Re: [gmx-users] DPD in Groamcs

[praveen kumar]

Thanks alot Goga N and Raman Preet Singh,

I have to simulate the polymer thin film of the order of sub nanometer
length scale, though I have gone through the DPDMacs, am able to run simple
DPD calculations, but haven't found any reference article that used
DPD-MACS. In addition to that we cannot simply calculate any thermodynamic
properties like Delta_G and Delta_H, using DPDMACS.  As Gromcs Approach of
free-enrgy calculation we cannot simply implement to It. I hope this would
topic of future interest those who want to develop.
However most of the references i have found either uses LAMMPS, DL_Meso and
Mesodyn. But post procssing needs to be coded on their own,I hope we should
go ahead with well tested LAMMPS.

Best
Praveen



On Tue, Oct 24, 2017 at 7:01 PM, <
gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:

> Send gromacs.org_gmx-users mailing list submissions to
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>
>
> Today's Topics:
>
>1. Contact map (sp...@iacs.res.in)
>2. Re: DPD in Groamcs (Raman Preet Singh)
>3. Re: DPD in Groamcs (Raman Preet Singh)
>4. Re: DPD in Groamcs (Goga, N.)
>5. (no subject) (limingru)
>6. Re: Drude polarizable simulations (Justin Lemkul)
>
>
> --
>
> Message: 1
> Date: Tue, 24 Oct 2017 17:28:38 +0530
> From: sp...@iacs.res.in
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Contact map
> Message-ID:
> <20171024172838.horde.dkozh3iro8jn-6chod0w...@mailweb.iacs.res.in>
> Content-Type: text/plain; charset=UTF-8; format=flowed; DelSp=Yes
>
> Hi all
> I want to generate a contact map for all the residues of lysozyme protein.
> I am using gmx mdmat to generate this. Can I generate a text file (which
> can be open in Grace) except the image files(eg: xpm file)? Please let me
> know the particular flag which I can use to get a *.xvg file.
>
> Thanks
> Sunipa Sarkar
>
>
> --
>
> Message: 2
> Date: Tue, 24 Oct 2017 12:27:09 +
> From: Raman Preet Singh 
> To: "gmx-us...@gromacs.org" 
> Subject: Re: [gmx-users] DPD in Groamcs
> Message-ID:
>  INDPRD01.PROD.OUTLOOK.COM>
>
> Content-Type: text/plain; charset="utf-8"
>
> I was looking for DPD in Gromacs too but in vain. You may try DPDmacs,
> POLY DL or LAMPPS.
>
> --
>
> Message: 3
> Date: Tue, 24 Oct 2017 12:32:19 +
> From: Raman Preet Singh 
> To: "gmx-us...@gromacs.org" 
> Subject: Re: [gmx-users] DPD in Groamcs
> Message-ID:
>  INDPRD01.PROD.OUTLOOK.COM>
>
> Content-Type: text/plain; charset="utf-8"
>
> Forgot to mention Materials Studio. An extremely easy-to-use software
> but comes at a hefty license fee.
>
> On Oct 24, 2017 5:57 PM, Raman Preet Singh  mailto:ramanpreetsi...@hotmail.com>> wrote:
>
> I was looking for DPD in Gromacs too but in vain. You may try DPDmacs,
> POLY DL or LAMPPS.
>
> --
>
> Message: 4
> Date: Tue, 24 Oct 2017 15:30:34 +0300
> From: "Goga, N." 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] DPD in Groamcs
> Message-ID:
> 

Re: [gmx-users] No performance increase with single vs multiple nodes

[Matthew W Hanley]

> There's several dozen lines of performance analysis at the end of the log

> file, which you need to inspect and compare if you want to start to
> understand what is going on :-)

Thank you for the feedback.  Fair warning, I'm more of a system administrator 
than a regular gromacs user.  What is it that I should be focused on, and more 
importantly how do I find the bottleneck?  Gromacs does recommend using 
AVX2_256, but I was unable to get Gromacs to build using that.  Here is more of 
the log file:


On 32 MPI ranks


 Computing:  Num   Num  CallWall time Giga-Cycles

 Ranks Threads  Count  (s) total sum%

-

 Domain decomp.321   1666  18.920   1509.802   3.8

 DD comm. load 321   1666   0.017  1.394   0.0

 DD comm. bounds   321   1666   0.206 16.406   0.0

 Vsite constr. 321  50001   4.624369.013   0.9

 Neighbor search   321   1667  19.646   1567.793   4.0

 Comm. coord.  321  48334   8.291661.640   1.7

 Force 321  50001 339.477  27090.350  68.6

 Wait + Comm. F321  50001  12.691   1012.783   2.6

 NB X/F buffer ops.321 146669  13.563   1082.352   2.7

 Vsite spread  321  50001   8.716695.518   1.8

 Write traj.   321  2   0.080  6.366   0.0

 Update321  50001  37.268   2973.983   7.5

 Constraints   321  50001  25.674   2048.789   5.2

 Comm. energies321   5001   0.965 77.013   0.2

 Rest   4.385349.931   0.9

-

 Total494.524  39463.132 100.0

-?



