the relevant portions and use a
proper subject line.

On 3/8/16 8:19 PM, Sana Saeed wrote:

dear Justin Lemkuli already run that without restraints, it has no problems.
even i used the gro file from the simple 5ns MD but still have these same
errors and warnings. when i set Lincs constraints to all-bonds , simulation
finishes fine but by using alchemical_analysis.py for free energies it gives
errors and warnings. (Warning: states 29 and 37 have the same energies on the
dataset.) i used 42 lambdas and about 32 states are having same energies. and
when i set constraints to h-bonds then LINCS warnings. i tried to use
different options for pressure coupling also because i read somewhere it also
affects simulation. i am quite confused where the problem is. is it possible
to send you topology file and you have a look?Thanks in advance


Now we're talking about half a million different things.  When reporting a 
problem, please keep it simple.  It's impossible for anyone on this mailing list 
to be inside your head and know what you've done.


If you want to troubleshoot distance restraints, we can do that.  But let's take 
things one at a time.  If you want to share files, please upload a tarball of 
*all* input files: coordinates, topology(ies), any relevant .mdp file(s), and a 
run script that lists all of your commands, exactly in sequence as you typed 
them.  Please do not send this information privately; share with the list so 
others can contribute (I'm frankly swamped lately and have little time to delve 
deeply into such issues but I'll try to make a little time).


-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] distance restraints in mdp

[Justin Lemkul]

On 3/7/16 10:35 PM, Sana Saeed wrote:

i am performing protein ligand binding free energy calculation MD. i have
applied distance restraint to 1 pair of atoms. now when i am running md it
gives me LINCS warnings. first i thought it is because of wrong geometry so i
changed complex, now i am doing it for Lysozyme+JZ4. but still same warning.
i am confused about the distance restraints to be introduced in mdp file.
disre = simple/ensemble? i read in manual, but still confused. i tried both
with "simple it gives me LINCS warning and with ensemble it says that this
version of gromacs doesnt support it. i am using 5.1 gromacs.


Then simplify further and make sure the system runs without restraints or 
anything else.  Just normal MD.  Start simple to avoid chasing the wrong problem.


-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 3/8/16 3:59 AM, mohammad r wrote:

Thank you Parham
You mean that it is not necessary to do QM/MM simulation?



The trivial task of adding ions to neutralize the net charge on the system 
certainly does not require anything like QM/MM.


-Justin


 On Tuesday, March 8, 2016 11:13 AM, Parham Jabbarzadeh (Department of Biomedical 
Science)  wrote:


  Dear Sir

Use this command:

gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -neutral

In this case, you don't need ​the number of ions​.
Kind Regards

Parham J. K.
​​==​==​=
​PhD candidate - Lecturer in drug discovery
Faculty of Medicine and Health SciencesUniversity Putra MalaysiaMalaysia
​==​===Publication ::: Featured Publication ::: Website ::: 
FaceBook
On Tue, Mar 8, 2016 at 3:32 PM, mohammad r  wrote:

Hi everybody, I’ve generated a water-peptide system, now I want to neutralize 
it. Is adding adequate number of ions sufficient for neutralizing process or I 
should do QM/MM simulation for the this process? Thank you, Mohammad.
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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] apply force on single molecule

[Smith, Micholas D.]

Yes. Take a look at the manual for information on using the Pulling code.


===
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Parvez Mh 

Sent: Tuesday, March 08, 2016 2:20 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] apply force on single molecule

Dear all,

I want look at change in potential energy profile, when i apply force on a
molecule on one end where other end fixed in a position. Is it possible do
it in gromacs. If yes, how may i proceed?

--Masrul
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[gmx-users] apply force on single molecule

[Parvez Mh]

Dear all,

I want look at change in potential energy profile, when i apply force on a
molecule on one end where other end fixed in a position. Is it possible do
it in gromacs. If yes, how may i proceed?

--Masrul
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Re: [gmx-users] unit cell vector warning

[Irem Altan]

Hi,

I'm generating the box from the.pdb file with pdb2gmx. The protein in question 
is 5e1k. I do the simulations in the protein unit cell. 

