[gmx-users] Umbrella Sampling - Changing force constant values between samples

[Dan Gil]

Hello,

I am wondering if it is valid to use different force constant (k) values
between samples for umbrella sampling.

It seems that gmx_wham accepts different k values in a set, but I wanted to
make sure this is OK. Should I be wary of any artifacts with these
simulations?

Best Regards,

Dan Gil
PhD Candidate
Department of Chemical and Biomolecular Engineering
Case Western Reserve University
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Re: [gmx-users] gmx select with coordinates

[Dan Gil]

Hi Shan,

Sorry it's been a while - I don't check this email too often. Did you
figure the problem out?

I use the Graphical Representations menu of VMD, although I am sure there
is a way to do it in the console too.

On Thu, Sep 27, 2018 at 9:35 PM Shan Jayasinghe <
shanjayasinghe2...@gmail.com> wrote:

> Dear Prof. Dan,
>
> Thank you very much for the suggestion. However, when I gave the command;
> gmx select -f run05.xtc -s run05.tpr -b 39 -e 40 -on index.ndx in
> VMD TkConsole, I didn't get any output.
>
> I didn't get the cursor in next line to type x > 45 and x < 90 and y > 90
> and y. What could be the reason for this? Appreciate, if you can reply me.
>
> Thank you.
>
> On Fri, Sep 28, 2018 at 12:00 AM Dan Gil  wrote:
>
> > Hi,
> >
> > I believe you are trying to select atoms/particles that are in an
> > infinitely tall box with the vertices (45, 90), (45, 125), (90, 90) and
> > (90, 125)?
> >
> > Gmx select uses commands that are similar in syntax to a software called
> > VMD. So I like to use VMD to figure out what I need to give to gmx select
> > in order to get the selections I want.
> >
> > For example, I think for what you want, I would do:
> >
> > gmx select -f run05.xtc -s run05.tpr -b 39 -e 40 -on index.ndx
> > [Press Enter]
> > x > 45 and x < 90 and y > 90 and y < 125 [Press Enter]
> >
> > If you want to include it in a script without manual user input:
> >
> > echo x > 45 and x < 90 and y > 90 and y < 125 | gmx select -f run05.xtc
> -s
> > run05.tpr -b 39 -e 40 -on index.ndx
> >
> > VMD is great! It's also free software if you haven't tried using it yet.
> > The only thing you gotta watch out for is that VMD uses Angstroms while
> GMX
> > uses nm.
> >
> > Dan
> >
> > On Thu, Sep 27, 2018 at 7:51 AM Shan Jayasinghe <
> > shanjayasinghe2...@gmail.com> wrote:
> >
> > > Dear Gromacs users,
> > >
> > > I want to make an index files with molecules in a particular area. I
> have
> > > four x,y coordinates [(45, 90), (45, 125), (90, 90) and (90, 125)]
> which
> > > define an area of the system. How can I do it with gmx_select?
> > >
> > > Can anyone help me?
> > >
> > > Thank you.
> > >
> > > On Thu, Sep 27, 2018 at 4:14 PM Shan Jayasinghe <
> > > shanjayasinghe2...@gmail.com> wrote:
> > >
> > > >
> > > > Dear Gromacs users,
> > > >
> > > > I want to make an index files with particular x and y coordinates.
> > There
> > > > is no restriction for z coordinates. How can I do it with
> gmx_select? I
> > > > already tried with the following command. However, it seems I don't
> get
> > > the
> > > > result I want.
> > > >
> > > > gmx select '[45, 90] and [45, 125] and [90, 90] and [90, 125]' -f
> > > > run05.xtc -s run05.tpr -b 39 -e 40 -on index.ndx
> > > >
> > > > Can anyone help me?
> > > >
> > > > Thank you.
> > > >
> > >
> > >
> > > --
> > > Best Regards
> > > Shan Jayasinghe
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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> > >
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> >
>
>
> --
> Best Regards
> Shan Jayasinghe
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Re: [gmx-users] Buckingham parameters to Lennard Jones Parameters

[Dan Gil]

Doesn't gmx sigeps do what you need?

Dan

On Wed, Sep 26, 2018 at 10:44 AM Sam David  wrote:

> What is your system?
> Try to do a fitting and check. I have the same problem and still trying
>
> Good luck
> Sam
>
> On Wed, Sep 26, 2018 at 9:08 AM sanjeet kumar singh ch16d012 <
> ch16d...@smail.iitm.ac.in> wrote:
>
> > Hello Group,
> >Can anyone please tell me as how can i convert Buckingham
> > potential parameters into Lennard Jones parameters?
> >
> > Thanks in advance.
> > --
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Re: [gmx-users] gmx select with coordinates

[Dan Gil]

Hi,

I believe you are trying to select atoms/particles that are in an
infinitely tall box with the vertices (45, 90), (45, 125), (90, 90) and
(90, 125)?

Gmx select uses commands that are similar in syntax to a software called
VMD. So I like to use VMD to figure out what I need to give to gmx select
in order to get the selections I want.

For example, I think for what you want, I would do:

gmx select -f run05.xtc -s run05.tpr -b 39 -e 40 -on index.ndx
[Press Enter]
x > 45 and x < 90 and y > 90 and y < 125 [Press Enter]

If you want to include it in a script without manual user input:

echo x > 45 and x < 90 and y > 90 and y < 125 | gmx select -f run05.xtc -s
run05.tpr -b 39 -e 40 -on index.ndx

VMD is great! It's also free software if you haven't tried using it yet.
The only thing you gotta watch out for is that VMD uses Angstroms while GMX
uses nm.

Dan

On Thu, Sep 27, 2018 at 7:51 AM Shan Jayasinghe <
shanjayasinghe2...@gmail.com> wrote:

> Dear Gromacs users,
>
> I want to make an index files with molecules in a particular area. I have
> four x,y coordinates [(45, 90), (45, 125), (90, 90) and (90, 125)] which
> define an area of the system. How can I do it with gmx_select?
>
> Can anyone help me?
>
> Thank you.
>
> On Thu, Sep 27, 2018 at 4:14 PM Shan Jayasinghe <
> shanjayasinghe2...@gmail.com> wrote:
>
> >
> > Dear Gromacs users,
> >
> > I want to make an index files with particular x and y coordinates. There
> > is no restriction for z coordinates. How can I do it with gmx_select? I
> > already tried with the following command. However, it seems I don't get
> the
> > result I want.
> >
> > gmx select '[45, 90] and [45, 125] and [90, 90] and [90, 125]' -f
> > run05.xtc -s run05.tpr -b 39 -e 40 -on index.ndx
> >
> > Can anyone help me?
> >
> > Thank you.
> >
>
>
> --
> Best Regards
> Shan Jayasinghe
> --
> Gromacs Users mailing list
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> * Please search the archive at
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> posting!
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 172, Issue 89

[Dan Gil]

I think that may indicate that their is something wrong with your input
files, possibly the configuration.

Did you check if the configuration has any bad contacts?

On Wed, Aug 29, 2018 at 7:15 AM sagar bathla  wrote:

> hi Dan,
>
> I got the warnings at the start of the mdrun.
>
> Regards
> Sagar
>
> On Wed, Aug 29, 2018 at 3:30 PM <
> gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:
>
> > Send gromacs.org_gmx-users mailing list submissions to
> > gromacs.org_gmx-users@maillist.sys.kth.se
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> >
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> > or, via email, send a message with subject or body 'help' to
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> >
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> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of gromacs.org_gmx-users digest..."
> >
> >
> > Today's Topics:
> >
> >1. free energy of complex system (abhisek Mondal)
> >2.  restrain ligand in free energy. (T?ng Ho?ng)
> >3. Re: rotation of atoms by more than 90 degrees & LINCS
> >   Warnings (Dan Gil)
> >4. Re: rotation of atoms by more than 90 degrees & LINCS
> >   Warnings (Dan Gil)
> >
> >
> > --
> >
> > Message: 1
> > Date: Wed, 29 Aug 2018 11:23:16 +0530
> > From: abhisek Mondal 
> > To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se
> > Subject: [gmx-users] free energy of complex system
> > Message-ID:
> >  > f3+ulyykpn2zi3xg38dctm...@mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > Hi,
> > I'm just trying to calculate free energy of a complex system using
> > following method:
> >
> >
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/03_workflow.html
> >
> > However, I'm facing some difficulties understanding how can I achieve the
> > goal. The tutorial goes on with a single entity from lambda=0 to 1 with
> > 0.05 spacing for data collection.
> >
> > Now, if I would like to calculate free energy of a complex (say, dimeric
> > protein) then how am I supposed to design the lambda states ?
> > I mean will it be like, one monomer will remain constant and the other
> > monomer goes from lambda=0 to 1 state ? If that be the case then please
> > suggest a way to customize the procedure.
> >
> > Please provide some suggestions.
> > I'm really willing to apply this method in my scenario.
> > Thank you.
> > --
> > Abhisek Mondal
> >
> > *Senior Research Fellow*
> > *Protein Crystallography Group*
> >
> > *Structural Biology and Bioinformatics Division*
> > *CSIR-Indian Institute of Chemical Biology*
> >
> > *Kolkata 700032*
> >
> > *INDIA*
> >
> >
> > --
> >
> > Message: 2
> > Date: Wed, 29 Aug 2018 14:06:31 +0700
> > From: T?ng Ho?ng 
> > To: gmx-us...@gromacs.org
> > Subject: [gmx-users]  restrain ligand in free energy.
> > Message-ID:
> > <
> > cafn5yuf4myt_q-xfn5qkdavn25oouj4srw-bele21grnoyk...@mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > Hello everyone,
> > i am trying to calculate free energy for complex protein-ligand. but in
> > tutorial it just have methane in water. So i find this
> >
> http://www.alchemistry.org/wiki/Absolute_Binding_Free_Energy_-_Gromacs_2016
> > but the problem is i don know how to restrain this ligand.
> > in file complex.top i see that intramolecular - interaction , bond,
> angle ,
> > diheral.  and in .mdp file i see bonds_lambda increase.  I wonder how i
> can
> > restrain like this . where i can find intramolecular -interaction/
> > Thank you for your help.
> >
> > Regrads,
> > Tung,
> >
> > --
> > Ho?ng T?ng / student
> > hoangtung9...@gmail.com / +(84) 0928 478 789
> >
> > University of Medicine and Pharmacy I Ho Chi Minh City
> > 197 Nguyen Thai Hoc, Pham Ngu Lao, District 1, HCM City
> > <https://htmlsig.com/signatures/0001DP594H>
> >
> > [image: Facebook] <https://htmlsig.com/t/01DK2V24>  [image: Skype]
> > <https://htmlsig.com/t/01DH4S28>
> >
> >
&

Re: [gmx-users] rotation of atoms by more than 90 degrees & LINCS Warnings

[Dan Gil]

Hi Sagar,

At which time step do you get LINCS warnings?

Also, please see:
http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings

Dan

On Tue, Aug 28, 2018 at 3:19 AM sagar bathla  wrote:

> Dear all,
>
> My system consists of 2 orthorhombic parallel graphene sheets in a big
> triclinic box filled with water. when i am trying to run equillibration
> then i am getting too many lincs warnings and simulation has been getting
> crashed everytime. i have put retraint on all atoms of graphene but still
> this problem is occuring again.
>
> My .mdp file looks like this
> title   = OPLS Graphene IN WATER NVT equilibration
> define  = -DPOSRES -DFLEXIBLE   ; position restrain the protein
>
> ; Run parameters
> integrator  = md; leap-frog integrator
> nsteps  = 50; 2 * 50 = 1000 ps
>
> dt  = 0.002 ; 2 fs
>
> ; Output control
> nstxout = 1000  ; save coordinates every 1.0 ps
> nstvout = 1000  ; save velocities every 1.0 ps
> nstenergy   = 1000  ; save energies every 1.0 ps
> nstlog  = 1000  ; update log file every 1.0 ps
>
> ; Bond parameters
> continuation= yes   ; first dynamics run
> constraint_algorithm= lincs ; holonomic constraints
> constraints = all-bonds ; all bonds (even heavy atom-H
> bonds) constrained
> lincs_iter  = 1 ; accuracy of LINCS
> lincs_order = 4 ; also related to accuracy
> lincs-warnangle = 90
>
> ; Neighborsearching
> vdw-modifier= Force-switch
> cutoff-scheme   = Verlet
> ns_type = grid  ; search neighboring grid cells
> nstlist = 10; 20 fs, largely irrelevant with
> Verlet
> rcoulomb= 1.2   ; short-range electrostatic cutoff
> (in nm)
> rvdw= 1.2
> rlist   = 1.2   ; short-range van der Waals cutoff
> (in nm)
> rvdw-switch = 1.0
> ; Electrostatics
> coulombtype = PME   ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order   = 4 ; cubic interpolation
> fourierspacing  = 0.16  ; grid spacing for FFT
>
> ; Temperature coupling is on
> tcoupl  = nose-hoover   ; nose-hoover thermostat
> tc-grps = GRA SOL   ; two coupling groups - more accurate
> tau_t   = 0.1 0.1   ; time constant, in ps
> ref_t   = 300 300   ; reference temperature, one for
> each group, in K
>
> ; Pressure coupling is off
> pcoupl  = no; no pressure coupling in NVT
>
> ; Periodic boundary conditions
> pbc = xyz   ; 3-D PBC
> periodic-molecules = yes
>
> ; Dispersion correction
> DispCorr= EnerPres  ; account for cut-off vdW scheme
>
> ; number of steps for center of mass motion removal =
> comm-mode= Linear
> nstcomm  = 1
> comm-grps= GRA SOL
> ; Velocity generation
> gen_vel = no; assign velocities from Maxwell
> distribution
> gen_temp= 300   ; temperature for Maxwell distribution
> gen_seed= -1; generate a random seed
>
> ;non equillibrium md
> freezegrps: GRA
> freezedim: Y Y Y
>  i have tried various things but nothing is working.
> please help to solve this problem
>
> Regards
> Sagar Bathla
> --
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Re: [gmx-users] No default Ryckaert-Bell. types

[Dan Gil]

Hello,

This is telling you that the OPLS-AA force field does not have the dihedral
force-field parameters for your molecule (topol_Other_chain_C.itp) of the
Ryckaert-Bell type. Your exact problem might be:
(1) There is something wrong with the molecule topology.
(2) OPLS-AA really doesn't have the dihedral force-field parameters, and
you need to use another force-field.