If that's not helpful, I would need more specifics on what part of the log file 
would be.  Failing that, if anyone could recommend some good documentation for 
optimizing performance I would greatly appreciate it, thank you!

-Matt


Matthew Hanley
IT Analyst
College of Engineering and Computer Science
Syracuse University
mwhan...@syr.edu


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Re: [gmx-users] GROMACS on a cluster

[Mark Abraham]

Hi,

This is a general issue with using MPI programs, not one specific to
GROMACS. Please read and follow the instructions for your cluster. The MPI
system needs to know how to find gmx_mpi on each rank on each node, but how
you should do this depends whether there's modules in use, or you have to
set the PATH, or you need to specify a full path to gmx_mpi.

Mark

On Tue, Oct 24, 2017 at 11:46 PM Ali Ahmed  wrote:

> Dear GROMACS users
>
> I need to work on a cluster which has 30 nodes, each has 8 processors
>
> I need to work on 8 nodes (64 processors). For mdrun I used this command:
>
>  mpirun -np 64 gmx_mpi mdrun ..
>
> but the simulation failed to start and here is the error
>
> --
> mpirun was unable to find the specified executable file, and therefore
> did not launch the job.  This error was first reported for process
> rank 0; it may have occurred for other processes as well.
>
> NOTE: A common cause for this error is misspelling a mpirun command
>   line parameter option (remember that mpirun interprets the first
>   unrecognized command line token as the executable).
>
> Node:   login-1
> Executable: gmx_mpi
> --
> 16 total processes failed to start
>
> I could not figur this error.
> Any suggestions will be appreciated
>
> Thanks in advance
> --
> Gromacs Users mailing list
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> * Please search the archive at
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[gmx-users] GROMACS on a cluster

[Ali Ahmed]

Dear GROMACS users

I need to work on a cluster which has 30 nodes, each has 8 processors

I need to work on 8 nodes (64 processors). For mdrun I used this command:

 mpirun -np 64 gmx_mpi mdrun ..

but the simulation failed to start and here is the error

--
mpirun was unable to find the specified executable file, and therefore
did not launch the job.  This error was first reported for process
rank 0; it may have occurred for other processes as well.

NOTE: A common cause for this error is misspelling a mpirun command
  line parameter option (remember that mpirun interprets the first
  unrecognized command line token as the executable).

Node:   login-1
Executable: gmx_mpi
--
16 total processes failed to start

I could not figur this error.
Any suggestions will be appreciated

Thanks in advance
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Re: [gmx-users] Conversion Amber to Gromacs

[Alan]

Please, get it here

svn checkout http://ccpn.svn.sourceforge.net/svnroot/ccpn/branches/
stable/ccpn/python/acpype acpype

Interestingly, but Google code still holds the correct information too:

https://code.google.com/archive/p/acpype/


On 24 October 2017 at 18:34, ABEL Stephane  wrote:

> Hello Elisa,
>
> "J'arrive après la bataille" To be sure that you have correct Amber
> parameters for GROMACS, you could also use the acpype suite*. This suite
> converts  Amber params in gromacs format. The program generates the
> (non)ffbonded.itp and top files in gromacs format from the Amber's LeaP
> tool. It also provides some gromacs and Amber files to perform and a single
> point energy to test if the conversion is correctly done.
>
> I used successfully this code  to convert the Amber lipid14 params for
> POPC lipid in the GROMACS format.
>
> *http://www.ccpn.ac.uk/v2-software/software/ACPYPE-folder
>
> HTH
>
> Stéphane
>
> --
>
> Message: 3
> Date: Tue, 24 Oct 2017 17:17:08 +0200
> From: Elisa Pieri 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Conversion Amber to Gromacs
> Message-ID:
> 

[gmx-users] Conversion Amber to Gromacs

[ABEL Stephane]

Hello Elisa, 

"J'arrive après la bataille" To be sure that you have correct Amber parameters 
for GROMACS, you could also use the acpype suite*. This suite converts  Amber 
params in gromacs format. The program generates the (non)ffbonded.itp and top 
files in gromacs format from the Amber's LeaP tool. It also provides some 
gromacs and Amber files to perform and a single point energy to test if the 
conversion is correctly done. 