Best,
Irem

> On Mar 8, 2016, at 11:39 AM, Mark Abraham  wrote:
> 
> Hi,
> 
> How are you actually generating the coordinate file, and/or the box
> vectors? As far as I know, nobody's written down the set of vectors that
> should work sensibly, but it's likely that the gmx tools will write boxes
> that will definitely work later on...
> 
> Mark
> 
>> On Tue, Mar 8, 2016 at 4:27 PM Irem Altan  wrote:
>> 
>> Hi,
>> 
>> An update on the unit cell problem: when I make small changes in the
>> angle, say change 89.45 to 89.00, the error disappears. I’m still getting
>> the same warning. This is with version 5.1.2. Could this be a numerical
>> precision issue (c_y is 0.05, see below) or a bug? I tried to run this
>> without the protein, by just putting water and a few ions in the box.
>> 
>> Best,
>> Irem
>> 
>>> On Mar 3, 2016, at 4:15 PM, Irem Altan  wrote:
>>> 
>>> Hi,
>>> 
>>> I am trying to simulate a protein in its triclinic unit cell. During the
>> energy minimization and MD simulation, GROMACS prints the following out at
>> every step:
>>> 
>>> WARNING: Found more than 12 triclinic correction vectors, ignoring some.
>>> There is probably something wrong with your box.
>>> 0.0e+00,  0.0e+00}
>>> 3.89470e-01,   2.50360e+00  3.41610e-01  Box[1]={
>> 3.41610e-01,  5.49000e-03,  5.26833e+00}
>>> 2.91510e+00 Box (3x3):
>>> 2.91510e+00, ,  0.0e+00}
>>>   Box[1]={ Box[0]={ 0.0e+00 2.50360e+00
>> 5.49000e-03,
>>> 
>>> I checked the .gro file to see the unit cell vectors are listed
>> correctly.
>>> 
>>> The protein has the following sides and angles:
>>> 
>>> a = 25.04, b = 29.41, c = 52.79, α = 89.45, β = 86.29, γ = 82.39
>>> 
>>> and I calculate the unit vectors to be:
>>> 
>>> a = [ 25.036,   0.   ,   0.   ]
>>> b = [  3.8947483 ,  29.15096972,   0.]
>>> c = [  3.41611372,   0.05486764,  52.6816]
>>> 
>>> and the .gro file has the line:
>>> 
>>>  2.50360   2.91510   5.26833   0.0   0.0   0.38947   0.0
>> 0.34161   0.00549
>>> 
>>> which seems to be correct.
>>> 
>>> I have also verified that the conditions 3.1-3.3 listed on page 12 on
>> the manual for 5.1 to be correct.
>>> 
>>> What could be the problem?
>>> 
>>> Best,
>>> Irem
>>> --
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>>> 
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>> posting!
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>> send a mail to gmx-users-requ...@gromacs.org.
>> 
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Re: [gmx-users] unit cell vector warning

[Mark Abraham]

Hi,

How are you actually generating the coordinate file, and/or the box
vectors? As far as I know, nobody's written down the set of vectors that
should work sensibly, but it's likely that the gmx tools will write boxes
that will definitely work later on...

Mark

On Tue, Mar 8, 2016 at 4:27 PM Irem Altan  wrote:

> Hi,
>
> An update on the unit cell problem: when I make small changes in the
> angle, say change 89.45 to 89.00, the error disappears. I’m still getting
> the same warning. This is with version 5.1.2. Could this be a numerical
> precision issue (c_y is 0.05, see below) or a bug? I tried to run this
> without the protein, by just putting water and a few ions in the box.
>
> Best,
> Irem
>
> > On Mar 3, 2016, at 4:15 PM, Irem Altan  wrote:
> >
> > Hi,
> >
> > I am trying to simulate a protein in its triclinic unit cell. During the
> energy minimization and MD simulation, GROMACS prints the following out at
> every step:
> >
> > WARNING: Found more than 12 triclinic correction vectors, ignoring some.
> >  There is probably something wrong with your box.
> > 0.0e+00,  0.0e+00}
> >  3.89470e-01,   2.50360e+00  3.41610e-01  Box[1]={
> 3.41610e-01,  5.49000e-03,  5.26833e+00}
> > 2.91510e+00 Box (3x3):
> > 2.91510e+00, ,  0.0e+00}
> >Box[1]={ Box[0]={ 0.0e+00 2.50360e+00
> 5.49000e-03,
> >
> > I checked the .gro file to see the unit cell vectors are listed
> correctly.
> >
> > The protein has the following sides and angles:
> >
> > a = 25.04, b = 29.41, c = 52.79, α = 89.45, β = 86.29, γ = 82.39
> >
> > and I calculate the unit vectors to be:
> >
> > a = [ 25.036,   0.   ,   0.   ]
> > b = [  3.8947483 ,  29.15096972,   0.]
> > c = [  3.41611372,   0.05486764,  52.6816]
> >
> > and the .gro file has the line:
> >
> >   2.50360   2.91510   5.26833   0.0   0.0   0.38947   0.0
>  0.34161   0.00549
> >
> > which seems to be correct.
> >
> > I have also verified that the conditions 3.1-3.3 listed on page 12 on
> the manual for 5.1 to be correct.
> >
> > What could be the problem?
> >
> > Best,
> > Irem
> > --
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Re: [gmx-users] unit cell vector warning

[Irem Altan]

Hi,

An update on the unit cell problem: when I make small changes in the angle, say 
change 89.45 to 89.00, the error disappears. I’m still getting the same 
warning. This is with version 5.1.2. Could this be a numerical precision issue 
(c_y is 0.05, see below) or a bug? I tried to run this without the protein, by 
just putting water and a few ions in the box.

Best,
Irem

> On Mar 3, 2016, at 4:15 PM, Irem Altan  wrote:
> 
> Hi,
> 
> I am trying to simulate a protein in its triclinic unit cell. During the 
> energy minimization and MD simulation, GROMACS prints the following out at 
> every step:
> 
> WARNING: Found more than 12 triclinic correction vectors, ignoring some.
>  There is probably something wrong with your box.
> 0.0e+00,  0.0e+00}
>  3.89470e-01,   2.50360e+00  3.41610e-01  Box[1]={ 3.41610e-01,  
> 5.49000e-03,  5.26833e+00}
> 2.91510e+00 Box (3x3):
> 2.91510e+00, ,  0.0e+00}
>Box[1]={ Box[0]={ 0.0e+00 2.50360e+00 
> 5.49000e-03,
> 
> I checked the .gro file to see the unit cell vectors are listed correctly.
> 
> The protein has the following sides and angles:
> 
> a = 25.04, b = 29.41, c = 52.79, α = 89.45, β = 86.29, γ = 82.39
> 
> and I calculate the unit vectors to be:
> 
> a = [ 25.036,   0.   ,   0.   ]
> b = [  3.8947483 ,  29.15096972,   0.]
> c = [  3.41611372,   0.05486764,  52.6816]
> 
> and the .gro file has the line:
> 
>   2.50360   2.91510   5.26833   0.0   0.0   0.38947   0.0   
> 0.34161   0.00549
> 
> which seems to be correct.
> 
> I have also verified that the conditions 3.1-3.3 listed on page 12 on the 
> manual for 5.1 to be correct.
> 
> What could be the problem?
> 
> Best,
> Irem
> -- 
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Re: [gmx-users] md of only water - obtaining different pressure in the x , y and z directions

[André Farias de Moura]

Hi,

pressure is an intrinsically macroscopic property (both in size and time),
which we may compute for such small systems during such short simulations,
but it does not behave ideally under these conditions. Remember that P and
V are thermodynamically coupled variables and that liquid compressibility
is low, so small volume fluctuations arising from pressure coupling to an
external bath will produce wild instantaneous pressure fluctuations.