If your molecule is a simple hydrocarbon, it is unlikely that OPLS-AA has
missing parameters.

Dan

On Sat, Aug 11, 2018 at 10:52 AM, Baolin Huang  wrote:

> Dear All,
>   I experienced an error as follows: (I used the OPLS-AA force field)
>   ERROR 48600 [file topol_Other_chain_C.itp, line 144934]:
>   No default Ryckaert-Bell. types
>
>
> Anyone can help?
> Kind regards,
>
>
> --
>
> Dr. Baolin Huang
> Lecturer, School of Life Sciences, Guangzhou University
> --
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Re: [gmx-users] ndx file with frames

[Dan Gil]

Hi,

I have used gmx select to create groups of atoms for each time frame - the
indices of the atoms in each group changed with each step. Then I used this
output in other gromacs utilities such as gmx rdf.

I haven't used plumed, but from your question I believe gmx select might be
a good start for you.

Dan

On Mon, Jul 30, 2018 at 9:29 AM, Stefano Guglielmo <
stefano.guglie...@unito.it> wrote:

> Dear all,
>
> I would like to generate an index file containing frame numbers selected
> according to a parameter contained in plumed output; I could select the
> desired frames from the output using any scripting/text manipulating tool,
> but I was wondering which should be the suitable format to be read by,
> let's say, trjconv.
> Does anyone have any suggestions?
>
> Thanks in advance
> Stefano
>
> --
> Stefano GUGLIELMO PhD
> Assistant Professor of Medicinal Chemistry
> Department of Drug Science and Technology
> Via P. Giuria 9
> 10125 Turin, ITALY
> ph. +39 (0)11 6707178
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Re: [gmx-users] zig-zag stacking

[Dan Gil]

Hi,

I haven't tried it, but I wonder if the gmx editconf utility can be used to
translate groups of atoms, where the group is defined with an index file
(make_ndx).

Dan

On Tue, Jul 31, 2018 at 1:21 PM, Nagasree Garapati <
nagasree.garap...@mail.wvu.edu> wrote:

> Hi All
>
>
> I am trying to look at the pore space availability and property
> differences between supercells created by stacking unitcells on top of each
> other and by zigzag stacking.
>
> In Gromacs genconf can be used to create a super cell by stacking unit
> cells on top of each other, is there a way to create zig zag stacking?
>
>
> Thank You
>
> With Regards
> Nagasree Garapati
> Research Assistant Professor
> Dept of Chemical and Biomedical Engineering
> West Virginia University
> PO Box 6102
> Morgantown, WV 26506-6102
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Re: [gmx-users] gmx select and gmx trjconv or gmx density

[Dan Gil]

Thank you Dr. Abraham!

I think I will write a script to do the analysis then.

Best Regards,

Dan

On Mon, Apr 9, 2018 at 12:57 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> Unfortunately not all tools support dynamic selection groups yet, so the
> only useful way to use that index file is by matching it with the correct
> single frame from the trajectory, which you might get from e.g. gmx trjconv
> split
>
> Mark
>
> On Fri, Apr 6, 2018, 21:37 Dan Gil <dan.gil9...@gmail.com> wrote:
>
> > Hi,
> >
> > I am trying to select particles that are z < 20 and z > 10 as a function
> of
> > time.
> >
> > I think I used gmx select correctly and generated an index file with
> group
> > names like "(z_<_.8_f2882_t23056.000)"
> >
> > Now I am unsure how I use this index file for gmx trjconv or gmx density.
> > Does anybody have some advice?
> >
> > Thanks in advance.
> >
> > Best Regards,
> >
> > Dan Gil
> > PhD Student
> > Case Western Reserve University
> > Department of Chemical and Biomolecular Engineering
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> >
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> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
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[gmx-users] gmx select and gmx trjconv or gmx density

[Dan Gil]

Hi,

I am trying to select particles that are z < 20 and z > 10 as a function of
time.

I think I used gmx select correctly and generated an index file with group
names like "(z_<_.8_f2882_t23056.000)"

Now I am unsure how I use this index file for gmx trjconv or gmx density.
Does anybody have some advice?

Thanks in advance.

Best Regards,

Dan Gil
PhD Student
Case Western Reserve University
Department of Chemical and Biomolecular Engineering
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Re: [gmx-users] Parmbsc1 force-field

[Dan Gil]

Hi Dr. Lindahl,

Thank you for clarifying - it helps a lot!

Best Regards,

Dan

On Tue, Mar 6, 2018 at 6:20 AM, Viveca Lindahl <vivecalind...@gmail.com>
wrote:

> Hi Dan,
>
> No, it can be confusing. After reading your email I even dug up an old
> email thread where we (confusedly) discussed this topic.
>
> Most importantly is to not use the Na-parameters that I think are by
> default present in the gromacs implementation, which leads to ion crystals
> (DOI: 10.1021/jp0765392). The two references you cite, Smith & Dang 1994
> and Dang 1995, are quite similar. I emailed with parmbsc1 developers and
> their experience was the same. Together with parmbsc0, other authors have
> used Dang 1995, so that's how our choice came about. To follow the parmbsc1
> authors you should indeed use the paper they cite.
>
>
>
> --
> Viveca
>
>
> On Mon, Mar 5, 2018 at 4:49 PM, Dan Gil <dan.gil9...@gmail.com> wrote:
>
> > Hi Dr. Lindahl,
> >
> > Thanks for putting the force-field together! It is helping my research
> very
> > much. Right now I am just checking over everything to make sure I didn't
> > make any silly mistakes, and that everything is justified.
> >
> > I might be just confusing myself, but the parmbsc1 paper is citing this
> > paper (http://aip.scitation.org/doi/pdf/10.1063/1.466363) for the Na+
> > parameters... whereas the citation for the force-field you put together
> is
> > this one (https://pubs.acs.org/doi/abs/10.1021/ja00131a018). They have
> > different values for the 12-6 sigma and epsilon.
> >
> > Same authors, but the one you chose is a newer work than the other one.
> Is
> > that why you chose the parameters from this paper?
> >
> > Best Regards,
> >
> > Dan
> >
> > On Mon, Mar 5, 2018 at 8:32 AM, Viveca Lindahl <vivecalind...@gmail.com>
> > wrote:
> >
> > > Hi Dan,
> > >
> > > I'm the author together (with Alessandra Villa). I hope it helps others
> > > providing the parameters on the website, but as Mark said, it's up to
> you
> > > to double-check it. If you do find actual errors, I'm interested in
> > hearing
> > > about it :)
> > >
> > > --
> > > Viveca
> > >
> > >
> > > On Fri, Mar 2, 2018 at 5:19 PM, Dan Gil <dan.gil9...@gmail.com> wrote:
> > >
> > > > Hello, update here.
> > > >
> > > > I think there is a possibility that the parmbsc1 force-field updated
> on
> > > the
> > > > gromacs website has some incorrect values.
> > > >
> > > > In the parmbsc1 paper (https://www.nature.com/
> articles/nmeth.3658.pdf)
> > > > they
> > > > say they use Na+ parameters from this paper (
> > > > http://aip.scitation.org/doi/pdf/10.1063/1.466363).
> > > >
> > > > .sigma (Å)epsilon (kcal/mol)
> > > > Na+   2.350  0.1300
> > > >
> > > > Here is what I find in the GROMACS force-field.
> > > >
> > > > .sigma (nm)epsilon (kJ/mol)
> > > > Na+   0.25840.4184
> > > >
> > > > I would like to directly contact the author, but I have no means at
> the
> > > > moment.
> > > >
> > > > Best Regards,
> > > >
> > > > Dan
> > > >
> > > > On Thu, Mar 1, 2018 at 7:00 PM, Dan Gil <dan.gil9...@gmail.com>
> wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > I am using the parmbsc1 force-field (http://www.gromacs.org/@api/d
> > > > > eki/files/260/=amber99bsc1.ff.tgz) in GROMACS. I am looking for
> the
> > > > > original paper where the Na+ and Cl- ion 12-6 Lennard-Jones are
> > coming
> > > > > from, but I am having trouble finding them.
> > > > >
> > > > > The Amber17 manual suggests that this paper (
> > > > https://pubs.acs.org/doi/pdf/
> > > > > 10.1021/ct500918t) is the source for monovalent ions. But, the
> values
> > > > > from the GROMACS parmbsc1 force-field (ffnonbonded.itp) does not
> > match
> > > > the
> > > > > values from the paper, I think.
> > > > >
> > > > > Could you point me to the right direction? Citing the original
> paper
> > is
> > > > > something important to me, but I have apparently hit a dead end.
> > > > >
> > > > > Best Regards,
> > > > >
> &g

Re: [gmx-users] Parmbsc1 force-field

[Dan Gil]

Hi Dr. Lindahl,

Thanks for putting the force-field together! It is helping my research very
much. Right now I am just checking over everything to make sure I didn't
make any silly mistakes, and that everything is justified.

I might be just confusing myself, but the parmbsc1 paper is citing this
paper (http://aip.scitation.org/doi/pdf/10.1063/1.466363) for the Na+
parameters... whereas the citation for the force-field you put together is
this one (https://pubs.acs.org/doi/abs/10.1021/ja00131a018). They have
different values for the 12-6 sigma and epsilon.

Same authors, but the one you chose is a newer work than the other one. Is
that why you chose the parameters from this paper?

Best Regards,

Dan

On Mon, Mar 5, 2018 at 8:32 AM, Viveca Lindahl <vivecalind...@gmail.com>
wrote:

> Hi Dan,
>
> I'm the author together (with Alessandra Villa). I hope it helps others
> providing the parameters on the website, but as Mark said, it's up to you
> to double-check it. If you do find actual errors, I'm interested in hearing
> about it :)
>
> --
> Viveca
>
>
> On Fri, Mar 2, 2018 at 5:19 PM, Dan Gil <dan.gil9...@gmail.com> wrote:
>
> > Hello, update here.
> >
> > I think there is a possibility that the parmbsc1 force-field updated on
> the
> > gromacs website has some incorrect values.
> >
> > In the parmbsc1 paper (https://www.nature.com/articles/nmeth.3658.pdf)
> > they
> > say they use Na+ parameters from this paper (
> > http://aip.scitation.org/doi/pdf/10.1063/1.466363).
> >
> > .sigma (Å)epsilon (kcal/mol)
> > Na+   2.350  0.1300
> >
> > Here is what I find in the GROMACS force-field.
> >
> > .sigma (nm)epsilon (kJ/mol)
> > Na+   0.25840.4184
> >
> > I would like to directly contact the author, but I have no means at the
> > moment.
> >
> > Best Regards,
> >
> > Dan
> >
> > On Thu, Mar 1, 2018 at 7:00 PM, Dan Gil <dan.gil9...@gmail.com> wrote:
> >
> > > Hi,
> > >
> > > I am using the parmbsc1 force-field (http://www.gromacs.org/@api/d
> > > eki/files/260/=amber99bsc1.ff.tgz) in GROMACS. I am looking for the
> > > original paper where the Na+ and Cl- ion 12-6 Lennard-Jones are coming
> > > from, but I am having trouble finding them.
> > >
> > > The Amber17 manual suggests that this paper (
> > https://pubs.acs.org/doi/pdf/
> > > 10.1021/ct500918t) is the source for monovalent ions. But, the values
> > > from the GROMACS parmbsc1 force-field (ffnonbonded.itp) does not match
> > the
> > > values from the paper, I think.
> > >
> > > Could you point me to the right direction? Citing the original paper is
> > > something important to me, but I have apparently hit a dead end.
> > >
> > > Best Regards,
> > >
> > > Dan Gil
> > > PhD Student
> > > Department of Chemical and Biomolecular Engineering
> > > Case Western Reserve University
> > >
> > --
> > 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.
> >
> --
> Gromacs Users mailing list
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> Support/Mailing_Lists/GMX-Users_List before posting!
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Re: [gmx-users] Parmbsc1 force-field

[Dan Gil]

Yes! Thank you so much.