I used successfully this code  to convert the Amber lipid14 params for POPC 
lipid in the GROMACS format.

*http://www.ccpn.ac.uk/v2-software/software/ACPYPE-folder

HTH 

Stéphane  

--

Message: 3
Date: Tue, 24 Oct 2017 17:17:08 +0200
From: Elisa Pieri 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Conversion Amber to Gromacs
Message-ID:

Re: [gmx-users] Order Parameter for HII phase

[Mohsen Ramezanpour]

Hi Everyone,

Like to know your thoughts on this.
I appreciate any comment on this in advance.

Cheers,
Mohsen

On Wed, Oct 18, 2017 at 7:26 PM, Mohsen Ramezanpour <
ramezanpour.moh...@gmail.com> wrote:

> Hi Justin, Tom, Antonio,
>
> I read the articles recommended in the previous emails.
> To get the order parameter, for any system and by any technique (e.g.
> g_angle), we need to calculate the C-D vector angle with respect to the
> "local normal vector" at the place of that lipid.
>
> For the bilayer, it is the Z direction which is the normal vector to the
> bilayer surface. Easy.
>
> For the HII, however, this "local normal vector" is challenging.
> The cylinders in HII (which is long enough) are not perfect cylinders and
> are bent (in a shape like a Tilda "~" ). Even when the cylinders are not
> bent (i.e.they are like "__", still a "local normal vector" need to be
> calculated in this calculation.
>
>
> Here are four solutions I am thinking about:
>
> 1) Using the "radial" option in g_order, but I am not sure if this will
> give what I want.
>
> 2) Slicing the HII cylinders in Z direction (i.e. the cylinder axis),
> calculating a center of mass for those lipids in each slice, and then using
> the g_angle and its "-g2 sphnorm". In this way, the COM of that slice will
> be taken as the center of the sphere (an approximation).
>
> 3) Using g_angle but using "-g1 plane": in this case, the coordinates of
> three atoms in that lipid at each frame will be used to make the local
> normal vector.
>
> 4) Maybe a combination of g_sgangle and g_angle/g_order. The
> g_sgangle seems to give the local normal vector for each time frame. This
> can be subsequently used in g_order or g_angle for angle calculation.
>
> One of the main problems in methods 3 and 4 is that: the way the three
> atoms on the lipid are selected, the normal vector will be different,
> especially if the lipid is tilted.
>
> Is there any other way which I could calculate the C-D angle and order
> parameter in HII phase?
>
> Please let me know your opinion. Any help is appreciated in advance.
>
> Cheers,
> Mohsen
>
> On Thu, Feb 23, 2017 at 4:55 PM, Mohsen Ramezanpour <
> ramezanpour.moh...@gmail.com> wrote:
>
>> Thanks Antonio.
>> I will give them a try :-)
>>
>> Cheers
>> Mohsen
>>
>> On Thu, Feb 23, 2017 at 4:15 PM, Antonio Baptista 
>> wrote:
>>
>>> Hi Mohsen,
>>>
>>> I suggest you have a look at the QRB 1977 review by Seelig, that Tom
>>> already mentioned. Like for the planar case, they discuss how spectra of
>>> cylindrical lipid phases are related to the order parameter tensor (but I
>>> never looked into the details for that case). Anyway, I don't know if you
>>> want to compare your simulations with experimental data or are just looking
>>> for a convenient structural parameter. But, whatever the case is, reading
>>> the literature and thinking about the geometry of your system (Duliez's
>>> papers are a good train for that) should give you some hints for a relevant
>>> parameter for your system.
>>>
>>> Once you have selected a parameter, you can compute it from stratch
>>> using other GROMACS tools besides g_order. In particular, you can use
>>> g_gangle to get several sorts of angles and then process them yourself. As
>>> an example, you can use this approach to compute SCD using the equation
>>> already mentioned by Tom, and then check if it agrees with the SCD given by
>>> g_order (I once did that, just to be sure).
>>>
>>> Good luck! :)
>>>
>>> Best,
>>> Antonio
>>>
>>>
>>>
>>> On Thu, 23 Feb 2017, Justin Lemkul wrote:
>>>
>>>

 On 2/23/17 1:25 PM, Mohsen Ramezanpour wrote:

> And I agree with Piggot. The paper by Chau is about on option in
> g_order.
>
>
 Yes, and if memory serves (been a while since I used the program, so
 perhaps I am confusing something), this is what -o provides you so I
 thought it was relevant.  -od gives you the deuterium order parameters.
 The documentation for gmx order is indeed very sparse.