If pressure matters for you for some reason, systems need to be much larger
and time needs to be much longer. How larger and longer should they be?
Take a look at your pressure fluctuations in a pressure-time plot or its
histogram and notice that it spreads over hundreds or thousands of bars, so
statistically meaningful averages can only be obtained if you manage to
decrease that fluctuations, but fluctuations decrease as 1/SQRT(N), so
increasing your system by a factor of 100 should decrease your pressure
fluctuation by  a factor of 10.

It is hard to afford such large systems, so most people usually do pressure
block averaging over long enough simulations.

I hope it helps

Andre

On Tue, Mar 8, 2016 at 7:19 AM, Diez Fernandez, Amanda <
amanda.die...@imperial.ac.uk> wrote:

> Hi,
>
> I am running a simulation which contains only water (using the spc216.gro
> coordinates and TIP3P model) in an NPT ensemble.
>  I get different values for the average pressure in the x y and z
> directions.
> I am running the simulation for up to 10s in a 4nm side cube unit cell.
> I am using a Nose Hoover thermostat and a Parrinello-Rahman barostat
> applied isotropically, with target pressure 1 bar.
>
> The averages after 1ns are:
>
>
> Energy  Average   Err.Est.   RMSD  Tot-Drift
>
>
> ---
>
> Temperature 299.9990.000986.07906 0.00504098  (K)
>
> Pressure 1.3174  0.066350.061   -0.14372  (bar)
>
> Box-X4.03960.00013 0.00874048 -5.7234e-06  (nm)
>
> Box-Y4.03960.00013 0.00874048 -5.7234e-06  (nm)
>
> Box-Z4.03960.00013 0.00874048 -5.7234e-06  (nm)
>
> Pres-XX 1.11668  2 485.28   0.288761  (bar)
>
> Pres-YY   -0.762405  1427.866-6.2632  (bar)
>
> Pres-ZZ 3.597922.4410.5465.54328  (bar)
>
>
> The averages over the 10 ns are :
>
>
> Energy  Average   Err.Est.   RMSD  Tot-Drift
>
>
> ---
>
> Temperature 300  8e-054.00951 0.000535848  (K)
>
> Pressure1.22566 0.0067275.993 -0.0289005  (bar)
>
> Box-X   4.039295.1e-05 0.00823878 0.000126042  (nm)
>
> Box-Y   4.039295.1e-05 0.00823878 0.000126042  (nm)
>
> Box-Z   4.039295.1e-05 0.00823878 0.000126042  (nm)
>
> Pres-XX 1.29387   0.73385.989  0.0898956  (bar)
>
> Pres-YY 1.35691   0.74378.8413.13618  (bar)
>
> Pres-ZZ 1.02621   0.84377.022   -3.31278  (bar)
>
>
>
> Why is the average pressure in the in each direction different?
>
> And why is the drift of the XX direction so much lower than in the YY and
> ZZ directions?
>
>
> Many thanks!
>
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-- 
_

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090
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[gmx-users] Pressure of an energy minimized system

[Rakesh Sharan]

Dear all,

I have a question regarding computation of pressure of an energy minimized
(using steepest decent) system. I would expect that the pressure of an
energy minimized system should have contribution only from the virial part
of the pressure expression (as there is no temperature). However, when I am
computing pressure using g_energy, the pressure (P_tot) and pressure
computed from virial (P_vir = (-1/3Vol)*(Vir_xx+Vir_yy+Vir_z)/3)) are
significantly different and P_tot is exactly six times P_vir. I am not able
to understand the origin of this discrepancy. I would highly appreciate
comments/suggestions from this forum. I would also very much appreciate any
alternate suggestion for computing pressure of energy minimized structures.

Thanks very much!