On Fri, Mar 2, 2018 at 11:37 AM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> This is not an official GROMACS offering, so as always, buyer beware. But
> the forcefield.doc file notes the source of the Na+ parameters as
> https://pubs.acs.org/doi/abs/10.1021/ja00131a018. Does that cover the
> question?
>
> Mark
>
> On Fri, Mar 2, 2018 at 5:20 PM Dan Gil <dan.gil9...@gmail.com> wrote:
>
> > Hello, update here.
> >
> > I think there is a possibility that the parmbsc1 force-field updated on
> the
> > gromacs website has some incorrect values.
> >
> > In the parmbsc1 paper (https://www.nature.com/articles/nmeth.3658.pdf)
> > they
> > say they use Na+ parameters from this paper (
> > http://aip.scitation.org/doi/pdf/10.1063/1.466363).
> >
> > .sigma (Å)epsilon (kcal/mol)
> > Na+   2.350  0.1300
> >
> > Here is what I find in the GROMACS force-field.
> >
> > .sigma (nm)epsilon (kJ/mol)
> > Na+   0.25840.4184
> >
> > I would like to directly contact the author, but I have no means at the
> > moment.
> >
> > Best Regards,
> >
> > Dan
> >
> > On Thu, Mar 1, 2018 at 7:00 PM, Dan Gil <dan.gil9...@gmail.com> wrote:
> >
> > > Hi,
> > >
> > > I am using the parmbsc1 force-field (http://www.gromacs.org/@api/d
> > > eki/files/260/=amber99bsc1.ff.tgz) in GROMACS. I am looking for the
> > > original paper where the Na+ and Cl- ion 12-6 Lennard-Jones are coming
> > > from, but I am having trouble finding them.
> > >
> > > The Amber17 manual suggests that this paper (
> > https://pubs.acs.org/doi/pdf/
> > > 10.1021/ct500918t) is the source for monovalent ions. But, the values
> > > from the GROMACS parmbsc1 force-field (ffnonbonded.itp) does not match
> > the
> > > values from the paper, I think.
> > >
> > > Could you point me to the right direction? Citing the original paper is
> > > something important to me, but I have apparently hit a dead end.
> > >
> > > Best Regards,
> > >
> > > Dan Gil
> > > PhD Student
> > > Department of Chemical and Biomolecular Engineering
> > > Case Western Reserve University
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> >
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> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] Parmbsc1 force-field

[Dan Gil]

Hello, update here.

I think there is a possibility that the parmbsc1 force-field updated on the
gromacs website has some incorrect values.

In the parmbsc1 paper (https://www.nature.com/articles/nmeth.3658.pdf) they
say they use Na+ parameters from this paper (
http://aip.scitation.org/doi/pdf/10.1063/1.466363).

.sigma (Å)epsilon (kcal/mol)
Na+   2.350  0.1300

Here is what I find in the GROMACS force-field.

.sigma (nm)epsilon (kJ/mol)
Na+   0.25840.4184

I would like to directly contact the author, but I have no means at the
moment.

Best Regards,

Dan

On Thu, Mar 1, 2018 at 7:00 PM, Dan Gil <dan.gil9...@gmail.com> wrote:

> Hi,
>
> I am using the parmbsc1 force-field (http://www.gromacs.org/@api/d
> eki/files/260/=amber99bsc1.ff.tgz) in GROMACS. I am looking for the
> original paper where the Na+ and Cl- ion 12-6 Lennard-Jones are coming
> from, but I am having trouble finding them.
>
> The Amber17 manual suggests that this paper (https://pubs.acs.org/doi/pdf/
> 10.1021/ct500918t) is the source for monovalent ions. But, the values
> from the GROMACS parmbsc1 force-field (ffnonbonded.itp) does not match the
> values from the paper, I think.
>
> Could you point me to the right direction? Citing the original paper is
> something important to me, but I have apparently hit a dead end.
>
> Best Regards,
>
> Dan Gil
> PhD Student
> Department of Chemical and Biomolecular Engineering
> Case Western Reserve University
>
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[gmx-users] Parmbsc1 force-field

[Dan Gil]

Hi,

I am using the parmbsc1 force-field (http://www.gromacs.org/@api/
deki/files/260/=amber99bsc1.ff.tgz) in GROMACS. I am looking for the
original paper where the Na+ and Cl- ion 12-6 Lennard-Jones are coming
from, but I am having trouble finding them.

The Amber17 manual suggests that this paper (
https://pubs.acs.org/doi/pdf/10.1021/ct500918t) is the source for
monovalent ions. But, the values from the GROMACS parmbsc1 force-field
(ffnonbonded.itp) does not match the values from the paper, I think.

Could you point me to the right direction? Citing the original paper is
something important to me, but I have apparently hit a dead end.

Best Regards,

Dan Gil
PhD Student
Department of Chemical and Biomolecular Engineering
Case Western Reserve University
-- 
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Re: [gmx-users] How can I check external electric field was applied?

[Dan Gil]

Hi,

You guessed correctly - gmx potential only calculates the electric field
and potential of the system. It does not take into account the applied
field.

Are you using walls in your system? If so, are you using the 3DC correction
along with PME for Ewald summation? If you answered yes to both of these
question, you need to use Gromacs version 2016.4 and forwards - there has
been an important bug fix.

As long as your gmx grompp didn't return any warning or errors, I would
expect it to be valid. You can share your MDP file with us and that might
help.

Dan

On Fri, Feb 23, 2018 at 11:45 AM, 이연경  wrote:

>
> Dear Gromacs users,
>
> I’m testing a simple system that has one sodium ion and one chloide ion to
> check external electric field.
> ( Apply strong field along z axis, so I added the line of E_z = 1 10 0 to
> .mdp file. )
>
> After a short simulation, I used ‘gmx potential’ to check the field.
>
> But the result graphs of potential.xvg and field.xvg were different from
> my expectation.
>
> Although I applied 10v/nm along z axis, the electrostatic potential and
> electric field was not around 10V.
>
> Does ‘gmx potential’ calculate electric field and electrostatic potential
> including external force I applied, or just a system’s?
>
> If ‘gmx potential’ does not calculate including external forces, is there
> any method to check external field was correctly applied?
>
> Thanks for your time :)
>
>  YK Lee
>
>
>
> --
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Re: [gmx-users] Using xy periodic boundary and 3dc Ewald summation

[Dan Gil]

The details are in the article you linked and it will do a much better job
of explaining it than I can.

Let me clarify what I have said in the previous message: Gromacs is using
the correction described in the paper.

On Thu, Feb 8, 2018 at 9:43 AM, Ben Tam <btam...@hotmail.co.uk> wrote:

> Hi Dan,
>
> Thank you for your answer. If gromacs' pbc =xy still calculate periodic in
> the z-direction, how does gromacs take care of the z-direction Ewald?
>
> Best regards,
>
> Ben
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Dan Gil <
> dan.gil9...@gmail.com>
> Sent: Tuesday, February 6, 2018 03:49
> To: gmx-us...@gromacs.org
> Cc: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] Using xy periodic boundary and 3dc Ewald summation
>
> I believe that the 3DC method still applies summations over Z. From the
> abstract of the paper: "The proposed method adds a correction term to the
> standard Ewald summation formula."
>
> What the 3DC method does is add a correction term so that unrealistic
> electrostatic interactions between periodic images in the Z direction is
> cancelled.
>
> From what I understand, Gromacs' pbc=xy is still periodic in the
> z-direction, hence the zfac option.
>
> Please use Gromacs 2016.4 version and newer, since the devs fixed a bug
> associated with the 3DC method and PME.
>
> Dan
>
> <http://www.avg.com/email-signature?utm_medium=email;
> utm_source=link_campaign=sig-email_content=webmail>
> Virus-free.
> www.avg.com<http://www.avg.com>
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>
> On Mon, Feb 5, 2018 at 11:57 AM, Ben Tam <btam...@hotmail.co.uk> wrote:
>
> > Dear GROMACS user,
> >
> > Currently I am simulating a Metal Organic Frameworks membrane, in which I
> > have applied vacuum space at z direction (3 times of the current
> non-vacuum
> > system). Following the instruction on GROMACS, I have set the pbc = xy
> and
> > ewald-geometry = 3dc. So here is my first question, how does GROMACS
> > calculated the electrostatic potential for z direction when pbc = xy?
> Does
> > it just use Columb's equations?
> >
> > Then following on with my second question. In this paper :
> >
> > http://aip.scitation.org/doi/abs/10.1063/1.479595
> >
> > As far as I understand, 3dc is done by Ewald summation for all xyz
> > direction then a pseudo term is applied to z direction. Then from my
> > understanding is that pbc = xy turn off Ewald summation at z direction,
> > thus how does GROMACS calculated 3dc with z direction periodic boundary
> > turn off (as the pseudo term have to based on full pbc system)?
> >
> > Thank you very much for your help.
> >
> > Best regards,
> >
> > Ben
> > PhD Student
> >
> > --
> > Gromacs Users mailing list
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Re: [gmx-users] Using xy periodic boundary and 3dc Ewald summation

[Dan Gil]

I believe that the 3DC method still applies summations over Z. From the
abstract of the paper: "The proposed method adds a correction term to the
standard Ewald summation formula."

What the 3DC method does is add a correction term so that unrealistic
electrostatic interactions between periodic images in the Z direction is
cancelled.

>From what I understand, Gromacs' pbc=xy is still periodic in the
z-direction, hence the zfac option.

Please use Gromacs 2016.4 version and newer, since the devs fixed a bug
associated with the 3DC method and PME.

Dan


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On Mon, Feb 5, 2018 at 11:57 AM, Ben Tam  wrote:

> Dear GROMACS user,
>
> Currently I am simulating a Metal Organic Frameworks membrane, in which I
> have applied vacuum space at z direction (3 times of the current non-vacuum
> system). Following the instruction on GROMACS, I have set the pbc = xy and
> ewald-geometry = 3dc. So here is my first question, how does GROMACS
> calculated the electrostatic potential for z direction when pbc = xy? Does
> it just use Columb's equations?
>
> Then following on with my second question. In this paper :
>
> http://aip.scitation.org/doi/abs/10.1063/1.479595
>
> As far as I understand, 3dc is done by Ewald summation for all xyz
> direction then a pseudo term is applied to z direction. Then from my
> understanding is that pbc = xy turn off Ewald summation at z direction,
> thus how does GROMACS calculated 3dc with z direction periodic boundary
> turn off (as the pseudo term have to based on full pbc system)?
>
> Thank you very much for your help.
>
> Best regards,
>
> Ben
> PhD Student
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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Re: [gmx-users] Installing gromacs on the windows 10 linux subsystem

[Dan Gil]

Yes! I have gromacs installed and running on my machine.

Dan

On Sat, Dec 9, 2017 at 4:02 AM A. Alamir  wrote:

> Dear all,
>
> I would like to know if using gromacs on the Windows 10 ubuntu Linux
> subsystem (WLS) is supported. On WLS the gromacs package can be directly
> installed via the Ubuntu apt-get command. I know there are other
> windows-based alternatives to installing/using gromacs (ex. Cygwin), but on
> WLS it is straightforward, providing access to an almost native-like Linux
> experience.
>
> I have noticed that Amber MD can be installed/used on WLS (see
> http://ambermd.org/amber_install.html). Please let me know if you’ve
> successfully tested this for gromacs.
>
> Cheers,
>
> Abbas
>
>
>
>
> --
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>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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>
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Re: [gmx-users] Ewald summation in 2 dimensions with correction

[Dan Gil]

Hi,

I tried using the regular PME method with and without corrections. The
results don't depend on the choice of ewald-geometry  at all!

I used (Gromacs 5.1):
wall-ewald-zfac = 3
ewald-geometry = 3d ; This prompts a warning because I am using 2 walls
- 2d system. I forced this with maxwarn.
E-z= 1 5 0

and I also used
wall-ewald-zfac = 3
ewald-geometry = 3dc   ; No warnings since this is recommended
E-z= 1 5 0

I checked that this input was being processing correctly on topol.tpr. For
the first case, I see ewald-geometry = 0 and the second case ewald-geometry
= 1.