 Anyway, a general question:
> Can we expect to find a published article for each/some module(s) in
> Gromacs?
>

 No.  Many of the tools are just implementations of simple algorithms
 used widely in simulations.  Some do have specific references and those are
 generally printed to the screen output in bold blocks of text.

 With regards to deuterium order parameters, there is a well accepted
 and ubiquitously used equation, which Tom posted.

 I mean how/where can we figure out the underlying algorithm and
> comprehensive description of each analysis tool?
>
>
 That's why GROMACS is open source :)  Efforts are certainly always made
 to provide references when possible.

 -Justin

 Cheers
> Mohsen
>
>
> On Thu, Feb 23, 2017 at 10:06 AM, Mohsen Ramezanpour <
> ramezanpour.moh...@gmail.com> wrote:
>
> Hi Justin, Piggot,
>>

Re: [gmx-users] User-specified potential functions

[Faezeh Pousaneh]

Solved!!

the constant can be added to the table, to g(r) or h(r).


Best regards


On Tue, Oct 24, 2017 at 7:05 PM, Faezeh Pousaneh 
wrote:

> Hi,
>
> I created a table for my own potential which has a 'constant' value. I
> added it to the g(r) or h(r) functions in the table, but it gives incorrect
> results.
> I also can not shift the potential after simulation, since the x>cut-off
> will be also shifted.
>
> Any suggestion?
>
> Best regards
>
>
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Re: [gmx-users] Regarding topology generation by using topologen_1.1.pl script

[Justin Lemkul]

On 10/24/17 1:11 PM, Dilip H N wrote:

Hello,
I want to create a topology file for ammonia molecule and run using oplsaa
FF. since ammonia molecule is not there in oplsaa FF, i created the
molecule in Avogadro software and saved it as .pdb format. Then using the
topolgen_1.1.pl pearl script (script by Justin Lemkul), i generated the
topology. But the net charge on the molecule is 0.18 (for one molecule of
ammonia).


TopolGen makes no attempt to intelligently parametrize any molecule; it 
makes guesses based on analogy to known molecules, and sometimes fails.


In fairness, the script does print out a really clear warning:

"Output topology has been written. An attempt has been made to assign 
charges and atom types based
on existing functional groups, but they may not be correct.  No charge 
calculations or other
parameterization calculations have been done.  Guesses have been made 
for charge groups.  Please
inspect and correct the topology before using it in any simulations.  
The author of the script does
NOT guarantee accuracy or usability of any of the content; TopolGen was 
written as a convenience

for outputting a skeleton topology, and nothing more."


1] So how do i neutralize the net charge (because it is difficult to add a
non-integer charge), and hence carry out the simulation as neutral
system..??


You don't. You can't use a topology with fractional charge.


2] Or is it possible to run by other scripts like mktop, acpype etc..??


Possibly. Try them.

-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] Regarding topology generation by using topologen_1.1.pl script

[Dilip H N]

Hello,
I want to create a topology file for ammonia molecule and run using oplsaa
FF. since ammonia molecule is not there in oplsaa FF, i created the
molecule in Avogadro software and saved it as .pdb format. Then using the
topolgen_1.1.pl pearl script (script by Justin Lemkul), i generated the
topology. But the net charge on the molecule is 0.18 (for one molecule of
ammonia).

1] So how do i neutralize the net charge (because it is difficult to add a
non-integer charge), and hence carry out the simulation as neutral
system..??

2] Or is it possible to run by other scripts like mktop, acpype etc..??

Any suggestions are appreciated.

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



 Sent with Mailtrack

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[gmx-users] User-specified potential functions

[Faezeh Pousaneh]

Hi,

I created a table for my own potential which has a 'constant' value. I
added it to the g(r) or h(r) functions in the table, but it gives incorrect
results.
I also can not shift the potential after simulation, since the x>cut-off
will be also shifted.

Any suggestion?

Best regards
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[gmx-users] Drude polarizable simulation

[limingru]

Dear all,  I want to use GMX to simulate ethanol molecules 
interaction with macromolecular in a polarizable force filed. Whether the 
macromolecular and ethanol PDB files need adding Drude particles, if any, how 
to do? In addition, how to produce an ethanol.itp file for Drude2013 force 
field? Do the Drude2013 force field can be ran in the GMX v4.6.5? Thanks in 
advance.  Best wishes!