Best,
Rakesh


Rakesh S. Singh, Ph.D.
Postdoctoral Research Associate,
Department of Chemical & Biological Engineering,
Princeton University,
Princeton, NJ 08544
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[gmx-users] Extend to Embedding a protein into a lipid box using CGMD

[khourshaeishargh]

Dear all


based on my last question, consider My simulation box file is md.gro and
my protein is CG.gro. now if you can, please write the desired command
for me to embed this two file and have a lipid bilayer membrane embedded
with protein please.


best regards


Ali


==


Ali khourshaei shargh (khourshaeisha...@mech.sharif.ir)


Department of Mechanical Engineering


Sharif University of Technology, Tehran, Iran

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[gmx-users] md of only water - obtaining different pressure in the x , y and z directions

[Diez Fernandez, Amanda]

Hi,

I am running a simulation which contains only water (using the spc216.gro 
coordinates and TIP3P model) in an NPT ensemble.
 I get different values for the average pressure in the x y and z directions.
I am running the simulation for up to 10s in a 4nm side cube unit cell.
I am using a Nose Hoover thermostat and a Parrinello-Rahman barostat applied 
isotropically, with target pressure 1 bar.

The averages after 1ns are:


Energy  Average   Err.Est.   RMSD  Tot-Drift

---

Temperature 299.9990.000986.07906 0.00504098  (K)

Pressure 1.3174  0.066350.061   -0.14372  (bar)

Box-X4.03960.00013 0.00874048 -5.7234e-06  (nm)

Box-Y4.03960.00013 0.00874048 -5.7234e-06  (nm)

Box-Z4.03960.00013 0.00874048 -5.7234e-06  (nm)

Pres-XX 1.11668  2 485.28   0.288761  (bar)

Pres-YY   -0.762405  1427.866-6.2632  (bar)

Pres-ZZ 3.597922.4410.5465.54328  (bar)


The averages over the 10 ns are :


Energy  Average   Err.Est.   RMSD  Tot-Drift

---

Temperature 300  8e-054.00951 0.000535848  (K)

Pressure1.22566 0.0067275.993 -0.0289005  (bar)

Box-X   4.039295.1e-05 0.00823878 0.000126042  (nm)

Box-Y   4.039295.1e-05 0.00823878 0.000126042  (nm)

Box-Z   4.039295.1e-05 0.00823878 0.000126042  (nm)

Pres-XX 1.29387   0.73385.989  0.0898956  (bar)

Pres-YY 1.35691   0.74378.8413.13618  (bar)

Pres-ZZ 1.02621   0.84377.022   -3.31278  (bar)



Why is the average pressure in the in each direction different?

And why is the drift of the XX direction so much lower than in the YY and ZZ 
directions?


Many thanks!

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[gmx-users] Embedding a protein into a lipid box using CGMD

[khourshaeishargh]

Dear all


during a part of martini tutorial it says: If a stable DPPC membrane 
with
the wanted box dimensions is already available,�genbox�will be able to insert 
the peptides in the
bilayer (the peptides have to be pre-centered and positioned to ensure
their presence inside the membrane).


so my question is that, now I have a solvated box ( 128 dppc with 2000 
CG
water ) and a pretein which is precentered as .gro file of solvated box.
how can I embed them using genbox? I tried to do that but I failed.


Any comment would be helpful and I really appreciate it.


best regards


Ali


==


Ali khourshaei shargh (khourshaeisha...@mech.sharif.ir)


Department of Mechanical Engineering


Sharif University of Technology, Tehran, Iran

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Re: [gmx-users] Neutralizing

[mohammad r]

Thank you Parham 
You mean that it is not necessary to do QM/MM simulation?

On Tuesday, March 8, 2016 11:13 AM, Parham Jabbarzadeh (Department of 
Biomedical Science)  wrote:
 

 Dear Sir

Use this command:

gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -neutral

In this case, you don't need ​the number of ions​.
Kind Regards

Parham J. K.
​​==​==​=
​PhD candidate - Lecturer in drug discovery
Faculty of Medicine and Health SciencesUniversity Putra MalaysiaMalaysia
​==​===Publication ::: Featured Publication ::: Website ::: 
FaceBook 
On Tue, Mar 8, 2016 at 3:32 PM, mohammad r  wrote:

Hi everybody, I’ve generated a water-peptide system, now I want to neutralize 
it. Is adding adequate number of ions sufficient for neutralizing process or I 
should do QM/MM simulation for the this process? Thank you, Mohammad.
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