The electric field from ionic liquid has a magnitude of ~7.5 V/nm in the
opposite direction to the applied electric field for both cases. This is
greater than the applied 5. I obtained the electric field using gmx
potential.

I would very much appreciate any recommendations.

Dan

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On Mon, Nov 13, 2017 at 10:22 AM, Dan Gil <dan.gil9...@gmail.com> wrote:

> Hi,
>
> I am using gmx potential to measure the electric field. I've reported the
> values from field.xvg in my previous email. The field at the edges of the
> ionic liquid near the walls will oscillate because of the electric double
> layer but it is the bulk field I am concerned with.
>
> I read the supporting information - I thought that the Ewald summation
> correction for 2 dimensions was supposed to cancel out interactions between
> periodic images in the z direction?
>
> Were you using the regular 3-D Ewald summation in this work? I might try
> carrying out the calculations that way.
>
> Dan
>
> On Mon, Nov 13, 2017 at 2:23 AM, David van der Spoel <sp...@xray.bmc.uu.se
> > wrote:
>
>> On 11/11/17 16:44, Dan Gil wrote:
>>
>>> Hi,
>>>
>>> Just wanted to see if anyone had any thoughts...
>>>
>>> For more information, if I use:
>>> wall-ewald-zfac = 3
>>> E-z= 1 5 0
>>> The electric field from ionic liquid has a magnitude of 7.5 V/nm in the
>>> opposite direction to the applied electric field. This makes no sense to
>>> me
>>> at all.
>>>
>>> With
>>> wall-ewald-zfac = 5
>>> E-z= 1 5 0
>>> The ionic liquid E is -6.2
>>>
>> How do you measure the electric field? Using gmx potential?
>> What numbers does the (optional?) file field.xvg contain?
>>
>> There can of course be a difference between applied field and effective
>> field, in particular with PBC. I sugges you read the supporting information
>> for our paper: Carl Caleman and David van der Spoel: Picosecond Melting of
>> Ice by an Infrared Laser Pulse - A Simulation Study Angew. Chem. Intl. Ed.
>> 47 pp. 1417-1420 (2008)
>>
>>>
>>> With
>>> wall-ewald-zfac = 10
>>> E-z= 1 5 0
>>> The electric field is still slightly above the expected 5 V/nm.
>>>
>>> The dimensions of the box is about 5x5x20 nm3.
>>>
>>> Reading various sources say that the wall factor should not matter as
>>> long
>>> as it is sufficiently large (x3) but in my case it seems to matter a lot.
>>> Should I report this as a bug or do you think I can investigate this
>>> further?
>>>
>>> Best Regards,
>>>
>>> Dan
>>>
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>>>
>>>
>>> On Wed, Nov 8, 2017 at 11:37 AM, Dan Gil <dan.gil9...@gmail.com> wrote:
>>>
>>> Hello,
>>>>
>>>> I am studying room-temperature ionic liquids in slab geometry and I am
>>>> experiencing that I cannot get rid of the interactions between periodic
>>>> images in the z-direction. Is there something wrong with what I am
>>>> doing or
>>>> is this inevitable?
>>>>
>>>> The reason I think this is because when I change "wall-ewald-zfac" the
>>>> results change also.
>>>>
>>>> Gromacs 5.1
>>>> - - - - - - - - - - - - - - - - - - - - - 

Re: [gmx-users] Ewald summation in 2 dimensions with correction

[Dan Gil]

Hi,

I am using gmx potential to measure the electric field. I've reported the
values from field.xvg in my previous email. The field at the edges of the
ionic liquid near the walls will oscillate because of the electric double
layer but it is the bulk field I am concerned with.

I read the supporting information - I thought that the Ewald summation
correction for 2 dimensions was supposed to cancel out interactions between
periodic images in the z direction?

Were you using the regular 3-D Ewald summation in this work? I might try
carrying out the calculations that way.

Dan

On Mon, Nov 13, 2017 at 2:23 AM, David van der Spoel <sp...@xray.bmc.uu.se>
wrote:

> On 11/11/17 16:44, Dan Gil wrote:
>
>> Hi,
>>
>> Just wanted to see if anyone had any thoughts...
>>
>> For more information, if I use:
>> wall-ewald-zfac = 3
>> E-z= 1 5 0
>> The electric field from ionic liquid has a magnitude of 7.5 V/nm in the
>> opposite direction to the applied electric field. This makes no sense to
>> me
>> at all.
>>
>> With
>> wall-ewald-zfac = 5
>> E-z= 1 5 0
>> The ionic liquid E is -6.2
>>
> How do you measure the electric field? Using gmx potential?
> What numbers does the (optional?) file field.xvg contain?
>
> There can of course be a difference between applied field and effective
> field, in particular with PBC. I sugges you read the supporting information
> for our paper: Carl Caleman and David van der Spoel: Picosecond Melting of
> Ice by an Infrared Laser Pulse - A Simulation Study Angew. Chem. Intl. Ed.
> 47 pp. 1417-1420 (2008)
>
>>
>> With
>> wall-ewald-zfac = 10
>> E-z= 1 5 0
>> The electric field is still slightly above the expected 5 V/nm.
>>
>> The dimensions of the box is about 5x5x20 nm3.
>>
>> Reading various sources say that the wall factor should not matter as long
>> as it is sufficiently large (x3) but in my case it seems to matter a lot.
>> Should I report this as a bug or do you think I can investigate this
>> further?
>>
>> Best Regards,
>>
>> Dan
>>
>> <http://www.avg.com/email-signature?utm_medium=email_
>> source=link_campaign=sig-email_content=webmail>
>> Virus-free.
>> www.avg.com
>> <http://www.avg.com/email-signature?utm_medium=email_
>> source=link_campaign=sig-email_content=webmail>
>> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>>
>>
>> On Wed, Nov 8, 2017 at 11:37 AM, Dan Gil <dan.gil9...@gmail.com> wrote:
>>
>> Hello,
>>>
>>> I am studying room-temperature ionic liquids in slab geometry and I am
>>> experiencing that I cannot get rid of the interactions between periodic
>>> images in the z-direction. Is there something wrong with what I am doing
>>> or
>>> is this inevitable?
>>>
>>> The reason I think this is because when I change "wall-ewald-zfac" the
>>> results change also.
>>>
>>> Gromacs 5.1
>>> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>>> ;Integration Method and Parameters
>>> integrator   = md
>>> nsteps   = 400
>>> dt= 0.002
>>> nstenergy= 100
>>> nstcalcenergy= 100
>>> nstlog   = 5000
>>>
>>> ;Output Control
>>> nstxout = 100
>>> nstvout = 1000
>>>
>>> ;Cutoff Schemes
>>> cutoff-scheme= verlet
>>> rlist= 1.0
>>> vdw-type = cut-off
>>> rvdw = 1.0
>>> DispCorr = EnerPres
>>>
>>> ;Coulomb interactions
>>> coulombtype  = pme
>>> rcoulomb = 1.0
>>> fourierspacing   = 0.4
>>>
>>> ;Constraints
>>> constraints  = all-bonds
>>>
>>> ;Temperature coupling
>>> gen-vel  = yes
>>> tcoupl   = v-rescale
>>> tc-grps  = System
>>> tau-t= 0
>>> ref-t= 300
>>>
>>> ;Walls
>>> pbc  = xy
>>> nwall= 2
>>> wall-type= 10-4
>>> ewald-geometry   = 3dc
>>> wall-atomtype= cp cm
>>> wall-density = 5 5
>>> wall-ewald-zfac  = 10
>>>
>>> ;Electric Field
>>> ;Cosine with fre

Re: [gmx-users] Ewald summation in 2 dimensions with correction

[Dan Gil]

Hi,

Just wanted to see if anyone had any thoughts...

For more information, if I use:
wall-ewald-zfac = 3
E-z= 1 5 0
The electric field from ionic liquid has a magnitude of 7.5 V/nm in the
opposite direction to the applied electric field. This makes no sense to me
at all.

With
wall-ewald-zfac = 5
E-z= 1 5 0
The ionic liquid E is -6.2

With
wall-ewald-zfac = 10
E-z= 1 5 0
The electric field is still slightly above the expected 5 V/nm.

The dimensions of the box is about 5x5x20 nm3.

Reading various sources say that the wall factor should not matter as long
as it is sufficiently large (x3) but in my case it seems to matter a lot.
Should I report this as a bug or do you think I can investigate this
further?

Best Regards,

Dan

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On Wed, Nov 8, 2017 at 11:37 AM, Dan Gil <dan.gil9...@gmail.com> wrote:

> Hello,
>
> I am studying room-temperature ionic liquids in slab geometry and I am
> experiencing that I cannot get rid of the interactions between periodic
> images in the z-direction. Is there something wrong with what I am doing or
> is this inevitable?
>
> The reason I think this is because when I change "wall-ewald-zfac" the
> results change also.
>
> Gromacs 5.1
> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> ;Integration Method and Parameters
> integrator   = md
> nsteps   = 400
> dt= 0.002
> nstenergy= 100
> nstcalcenergy= 100
> nstlog   = 5000
>
> ;Output Control
> nstxout = 100
> nstvout = 1000
>
> ;Cutoff Schemes
> cutoff-scheme= verlet
> rlist= 1.0
> vdw-type = cut-off
> rvdw = 1.0
> DispCorr = EnerPres
>
> ;Coulomb interactions
> coulombtype  = pme
> rcoulomb = 1.0
> fourierspacing   = 0.4
>
> ;Constraints
> constraints  = all-bonds
>
> ;Temperature coupling
> gen-vel  = yes
> tcoupl   = v-rescale
> tc-grps  = System
> tau-t= 0
> ref-t= 300
>
> ;Walls
> pbc  = xy
> nwall= 2
> wall-type= 10-4
> ewald-geometry   = 3dc
> wall-atomtype= cp cm
> wall-density = 5 5
> wall-ewald-zfac  = 10
>
> ;Electric Field
> ;Cosine with freq=0, Field V/nm, Phase=n/a
> E-z  = 1 0 0
> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>
> Best Regards,
>
> Dan
>
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Re: [gmx-users] walls and E-z

[Dan Gil]

I simulated ionic liquids with walls and electric field. The field was
processed in my case.

On Thu, Nov 9, 2017 at 4:13 PM, Alex <nedoma...@gmail.com> wrote:

> David, not sure this is a bug. For the moment, can someone simply tell me
> if external field directive is processed when walls are used?
> I fixed the issue by introducing an actual wall as part of the system and I
> think this behavior may be by design. I mean, why apply driving fields when
> the system is impermeable?
>
> Alex
>
> On Thu, Nov 9, 2017 at 12:03 AM, David van der Spoel <sp...@xray.bmc.uu.se
> >
> wrote:
>
> > On 08/11/17 22:29, Alex wrote:
> >
> >> Okay, same thing with 0.5V/nm. I think it's fairly safe to say that
> >> there's
> >> something wrong here...
> >>
> > Haven't followed but if a bug is suspected please file a report at
> > redmine.gromacs.org.
> >
> >
> >> Alex
> >>
> >> On Wed, Nov 8, 2017 at 12:25 PM, Alex <nedoma...@gmail.com> wrote:
> >>
> >> Good question. Dielectric breakdown of water is generally poorly
> >>> understood and the threshold depends on the ionic strength, but
> >>> 0.4-0.5V/nm
> >>> is generally where the fun begins. MD modelers working with solvated
> >>> systems casually ignore this, unless they have the great misfortune of
> >>> getting me as a reviewer. :)
> >>> That aside, I believe your suggestion is sound, at least to see if
> what I
> >>> observe is an outright bug.
> >>>
> >>> Thanks,
> >>>
> >>> Alex
> >>>
> >>> On Wed, Nov 8, 2017 at 10:39 AM, Dan Gil <dan.gil9...@gmail.com>
> wrote:
> >>>
> >>> Yes I saw your plot and it is simply around 0 with walls.
> >>>>
> >>>> What is the field required for dielectric breakdown?
> >>>>
> >>>> On Wed, Nov 8, 2017 at 12:18 PM, Alex <nedoma...@gmail.com> wrote:
> >>>>
> >>>> Hi Dan,
> >>>>>
> >>>>> Yup, periodic, continuous, and electrically neutral. I suggested a
> >>>>>
> >>>> similar
> >>>>
> >>>>> thought in my question, i.e. with walls any transport would
> definitely
> >>>>>
> >>>> be
> >>>>
> >>>>> transient and self-limited. However, nothing is transported even in
> the
> >>>>> perturbative sense, as you can see from the flux. The behavior is
> that
> >>>>>
> >>>> of a
> >>>>
> >>>>> system without any driving field.
> >>>>>
> >>>>> The electric field is already quite high (0.1 V/nm) and of course I
> >>>>>
> >>>> could
> >>>>
> >>>>> go completely nuts and exceed the experimental dielectric breakdown
> >>>>> threshold values for water, but the question remains, no?
> >>>>>
> >>>>> Thanks,
> >>>>>
> >>>>> Alex
> >>>>>
> >>>>>
> >>>>>
> >>>>> On 11/8/2017 9:58 AM, Dan Gil wrote:
> >>>>>
> >>>>> Hi Alex,
> >>>>>>
> >>>>>> Is your system without walls periodic and continuous in all
> >>>>>>
> >>>>> directions? I
> >>>>
> >>>>> can see a scenario where this sort of system will maintain charge
> >>>>>> neutrality in the different reservoirs separated by the semi-porous
> >>>>>> membrane. While cations will be transported, the charge in each
> >>>>>>
> >>>>> reservoir
> >>>>
> >>>>> will be maintained constant because as one cation leaves, its
> periodic
> >>>>>> image enters the same reservoir. It is a steady-state process.
> >>>>>>
> >>>>>> In the system with walls, charge neutrality will be broken if
> cations
> >>>>>>
> >>>>> are
> >>>>
> >>>>> transported across the membrane because it won't have a periodic
> image
> >>>>>> that
> >>>>>> enters the same reservoir as it leaves. I think that the cation
> >>>>>>
> >>>>> transport
> >>>>
> >>>>> would be more lik

Re: [gmx-users] walls and E-z

[Dan Gil]

Yes I saw your plot and it is simply around 0 with walls.