School of Nuclear Sci and Tec,
Beijing Normal University

Room.110,Teaching-Research Complex,
NO.10 WenHuiYuan St,Haiding District,
Beijing 100089,China  





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Re: [gmx-users] Contact map

[Justin Lemkul]

On 10/24/17 7:58 AM, sp...@iacs.res.in wrote:

Hi all
I want to generate a contact map for all the residues of lysozyme 
protein.

I am using gmx mdmat to generate this. Can I generate a text file (which
can be open in Grace) except the image files(eg: xpm file)? Please let me
know the particular flag which I can use to get a *.xvg file.



.xvg files are for time series. XmGrace will not plot matrix data.

-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] Drude polarizable simulations

[Justin Lemkul]

On 10/24/17 12:08 AM, limingru wrote:

Hello Justin,   Many thanks for your answer. Another question 
is that whether I need adding some Drude particles in my PDB file of DNA or 
Protein in the simulation process, if any, how to modify the PDB file?  I


pdb2gmx will build everything for you.


have been using the gmx v4.6.5 to do something. I don't know if this version 
can run Drude polarizable simulations.


No, you need to check out the developmental version of the code and use 
the Drude branch.


-Justin


I am going to do protein interaction with organic solution (e.g. ethanol or 
methanol, etc) in Drude2013 force filed using gromacs software. Would you 
please give me some warnings? I think it will give me more clear direction and 
bring me convenience in simulation process. Thanks a lot.
Best wishes!



School of Nuclear Sci and Tec,
Beijing Normal University

Room.110,Teaching-Research Complex,
NO.10 WenHuiYuan St,Haiding District,
Beijing 100089,China






- Original Message -
From: gromacs.org_gmx-users-requ...@maillist.sys.kth.se
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: gromacs.org_gmx-users Digest, Vol 162, Issue 88
Date: 2017-10-24 01:10


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Today's Topics:
1. Re: DPD in Groamcs (Goga, N.)
2. Re: Conversion Amber to Gromacs (Thomas Piggot)
3. Re: Conversion Amber to Gromacs (Mark Abraham)
4. Drude polarizable simulations (limingru)
5. Re: Drude polarizable simulations (Justin Lemkul)
6. Doubt about thermostat in MD (Varvdekar Bhagyesh Rajendra)
--
Message: 1
Date: Mon, 23 Oct 2017 13:54:20 +0300
From: "Goga, N." 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] DPD in Groamcs
Message-ID:

[gmx-users] (no subject)

[limingru]

Dear all,  I want to use GMX to simulate ethanol solution 
interaction with macromolecular in a polarizable force filed. Whether the 
macromolecular and ethanol PDB files need adding Drude particles? and how to 
produce an ethanol.itp file for Drude2013 force field? Do the Drude2013 force 
field can be ran in the GMX v4.6.5? Thanks in advance.   Best 
wishes!



School of Nuclear Sci and Tec,
Beijing Normal University

Room.110,Teaching-Research Complex,
NO.10 WenHuiYuan St,Haiding District,
Beijing 100089,China  





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Re: [gmx-users] DPD in Groamcs

[Goga, N.]

Friend,

I may have some older version of DPD-gromacs. However, I am not sure for
what you need it. Being trial, that version might not be completely free of
errors.

Nicu

On Tue, Oct 24, 2017 at 3:27 PM, Raman Preet Singh <
ramanpreetsi...@hotmail.com> wrote:

> I was looking for DPD in Gromacs too but in vain. You may try DPDmacs,
> POLY DL or LAMPPS.
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Re: [gmx-users] DPD in Groamcs

[Raman Preet Singh]

Forgot to mention Materials Studio. An extremely easy-to-use software but 
comes at a hefty license fee.

On Oct 24, 2017 5:57 PM, Raman Preet Singh 
> wrote:

I was looking for DPD in Gromacs too but in vain. You may try DPDmacs, POLY DL 
or LAMPPS.
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Re: [gmx-users] DPD in Groamcs

[Raman Preet Singh]

I was looking for DPD in Gromacs too but in vain. You may try DPDmacs, POLY DL 
or LAMPPS.
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[gmx-users] Contact map

[spss4]

Hi all
I want to generate a contact map for all the residues of lysozyme protein.
I am using gmx mdmat to generate this. Can I generate a text file (which
can be open in Grace) except the image files(eg: xpm file)? Please let me
know the particular flag which I can use to get a *.xvg file.

Thanks
Sunipa Sarkar
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[gmx-users] tc-groups in mdp file

[Amali Guruge]

Dear gmx users,

My system contains ~ 700 polyethylene glycol (PEG) molecules and ~96000
water molecules (SOL). I would like to know that, do I have to use two
groups to control the temperature or just use one?

Can anyone help me?

Thank you.

Sincerely,
A. G. G
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