What is the field required for dielectric breakdown?

On Wed, Nov 8, 2017 at 12:18 PM, Alex <nedoma...@gmail.com> wrote:

> Hi Dan,
>
> Yup, periodic, continuous, and electrically neutral. I suggested a similar
> thought in my question, i.e. with walls any transport would definitely be
> transient and self-limited. However, nothing is transported even in the
> perturbative sense, as you can see from the flux. The behavior is that of a
> system without any driving field.
>
> The electric field is already quite high (0.1 V/nm) and of course I could
> go completely nuts and exceed the experimental dielectric breakdown
> threshold values for water, but the question remains, no?
>
> Thanks,
>
> Alex
>
>
>
> On 11/8/2017 9:58 AM, Dan Gil wrote:
>
>> Hi Alex,
>>
>> Is your system without walls periodic and continuous in all directions? I
>> can see a scenario where this sort of system will maintain charge
>> neutrality in the different reservoirs separated by the semi-porous
>> membrane. While cations will be transported, the charge in each reservoir
>> will be maintained constant because as one cation leaves, its periodic
>> image enters the same reservoir. It is a steady-state process.
>>
>> In the system with walls, charge neutrality will be broken if cations are
>> transported across the membrane because it won't have a periodic image
>> that
>> enters the same reservoir as it leaves. I think that the cation transport
>> would be more like capacitance since a constant electric field will only
>> be
>> able to hold a finite number of cations across the membrane. This is an
>> equilibrium process.
>>
>> Maybe try higher electric field?
>>
>> Dan
>>
>> On Fri, Nov 3, 2017 at 2:43 AM, Alex <nedoma...@gmail.com> wrote:
>>
>> Hi all,
>>>
>>> It appears that the external field is refusing to move the ions when
>>> walls
>>> are present. I am comparing two setups of a system that has an aqueous
>>> bath
>>> (1M KCl) split by a semi-porous (infinitely selective for cations)
>>> membrane
>>> in XY. The only difference between them is that one is periodic in XYZ
>>> and
>>> the other has two walls. The difference isn't minor -- consider K+ fluxes
>>> with and without walls: https://www.dropbox.com/s/jve0
>>> hqqpfkn4ui6/flux.jpg?dl=0
>>>
>>> Initially, ionic populations in each case are homogeneous. I realize that
>>> with walls the process will stop when all cations end up at the top of
>>> the
>>> box (and that's the goal). However, there is no flux right from the
>>> start.
>>> Relevant portion of the mdp with walls below (not sure if this is
>>> important, but 'ewald-geometry' directive isn't in the mdp without
>>> walls):
>>>
>>> pbc = xy
>>> nwall   = 2
>>> wall-type   = 12-6
>>> wall-r-linpot   = 0.25
>>> wall_atomtype   = opls_996 opls_996
>>> wall-ewald-zfac = 3
>>> periodic_molecules  = yes
>>> ns_type =  grid
>>> rlist   =  1.0
>>> coulombtype =  pme
>>> ewald-geometry  =  3dc
>>> fourierspacing  =  0.135
>>> rcoulomb=  1.0
>>> rvdw=  1.0
>>> vdwtype =  cut-off
>>> cutoff-scheme   = Verlet
>>>
>>> Any ideas?
>>>
>>> Thanks,
>>>
>>> Alex
>>>
>>> --
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>>>
>>> * Please search the archive at http://www.gromacs.org/Support
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>>>
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[gmx-users] Ewald summation in 2 dimensions with correction

[Dan Gil]

Hello,

I am studying room-temperature ionic liquids in slab geometry and I am
experiencing that I cannot get rid of the interactions between periodic
images in the z-direction. Is there something wrong with what I am doing or
is this inevitable?

The reason I think this is because when I change "wall-ewald-zfac" the
results change also.

Gromacs 5.1
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;Integration Method and Parameters
integrator   = md
nsteps   = 400
dt= 0.002
nstenergy= 100
nstcalcenergy= 100
nstlog   = 5000

;Output Control
nstxout = 100
nstvout = 1000

;Cutoff Schemes
cutoff-scheme= verlet
rlist= 1.0
vdw-type = cut-off
rvdw = 1.0
DispCorr = EnerPres

;Coulomb interactions
coulombtype  = pme
rcoulomb = 1.0
fourierspacing   = 0.4

;Constraints
constraints  = all-bonds

;Temperature coupling
gen-vel  = yes
tcoupl   = v-rescale
tc-grps  = System
tau-t= 0
ref-t= 300

;Walls
pbc  = xy
nwall= 2
wall-type= 10-4
ewald-geometry   = 3dc
wall-atomtype= cp cm
wall-density = 5 5
wall-ewald-zfac  = 10

;Electric Field
;Cosine with freq=0, Field V/nm, Phase=n/a
E-z  = 1 0 0
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Best Regards,

Dan
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Re: [gmx-users] Software for PDB input for GROMACS

[Dan Gil]

Thank you, it works great! I just had to rename the nucleic acids with the
prefix "D" (e.g. A to DA, G to DG ...).

On Fri, Nov 3, 2017 at 7:44 PM, Thomas Piggot <t.pig...@soton.ac.uk> wrote:

> The nucleic acid builder should do what you want:
>
> http://structure.usc.edu/make-na/
>
> Cheers
>
> Tom
>
>
> On 03/11/17 19:54, Dan Gil wrote:
>
>> Hi,
>>
>> I would like to use the parmbsc1 force field to simulate DNA. I installed
>> the force-field and am now actually running a simulation with a Drew
>> Dickerson Dodecamer structure I downloaded from the RCSB database.
>>
>> Now I would like to generate my own structures and simulate them. I tried
>> using Avogadro, but the software is not following the same conventions as
>> parmbsc1 and therefore failing at pdb2gmx.
>>
>> Do you have recommendations on how to generate a PDB structure for nucleic
>> acids? I suppose I could do this by hand, but I would very much like to
>> avoid this path if I can.
>>
>> Best Regards,
>>
>> Dan
>>
>
> --
> Dr Thomas Piggot
> Visiting Fellow
> University of Southampton, UK.
>
> --
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[gmx-users] Software for PDB input for GROMACS

[Dan Gil]

Hi,

I would like to use the parmbsc1 force field to simulate DNA. I installed
the force-field and am now actually running a simulation with a Drew
Dickerson Dodecamer structure I downloaded from the RCSB database.

Now I would like to generate my own structures and simulate them. I tried
using Avogadro, but the software is not following the same conventions as
parmbsc1 and therefore failing at pdb2gmx.

Do you have recommendations on how to generate a PDB structure for nucleic
acids? I suppose I could do this by hand, but I would very much like to
avoid this path if I can.

Best Regards,

Dan
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Re: [gmx-users] Surface tension for water

[Dan Gil]

Iman,

You get the error message in the terminal if you are running it on your own
machine. If you are running on a supercomputer, the error messages will be
directed to a file. How do you know the simulation is crashing without the
software telling you? Please find the message (check all outputs), wherever
it might be, and share it with us. Otherwise I don't know what the problem
could be.

Dan

On Tue, Aug 29, 2017 at 4:14 PM, Iman Ahmadabadi  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 = 0.5
> >> ref_p  = 1.0  1.0
> >> compressibility = 4.46e-5  0
> >>
> >> Could I have any recommendation about my problem with surface-tension
> >> pcoupltyp? Am I right with semiisotropic options?
> >>
> >>
> >> Respectfully,
> >> Iman Ahmadabadi
> >>
> >
> >
> >
> > --
> > Iman Ahmadabadi
> >
> > Sharif University of Technology, Tehran, Iran
> >
> > Department of Physics and Chemistry
> >
> > Phone: (+98) 9156125273
> >
> > Email: imanahmadabad...@gmail.com , ahmadabad...@ch.sharif.edu
> >
>
>
>
> --
> Iman Ahmadabadi
>
> Sharif University of Technology, Tehran, Iran
>
> Department of Physics and Chemistry
>
> Phone: (+98) 9156125273
>
> Email: imanahmadabad...@gmail.com , ahmadabad...@ch.sharif.edu
> --
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Re: [gmx-users] Surface Tension Calculation

[Dan Gil]

Hi Lei,

1. In the Gromacs manual you can find the formula that the software uses to
calculate surface tension. It is just based on a few components of the
pressure tensor, so I imagine you can just use gmx energy (or g_energy
depending on the version of Gromacs you are using).
2. Freezing doesn't sound like a good idea if you are trying to calculate
the surface tension from equilibrium states. Here is a quote from the
online gromacs manual:

> Non-equilibrium MDnon-equilibrium MD*freezegrps:*Groups that are to be
> frozen (i.e. their X, Y, and/or Z position will not be updated; e.g. Lipid
> SOL). *freezedim* specifies for which dimension the freezing applies. To
> avoid spurious contibrutions to the virial and pressure due to large forces
> between completely frozen atoms you need to use energy group exclusions
> , this also saves
> computing time. Note that coordinates of frozen atoms are not scaled by
> pressure-coupling algorithms.


In essence, you have to be very knowledgeable about what you are doing.
First of all, this section is under non-equilibrium MD so it already seems
like a bad idea. Freezing the solid phase seems like a bad idea because it
will affect how the solid lattice responds to pressure changes. If you
really know what you are doing, perhaps you can use energy group exclusions
as the manual suggests. But I think that if you have a good force-field for
the solid phase it should be stable even without freezing. Have you tried
simulating without freeze? After careful equilibration and then a
sufficiently long production run, what result do you get for the
interfacial tension from gmx energy?
3. I don't yet see why anything like position restraints or freeze is
necessary.

Dan

On Mon, Aug 28, 2017 at 4:39 PM, Lei  wrote:

> Hi, gmx users,
> I have some questions regarding the surface tension calculation in gromacs.
> I was running simulations about interface between phase 1 (solid) and phase
> 2 (liquid). In my production run, the phase 1 molecules are frozen and I
> need to calculate the interfacial tension between phase 1 and phase 2.  I
> followed the typical procedure to calculate the surface tension: phase 1 is
> sandwiched by phase 2 and the interface is planar.
> So my questions are:
> 1. Is there a way to calculate the interfacial tension between phase 1 and
> phase 2?
> 2. Does the freeze command affect the calculation of tension? Do I need to
> freeze phase 1 atoms in the simulation to calculate the interfacial tension
> between phase 1 and phase 2?
> 3. What if I applied the position restraints on the phase 1 atoms instead
> of freezing them?
> Thank you all and enjoy simulating.
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Re: [gmx-users] Surface tension for water

[Dan Gil]

What is the error message?
What version of Gromacs are you using?
Can you post the entire .mdp file?


On Tue, Aug 29, 2017 at 9:34 AM, Iman Ahmadabadi  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 = 0.5
> ref_p  = 1.0  1.0
> compressibility = 4.46e-5  0
>
> Could I have any recommendation about my problem with surface-tension
> pcoupltyp? Am I right with semiisotropic options?
>
>
> Respectfully,
> Iman Ahmadabadi
> --
> Gromacs Users mailing list
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> * Please search the archive at http://www.gromacs.org/
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Re: [gmx-users] RDF

[Dan Gil]

>
> I have come across people describing RDF analysis between water and water
> and I always wonder what does it means. RDF can be done between protein and
> water to know the distribution of water around protein with default center
> of mass(My little knowledge) and what co-ordination number contribute to
> RDF has always been a puzzle for me.
>

what do you mean by  two component system?
>

These questions be answered together at once. Imagine that a protein is
dissolved in water and urea solution. This system has 3 components (water,
urea, and protein). So there can be 6 RDFs: g_ww, g_uu, g_pp, g_wu, g_wp,
g_up. "w" means water, "u" means urea, "p" means protein (If there is only
one protein molecule, than g_pp should be zero).

Like you said, we can study the distribution of water around proteins. You
can also use RDFs far more things than just protein systems. It can be used
for salts in water, mixtures of organic solvents, etc.

Coordination number is related to the radial distribution function. This
Wikipedia page (https://en.wikipedia.org/wiki/Coordination_number) has a
one method of calculating the coordination number from RDFs. For example,
in a protein + water + urea system, you may be able to find the number of
water molecules and the number of urea molecules around the protein in each
solvation shell. These numbers are averages over time, not the actual
number at a moment in time. I think this method of calculating CN might be
a quick and easy way to see if its worth using better methods (e.g.
deconvoluting each solvation shell before integration). If your protein is
very large, I can imagine this being a more difficult problem, but I don't
know for sure.

On Fri, Aug 18, 2017 at 7:47 AM, RAHUL SURESH <drrahulsur...@gmail.com>
wrote:

> Hi Dan
>
> Thank you so much for you descriptive answers. I have few clarifications
> that I have posted here. I will go through the papers here.
>
> On Fri, Aug 18, 2017 at 5:01 PM, Dan Gil <dan.gil9...@gmail.com> wrote:
>
> > Hi Rahul,
> >
> > I can't find the exact papers right now, but I remember seeing some
> > inconsistency in how people name these functions especially the radial
> > distribution function and pair correlation functions.
> >
> > If we go far back into literature, we can see JG Kirkwood using pair
> > correlation functions as functions of both the distance and the relative
> > orientation between the pairs [The Journal of Chemical Physics 19, 774
> > (1951); doi: 10.1063/1.1748352]. I don't know if he is the "inventor" of
> > the RDF, but he was one of the earliest to use it extensively in
> theories.
> > When you average the pair correlation functions over the relative
> > orientations, you get the radial distribution function which is a
> function
> > of distance only.
>
>
> That was very informative. But as now it can be calculated as a whole
> easily using various tools.
>
>
> > I think I've seen newer papers use RDF/PCF/PDF somewhat
> > interchangeably although I can't find these right now... Most people mean
> > the RDF but you can always look at the data to know what they mean.
> >
>
> I have come across people describing RDF analysis between water and water
> and I always wonder what does it means. RDF can be done between protein and
> water to know the distribution of water around protein with default center
> of mass(My little knowledge) and what co-ordination number contribute to
> RDF has always been a puzzle for me.
>
> >
> > I never used surface distribution functions, hopefully someone else can
> > bring you up to date on that one (How is the surface defined?).
> >
>
> I will be happy if some one can explain SDF and any particular tool to
> analyze it.
>
> >
> > But there is also the spatial distribution functions, which now a
> function
> > in 3D spherical coordinates. It gives the average density of particles at
> > given (r, theta, phi). In this paper they normalize it by the bulk
> density,
> > I am not sure if everyone does the same. (doi: 10.1063/1.465158)
> >
>
> Thank you. I guess it can be calculated using gmx spatial
>
> >
> > I think "radial pair distribution function" is synonymous with the RDF
> like
> > you said.
> >
>
> Yeah VMD use it as Radial pair distribution function.
>
> >
> > Partial radial distribution function is for multicomponent systems. In a
> > single component system, there is only one RDF and that is the total RDF.
> > In a two component system,
>
>
> what do you mean by  two component system?
>
>
> > there are 3 (AA, AB, BB) partial radial
> > distribution functions.

Re: [gmx-users] RDF

[Dan Gil]

Hi Rahul,

I can't find the exact papers right now, but I remember seeing some
inconsistency in how people name these functions especially the radial
distribution function and pair correlation functions.

If we go far back into literature, we can see JG Kirkwood using pair
correlation functions as functions of both the distance and the relative
orientation between the pairs [The Journal of Chemical Physics 19, 774
(1951); doi: 10.1063/1.1748352]. I don't know if he is the "inventor" of
the RDF, but he was one of the earliest to use it extensively in theories.
When you average the pair correlation functions over the relative
orientations, you get the radial distribution function which is a function
of distance only. I think I've seen newer papers use RDF/PCF/PDF somewhat
interchangeably although I can't find these right now... Most people mean
the RDF but you can always look at the data to know what they mean.

I never used surface distribution functions, hopefully someone else can
bring you up to date on that one (How is the surface defined?).

But there is also the spatial distribution functions, which now a function
in 3D spherical coordinates. It gives the average density of particles at
given (r, theta, phi). In this paper they normalize it by the bulk density,
I am not sure if everyone does the same. (doi: 10.1063/1.465158)

I think "radial pair distribution function" is synonymous with the RDF like
you said.

Partial radial distribution function is for multicomponent systems. In a
single component system, there is only one RDF and that is the total RDF.
In a two component system, there are 3 (AA, AB, BB) partial radial
distribution functions.

Hope that helps!

Dan

On Fri, Aug 18, 2017 at 2:19 AM, RAHUL SURESH 
wrote:

> Radial Distribution Function, Surface Distribution Function(SDF), Radial
> Pair Distribution Function and Partial Radial Distribution Function.
>
> What makes the difference in all the four?
>
> Have gone through lot pages and literature. Somehow one or the other piece
> of explanation confuses me.
>
> Can I have a short explanation of all?
>
> RDF and R-pair DF one and the same?
>
> How do I calculate SDF and Partial-RDF if it is different from others?
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
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Re: [gmx-users] non zero free energy values in mass transformation

[Dan Gil]

Hi Deepak,

I'd like to share a reference with you. http://www.tandfonline.
com/doi/abs/10.1080/00268970600893060

If you could take a look at results (14) versus (15), and results (28)
versus (29)... You see that when only the potential energy is considered,
the mass doesn't contribute to the free energy. However this is based on
the assumption that the mass between the two states are equal. The mass
between Li+ and Cl- are rather different.

Please correct me if I am wrong, but I believe TPI compares between two
states, a solute in the ideal gas phase and the same solute in water (in
your case). E.g. [Li]_idealGas -> [Li]_aqueous. The mass is not changing
here.

On the other hand TI considers two states with different species. In your
case, it is [Li]_aqueous -> [Cl]_aqueous. The two states being compared is
different than TPI. In TI, the masses of the solutes are different. I think
the idea is that when you do a TI in water and do a TI in gas, the mass
contributions to the free energy cancel out. Can you also try doing
[Li]_idealGas -> [Cl]_idealGas? Hopefully, the free energy change due to
the mass perturbation for the two transformations cancel out to zero.

A disclaimer though, I am also working on a very similar problem without
success (yet). I am very curious to see if this works out for you.

Dan


On Sun, Aug 13, 2017 at 11:08 PM, deepak bapat <duba...@gmail.com> wrote:

> Hi
>
> To study the efect of particle mass on excess chemical potential i did test
> particle insertion  (tpi) in SPC/E water. I created a lennard jones
> particle with very small LJ parameters so that the probability of gettining
> it inside the cavity increases.
>
> In one case I kept mass of tpi particle equal to that of Lithium. In second
> simulation the mass was equal to that of Chlorine atome.
>
> LJ parameters for tpi particles in both cases were 2.0e-02  7.64793e-02.
>
> In both cases the excess chemical potential was in the range of 0.0798
> kJ/mol.
>
> tpi only considers energy as a function of coordinates only so i assume
> that it would depend only on LJ parameters as long as we are delaing with
> neutral systems.
>
> So looking at this I again come back to the mass perturbation which started
> all this.
>
> Since I was doing NPT calculations at 300 K I expected that average total
> kinetic energy of the system should not be different. The themostat would
> just adjust velocity distribution so that it brings the temperature of the
> system to the set temperature. Any increase or decrease in mass should be
> accounted for by the thermostat.
>
> As I said, in free energy calculations I got non zero value. (~ +6.2
> kJ/mol). So I am still worried about this non zero behavior.
>
> Thanks and regards
>
> Deepak
>
>
>
>
>
>
>
>
>
>
>
> On Sat, Aug 12, 2017 at 10:11 AM, deepak bapat <duba...@gmail.com> wrote:
>
> > Thank you Andre and Dan.
> >
> > I'll read more about.
> >
> > Deepak
> >
> > On Fri, Aug 11, 2017 at 7:35 PM, Dan Gil <dan.gil9...@gmail.com> wrote:
> >
> >> Hi Deepak,
> >>
> >> I am battling the same problem too. I am doing free energy calculation
> for
> >> heptane -> perfluoro-heptane in water. Also SPC/E water, Gromacs 5.1.
> >>
> >> Like Andre said, there is expected to be a free energy change when you
> >> change the mass of a particle. But if you do the same transformation
> from
> >> Li+ to Cl- in the gas phase, hopefully the free energy change will be
> >> opposite and (approximately) equal. Have you tried doing this second
> >> calculation [Li+ -> Cl-] in the gas phase? I think this website:
> >> http://www.alchemistry.org/wiki/Thermodynamic_Cycle explains why this
> >> second step might be needed better.
> >>
> >> Dan
> >>
> >> On Fri, Aug 11, 2017 at 9:37 AM, André Farias de Moura <mo...@ufscar.br
> >
> >> wrote:
> >>
> >> > Deepak,
> >> >
> >> > I never did a mass perturbation myself, but I would expect some free
> >> energy
> >> > change, since the translational partition function depends on the mass
> >> of
> >> > the molecules.
> >> >
> >> > Also, having the same kinetic energy is not meaningful at all, the
> >> correct
> >> > quantity you should always use in statistical mechanics reasoning is
> the
> >> > momentum of the particle, p=mv, which clearly changes during your
> >> > alchemical transformation. Put in another way: the phase space of the
> >> > system is a 6N dimensional space of positions and momenta, and you
> have
> >

Re: [gmx-users] Non bonded interaction mapping

[Dan Gil]

Hi Sameer,

There is a quick and easy way to visualize hydrogen bonds. Convert your
traj.trr file to .gro and open it in VMD software. You can then manipulate
VMD options to show hydrogen bonds.

Dan

On Sun, Aug 6, 2017 at 10:57 AM, Sameer Edirisinghe 
wrote:

> Dear all,
>
> I have done 200ns simulation for my polymeric system and I want to map all
> existing nonbonded interactions (i.e. H bonds) in my system over the time.
> Can anyone suggest me a method for this?
>
>
> Regards
> Bhagya karunarathna
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Re: [gmx-users] (no subject)

[Dan Gil]

Hi Iman,

If I understand, you are planning on calculating the surface tension of
water?

To me, it seems odd that you would try to apply a surface-tension couple to
your system, and then calculate the surface tension.

Dan

On Thu, Aug 10, 2017 at 5:42 AM, Iman Ahmadabadi  wrote:

> Dear Users,
>
> I'm determining my .mdp file for NPT equilibration, but I don't know how to
> determine the ref_p section of mdp.
>
> pcoupl = berendsen
> pcoupltype = surface-tension
> tau_p = 0.5 0.5
> ref_p = 1.0 1.0
> compressibility = 4.46e-5 4.46e-5
>
> I'm gonna to calculate surface tension for a layer of water.
>
> Sincerely,
> Iman
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Re: [gmx-users] non zero free energy values in mass transformation

[Dan Gil]

Hi Deepak,

I am battling the same problem too. I am doing free energy calculation for
heptane -> perfluoro-heptane in water. Also SPC/E water, Gromacs 5.1.

Like Andre said, there is expected to be a free energy change when you
change the mass of a particle. But if you do the same transformation from
Li+ to Cl- in the gas phase, hopefully the free energy change will be
opposite and (approximately) equal. Have you tried doing this second
calculation [Li+ -> Cl-] in the gas phase? I think this website:
http://www.alchemistry.org/wiki/Thermodynamic_Cycle explains why this
second step might be needed better.

Dan

On Fri, Aug 11, 2017 at 9:37 AM, André Farias de Moura 
wrote:

> Deepak,
>
> I never did a mass perturbation myself, but I would expect some free energy
> change, since the translational partition function depends on the mass of
> the molecules.
>
> Also, having the same kinetic energy is not meaningful at all, the correct
> quantity you should always use in statistical mechanics reasoning is the
> momentum of the particle, p=mv, which clearly changes during your
> alchemical transformation. Put in another way: the phase space of the
> system is a 6N dimensional space of positions and momenta, and you have
> just perturbed the momenta part.
>
> And by the way: that is a typical case in which Monte Carlo methods would
> fail to reproduce an MD result, since only the configurational phase space
> is sampled in MC (masses effects would have to be added afterwards,
> assuming that some analytical result could be computed)
>
> I hope it helps
>
> Andre
>
> On Fri, Aug 11, 2017 at 6:36 AM, deepak bapat  wrote:
>
> > Dear Gmx Users
> >
> > I am trying to find out free energy of transforming one neutral LI to one
> > CL in aqueous solution.
> >
> > Water model is SPC/E. Gromacs version: 5.1.2
> >
> > I am doing something like this
> >
> > Insert 1 Li  olecule in water. (Li parameters were taken from Kasper P.
> > Jensen and William L. Jorgensen 2006.)
> >
> > step 1: increase mass of atom from 6.94100 to 35.45300.
> >
> > Step 2: change LJ parameters of LI to LJ of CL
> >
> >
> > Now my doubt is in step 1:  i get non zero free energy values.
> >
> > *required nonbonded.itp file content is*
> >
> > ;LI+
> > opls_406   LI  3   6.94100 0.000   A2.8700e-01 2.0929e-03
> > ; Li+ parameters from jensen and jorgensen JCTC 2006 2 1499-1509
> >
> > ;LI+ grown
> > opls_407   LI  17   35.45300 0.000   A2.8700e-01 2.0929e-03
> > ; Li+ parameters from jensen and jorgensen JCTC 2006 2 1499-1509 ;; Mass
> of
> > chlorine
> >
> >
> > *LI.itp file content of alchemical transformation for mass is*
> > [ atoms ]
> > ; idat type res nr  residu name at name  cg nr  charge   mass
> > 1   opls_4061   LI  LI   1  0.06.941
> > opls_407 0.0 35.45300
> >
> >
> > *.mdp file used is as follows*
> >
> >
> > integrator = sd
> > tinit  = 0
> > dt = 0.001
> > nsteps  = 100
> > nstcomm  = 100
> > nstxout = 0
> > nstvout = 0
> > nstfout  = 0
> > nstlog   = 5000
> > nstenergy = 5000
> > nstxtcout  = 500
> > cutoff-scheme= verlet
> > nstlist  = 10
> > ns_type  = grid
> > pbc  = xyz
> > rlist= 1.0
> > coulombtype  = PME
> > rcoulomb = 1.0
> > vdwtype  = cutoff
> > rvdw = 1.0
> > DispCorr  = EnerPres
> > fourierspacing   = 0.12
> > pme_order= 6
> > tc_grps  = system
> > tau_t= 1.0
> > ref_t= 300
> > Pcoupl   = Parrinello-Rahman
> > tau_p= 1.0
> > compressibility  = 4.5e-05
> > ref_p= 1.0
> > free_energy  = yes
> > init_lambda  = 0.05 ;;; depending on state, lambda value to be changed
> from
> > 0 to 1 ;
> > delta_lambda = 0
> > nstdhdl  = 10
> > gen_vel  = no
> > constraints  = h-bonds
> > constraint-algorithm = lincs
> > continuation = yes
> > lincs-order  = 12
> >
> >
> > Free enegy of step 1: i.e. mass transfomation is around +6.2 kJ/mol.
> >
> > In Gromacs 5.1.2 manual section 4.5 p.no 99 dependance of free energy on
> > lambda equation is given.
> >
> > Now my doubt is if I am using the NPT ensemble then the total kinetic
> > energy of the system should be constant i.e. summation(p^2/2m) which is
> > being controlled by the thermostat.
> >
> > But i am getting non zero value in this case? Is it normal to get
> something
> > like this or i have blundered somewhere?
> >
> > Will be happy to share input files if it helps.
> >
> > Thanks and Regards
> >
> > --
> > 

Re: [gmx-users] Perturbation Thermodynamic Integration

[Dan Gil]

mbda = 0
fep-lambdas  =
calc-lambda-neighbors= 1
vdw_lambdas  = 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
coul_lambdas = 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
bonded_lambdas   = 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
restraint_lambdas= 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
mass_lambdas = 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
nstdhdl  = 10

--Results--
A(aq)->B(aq)
Means
; mass-lambda | coul-lambda | vdw-lambda | bonded-lambda | restraint-lambda
| dH/dlambda to before | dH/dlambda to this | dH/dlambda to next | pV |
lambda
585.258 29.695 138.389 -106.111 0.000 0.000 0.000 78.180 14.434 0.0
194.905 27.926 109.373 -113.567 0.000 -8.514 0.000 35.428 14.433 0.1
201.785 23.966 90.522 -123.135 0.000 -5.856 0.000 32.987 14.437 0.2
101.067 21.244 76.286 -130.204 0.000 6.727 0.000 20.621 14.435 0.3
67.782 19.301 64.038 -136.090 0.000 12.170 0.000 15.391 14.436 0.4
54.102 17.403 54.579 -140.360 0.000 15.207 0.000 12.567 14.438 0.5
45.855 14.376 46.120 -146.966 0.000 17.949 0.000 10.041 14.437 0.6
39.769 11.953 39.144 -151.300 0.000 20.040 0.000 8.168 14.438 0.7
35.384 11.090 33.911 -151.862 0.000 21.252 0.000 7.172 14.439 0.8
31.411 9.077 28.113 -154.575 0.000 22.809 0.000 5.829 14.440 0.9
28.398 9.974 24.842 -151.347 0.000 23.126 0.000 0.000 14.439 1.0
Variances
; mass-lambda | coul-lambda | vdw-lambda | bonded-lambda | restraint-lambda
| dH/dlambda to before | dH/dlambda to this | dH/dlambda to next | pV |
lambda
17764.592 28.101 889.212 7624.759 0.000 0.000 0.000 265.656 0.002 0.0
1580.485 25.381 492.489 7085.318 0.000 93.157 0.000 95.406 0.002 0.1
4269.905 26.694 347.400 7025.386 0.000 118.370 0.000 120.552 0.002 0.2
1329.740 26.648 259.096 7083.151 0.000 85.371 0.000 87.603 0.002 0.3
249.921 24.406 195.233 7149.494 0.000 77.239 0.000 79.441 0.002 0.4
121.269 17.111 156.460 7039.120 0.000 74.030 0.000 76.206 0.002 0.5
87.000 15.901 128.267 7054.185 0.000 73.556 0.000 75.723 0.002 0.6
65.818 14.577 104.742 7096.497 0.000 73.225 0.000 75.402 0.002 0.7
55.143 14.713 91.124 7081.810 0.000 72.768 0.000 74.919 0.002 0.8
41.118 13.472 76.214 7198.105 0.000 73.496 0.000 75.675 0.002 0.9
33.836 15.572 65.528 7162.912 0.000 72.932 0.000 0.000 0.002 1.0

A(gas)->B(gas)
Means
; mass-lambda | coul-lambda | vdw-lambda | bonded-lambda | restraint-lambda
| dH/dlambda to before | dH/dlambda to this | dH/dlambda to next | pV |
lambda
1110.166 32.509 114.451 -115.748 0.000 0.000 0.000 127.586 4.377 0.0
398.592 26.708 101.772 -133.086 0.000 -26.055 0.000 52.957 3.912 0.1
237.629 27.141 84.628 -137.244 0.000 -7.766 0.000 34.879 5.057 0.2 84.897
20.358 76.144 -133.012 0.000 8.728 0.000 18.621 14.436 0.3 131.475 20.205
64.964 -158.091 0.000 7.811 0.000 19.736 3.927 0.4 107.720 20.655 57.763
-156.171 0.000 10.776 0.000 16.984 4.815 0.5 91.054 25.769 51.617 -146.044
0.000 11.632 0.000 16.326 4.020 0.6 78.003 21.697 45.907 -154.841 0.000
14.905 0.000 13.273 4.114 0.7 69.346 15.392 41.194 -167.694 0.000 18.277
0.000 10.139 6.244 0.8 62.263 17.129 37.528 -164.429 0.000 18.954 0.000
9.667 6.133 0.9 56.582 18.052 34.094 -162.977 0.000 19.727 0.000 0.000
4.456 1.0
Variances
; mass-lambda | coul-lambda | vdw-lambda | bonded-lambda | restraint-lambda
| dH/dlambda to before | dH/dlambda to this | dH/dlambda to next | pV |
lambda
40348.430 3.943 514.703 7085.063 0.000 0.000 0.000 481.126 0.030 0.0
6978.993 1.390 352.654 7972.572 0.000 151.629 0.000 154.128 0.000 0.1
2160.691 4.261 219.874 7020.561 0.000 94.026 0.000 96.219 0.263 0.2
301.074 32.826 249.228 7137.750 0.000 78.224 0.000 80.446 0.002 0.3
694.265 1.765 123.119 7225.511 0.000 80.863 0.000 83.117 0.000 0.4
452.408 7.903 97.154 7151.103 0.000 78.148 0.000 80.364 0.099 0.5
347.707 1.124 69.253 7024.693 0.000 74.678 0.000 76.844 0.004 0.6
230.115 4.723 56.425 7208.842 0.000 75.247 0.000 77.443 0.009 0.7
194.552 3.213 56.178 7169.195 0.000 74.497 0.000 76.669 2.824 0.8
154.875 4.498 47.516 7205.079 0.000 74.482 0.000 76.649 0.711 0.9
128.781 1.370 36.130 7231.535 0.000 74.006 0.000 0.000 0.155 1.0




On Tue, May 16, 2017 at 3:50 PM, Hannes Loeffler <hannes.loeff...@stfc.ac.uk
> wrote:

> On Tue, 16 May 2017 15:13:10 -0400
> Dan Gil <dan.gil9...@gmail.com> wrote:
>
>
> > If you do this via decoupling ("absolute" transformation) you do that
> > > once for molecule A and once for molecule B.
> >
> >
> > I believe you are referring to the BAR method? I am trying to see if
> > I get the same results as another group. They used thermodynamic
> > integration from A to B, so I decided to spend some more time with
> > this. I will try later if I get consistent results for both methods.
>
> No, I am not referring to a specific analysis methods.  I commented on
> an alternative pathway.
>
>
> > transforming the masses may interact badly
> > > with bond constraints that are applied to 

Re: [gmx-users] Perturbation Thermodynamic Integration

[Dan Gil]

>
> What does grompp from 2016.3 report?
>

ERROR 1 [file topol.top, line 10]:
  Atom 1 in molecule type 'HEPT' has different A and B state charges and/or
  atom types set in the topology file as well as through the mdp option
  'couple-moltype'. You can not use both these methods simultaneously.

If you do this via decoupling ("absolute" transformation) you do that
> once for molecule A and once for molecule B.


I believe you are referring to the BAR method? I am trying to see if I get
the same results as another group. They used thermodynamic integration from
A to B, so I decided to spend some more time with this. I will try later if
I get consistent results for both methods.

If you want to do this via a relative transformation you would not use
> couple-moltype at all but fill in the B columns in your topology file
> for all force field parameters that change.


I've filled in the B columns, but I didn't realize that I should not use
couple-moltype. I will remove the following lines from mdp file.

couple-moltype   = HEPT
> couple-lambda0   = vdwq
> couple-lambda1   = none
> couple-intramol  = no


Then, grompp reports no errors.

transforming the masses may interact badly
> with bond constraints that are applied to alchemically transformed
> bonds


Thank you for this information! Do you know if there are there publications
that refer to this issue?

On Tue, May 16, 2017 at 10:46 AM, Hannes Loeffler <
hannes.loeff...@stfc.ac.uk> wrote:

> On Tue, 16 May 2017 10:28:08 -0400
> Dan Gil <dan.gil9...@gmail.com> wrote:
>
> > Thank you for the advice on the cut-off schemes and PME methods.
> >
> > What is the physical meaning of a non-interacting final state
> > > that has different masses from the initial state?
> >
> >
> > These free energy options was just from me trying to figure out why
> > mass has any contributions at all. I am going from molecule A to B
> > described in the topology. In the actual simulations, I am planning
> > on using this: vdw_lambdas  = 0 0.1 0.2 0.3 0.4 0.5 0.6
> > 0.7 0.8 0.9 1 coul_lambdas = 0 0.1 0.2 0.3 0.4 0.5 0.6
> > 0.7 0.8 0.9 1 bonded_lambdas   = 0 0.1 0.2 0.3 0.4 0.5 0.6
> > 0.7 0.8 0.9 1 restraint_lambdas= 0 0.1 0.2 0.3 0.4 0.5 0.6
> > 0.7 0.8 0.9 1 mass_lambdas = 0 0.1 0.2 0.3 0.4 0.5 0.6
> > 0.7 0.8 0.9 1
> >
> > To get the solvation free energy difference between molecule A and B.
>
> If you do this via decoupling ("absolute" transformation) you do that
> once for molecule A and once for molecule B.  I don't see why you would
> want to change masses in this case.
>
> If you want to do this via a relative transformation you would not use
> couple-moltype at all but fill in the B columns in your topology file
> for all force field parameters that change.  In this case you _can_
> change the masses but you would have to do the same transformation in
> vacuum. Then the mass contributions should cancel perfectly (at least in
> the limit of infinite sampling, I guess).  But Michael Shirts has
> commented a while back that transforming the masses may interact badly
> with bond constraints that are applied to alchemically transformed
> bonds (we have seen problems with this too). So it is just simplest to
> not use mass-lambdas precisely because of the aforementioned argument.
>
>
> Cheers,
> Hannes.
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Re: [gmx-users] Perturbation Thermodynamic Integration

[Dan Gil]

Thank you for the advice on the cut-off schemes and PME methods.

What is the physical meaning of a non-interacting final state
> that has different masses from the initial state?


These free energy options was just from me trying to figure out why mass
has any contributions at all. I am going from molecule A to B described in
the topology. In the actual simulations, I am planning on using this:
vdw_lambdas  = 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
coul_lambdas = 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
bonded_lambdas   = 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
restraint_lambdas= 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
mass_lambdas = 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1

To get the solvation free energy difference between molecule A and B.

You'd need the latest grompp, as I've mentioned twice.


Sorry, I wasn't sure if I had the right version of grompp or not. I am
seeing if I can download the newest version of Gromacs to check.

On Tue, May 16, 2017 at 10:10 AM, Hannes Loeffler <
hannes.loeff...@stfc.ac.uk> wrote:

> I have not really followed the previous email exchange but from this
> mdp file I wonder what you are trying to achieve.  You seem to want to
> decouple all atoms of your HEPT molecule (couple-moltype,
> couple-intramol) from its environment but then you also change the
> masses.  What is the physical meaning of a non-interacting final state
> that has different masses from the initial state?  I believe the mass
> contributions are supposed to cancel in a closed thermodynamic cycle
> but what is the cycle you are simulating?
>
>
> On Tue, 16 May 2017 09:30:08 -0400
> Dan Gil <dan.gil9...@gmail.com> wrote:
>
> > Sorry, here is the mdp file:
> >
> > ;Integration Method and Parameters
> > integrator   = sd
> > nsteps   = 10
> > dt = 0.002
> > nstenergy= 1000
> > nstlog   = 5000
> >
> > ;Output Control
> > nstxout = 0
> > nstvout = 0
> >
> > ;Cutoff Schemes
> > cutoff-scheme= group
> > rlist= 1.0
> > vdw-type = cut-off
> > rvdw = 2.0
> >
> > ;Coulomb interactions
> > coulombtype  = pme
> > rcoulomb = 1.0
> > fourierspacing   = 0.4
> >
> > ;Constraints
> > constraints  = all-bonds
> >
> > ;Temperature coupling
> > tcoupl   = v-rescale
> > tc-grps  = system
> > tau-t= 0.1
> > ref-t= 300
> >
> > ;Pressure coupling
> > pcoupl = parrinello-rahman
> > ref-p = 1.01325
> > compressibility = 4.5e-5
> > tau-p = 5
> >
> > ;Free energy calculation
> > free-energy  = yes
> > init-lambda-state= 8
> > delta-lambda = 0
> > fep-lambdas  =
> > calc-lambda-neighbors= 1
> > vdw_lambdas  = 0 0   0   0   0   0   0   0   0   0   0
> > coul_lambdas = 0 0   0   0   0   0   0   0   0   0   0
> > bonded_lambdas   = 0 0   0   0   0   0   0   0   0   0   0
> > restraint_lambdas= 0 0   0   0   0   0   0   0   0   0   0
> > mass_lambdas = 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
> > couple-moltype   = HEPT
> > couple-lambda0   = vdwq
> > couple-lambda1   = none
> > couple-intramol  = no
> > nstdhdl  = 10
> >
> >
> > On Tue, May 16, 2017 at 1:02 AM, Mark Abraham
> > <mark.j.abra...@gmail.com> wrote:
> >
> > > Hi,
> > >
> > > What use are you making of constraints? Justin suggested sharing a
> > > full mdp file, which I think may help. We discovered last year that
> > > you can get equipartition failure for (IIRC) all-bonds constraints
> > > for moieties like -CH2Cl, and latest grompp now detects this.
> > >
> > > Mark
> > >
> > > On Tue, 16 May 2017 01:16 Dan Gil <dan.gil9...@gmail.com> wrote:
> > >
> > > > Hello,
> > > >
> > > > The last thread was getting too big, and the conversation evolved
> > > > to a topic different from my original question, so I decided to
> > > > start a new thread.
> > > >
> > > > We were discussing thermodynamic integration, and why the
> > > > mass_lambdas would have any contribution to the derivative of the
> > > > Hamiltonian.
> > > >
> > > > I found a source (link below) which derives the Gibbs f

Re: [gmx-users] Perturbation Thermodynamic Integration

[Dan Gil]

Hi,

The latest version of Gromacs I have is 5.1. Using this version, grompp
produces no warnings or errors.

I am using OPLS-AA, and I didn't have any issues with it thus far. I
inherited this research project though 3 years ago. Is there something you
think I should look at with scrutiny?

On Tue, May 16, 2017 at 9:42 AM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> Yes that looks like it is the envelope of the new warning. What does grompp
> from 2016.3 report?
>
> (Aside, that looks like an ad hoc non-bonded scheme. As a reviewer, I'd
> reject that method immediately unless there was evidence that it worked
> well for a range of observables, and was consistent with other practice for
> that force field. If there is such evidence, for my information, what model
> / force field does it like that?)
>
> Mark
>
> On Tue, May 16, 2017 at 3:30 PM Dan Gil <dan.gil9...@gmail.com> wrote:
>
> > Sorry, here is the mdp file:
> >
> > ;Integration Method and Parameters
> > integrator   = sd
> > nsteps   = 10
> > dt = 0.002
> > nstenergy= 1000
> > nstlog   = 5000
> >
> > ;Output Control
> > nstxout = 0
> > nstvout = 0
> >
> > ;Cutoff Schemes
> > cutoff-scheme= group
> > rlist= 1.0
> > vdw-type = cut-off
> > rvdw = 2.0
> >
> > ;Coulomb interactions
> > coulombtype  = pme
> > rcoulomb = 1.0
> > fourierspacing   = 0.4
> >
> > ;Constraints
> > constraints  = all-bonds
> >
> > ;Temperature coupling
> > tcoupl   = v-rescale
> > tc-grps  = system
> > tau-t= 0.1
> > ref-t= 300
> >
> > ;Pressure coupling
> > pcoupl = parrinello-rahman
> > ref-p = 1.01325
> > compressibility = 4.5e-5
> > tau-p = 5
> >
> > ;Free energy calculation
> > free-energy  = yes
> > init-lambda-state= 8
> > delta-lambda = 0
> > fep-lambdas  =
> > calc-lambda-neighbors= 1
> > vdw_lambdas  = 0 0   0   0   0   0   0   0   0   0   0
> > coul_lambdas = 0 0   0   0   0   0   0   0   0   0   0
> > bonded_lambdas   = 0 0   0   0   0   0   0   0   0   0   0
> > restraint_lambdas= 0 0   0   0   0   0   0   0   0   0   0
> > mass_lambdas = 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
> > couple-moltype   = HEPT
> > couple-lambda0   = vdwq
> > couple-lambda1   = none
> > couple-intramol  = no
> > nstdhdl  = 10
> >
> >
> > On Tue, May 16, 2017 at 1:02 AM, Mark Abraham <mark.j.abra...@gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > What use are you making of constraints? Justin suggested sharing a full
> > mdp
> > > file, which I think may help. We discovered last year that you can get
> > > equipartition failure for (IIRC) all-bonds constraints for moieties
> like
> > > -CH2Cl, and latest grompp now detects this.
> > >
> > > Mark
> > >
> > > On Tue, 16 May 2017 01:16 Dan Gil <dan.gil9...@gmail.com> wrote:
> > >
> > > > Hello,
> > > >
> > > > The last thread was getting too big, and the conversation evolved to
> a
> > > > topic different from my original question, so I decided to start a
> new
> > > > thread.
> > > >
> > > > We were discussing thermodynamic integration, and why the
> mass_lambdas
> > > > would have any contribution to the derivative of the Hamiltonian.
> > > >
> > > > I found a source (link below) which derives the Gibbs free energy
> > change
> > > as
> > > > a function of lambda. I learned that the mass contribution is often
> > > assumed
> > > > to be small and negligible, given that the mass difference between
> the
> > > two
> > > > lambda states are small.
> > > > http://www.tandfonline.com/doi/abs/10.1080/00268970600893060
> > > >
> > > > I think that the mass of the two lambda states that equation (14) is
> > > > referring to is the total mass (mass of solvent plus solute). My
> system
> > > is
> > > > 1 solute (~40 atoms) infinitely diluted in solvent (23500). I wonder
> > if I
> > > > am getting nonzero mass contributions (in 

Re: [gmx-users] Perturbation Thermodynamic Integration

[Dan Gil]

Sorry, here is the mdp file:

;Integration Method and Parameters
integrator   = sd
nsteps   = 10
dt = 0.002
nstenergy= 1000
nstlog   = 5000

;Output Control
nstxout = 0
nstvout = 0

;Cutoff Schemes
cutoff-scheme= group
rlist= 1.0
vdw-type = cut-off
rvdw = 2.0

;Coulomb interactions
coulombtype  = pme
rcoulomb = 1.0
fourierspacing   = 0.4

;Constraints
constraints  = all-bonds

;Temperature coupling
tcoupl   = v-rescale
tc-grps  = system
tau-t= 0.1
ref-t= 300

;Pressure coupling
pcoupl = parrinello-rahman
ref-p = 1.01325
compressibility = 4.5e-5
tau-p = 5

;Free energy calculation
free-energy  = yes
init-lambda-state= 8
delta-lambda = 0
fep-lambdas  =
calc-lambda-neighbors= 1
vdw_lambdas  = 0 0   0   0   0   0   0   0   0   0   0
coul_lambdas = 0 0   0   0   0   0   0   0   0   0   0
bonded_lambdas   = 0 0   0   0   0   0   0   0   0   0   0
restraint_lambdas= 0 0   0   0   0   0   0   0   0   0   0
mass_lambdas = 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
couple-moltype   = HEPT
couple-lambda0   = vdwq
couple-lambda1   = none
couple-intramol  = no
nstdhdl  = 10


On Tue, May 16, 2017 at 1:02 AM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> What use are you making of constraints? Justin suggested sharing a full mdp
> file, which I think may help. We discovered last year that you can get
> equipartition failure for (IIRC) all-bonds constraints for moieties like
> -CH2Cl, and latest grompp now detects this.
>
> Mark
>
> On Tue, 16 May 2017 01:16 Dan Gil <dan.gil9...@gmail.com> wrote:
>
> > Hello,
> >
> > The last thread was getting too big, and the conversation evolved to a
> > topic different from my original question, so I decided to start a new
> > thread.
> >
> > We were discussing thermodynamic integration, and why the mass_lambdas
> > would have any contribution to the derivative of the Hamiltonian.
> >
> > I found a source (link below) which derives the Gibbs free energy change
> as
> > a function of lambda. I learned that the mass contribution is often
> assumed
> > to be small and negligible, given that the mass difference between the
> two
> > lambda states are small.
> > http://www.tandfonline.com/doi/abs/10.1080/00268970600893060
> >
> > I think that the mass of the two lambda states that equation (14) is
> > referring to is the total mass (mass of solvent plus solute). My system
> is
> > 1 solute (~40 atoms) infinitely diluted in solvent (23500). I wonder if I
> > am getting nonzero mass contributions (in my dhdl.xvg output) because of
> > finite-size effects? Would completely neglecting the mass contributions
> be
> > acceptable? Does doing this technically change the system to one that is
> 1
> > solute and an infinite number of solvent molecules where the mass
> > contributions limit is zero?
> >
> > Best Regards,
> >
> > Dan
> > --
> > 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.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
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>
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[gmx-users] Perturbation Thermodynamic Integration

[Dan Gil]

Hello,

The last thread was getting too big, and the conversation evolved to a
topic different from my original question, so I decided to start a new
thread.

We were discussing thermodynamic integration, and why the mass_lambdas
would have any contribution to the derivative of the Hamiltonian.

I found a source (link below) which derives the Gibbs free energy change as
a function of lambda. I learned that the mass contribution is often assumed
to be small and negligible, given that the mass difference between the two
lambda states are small.
http://www.tandfonline.com/doi/abs/10.1080/00268970600893060

I think that the mass of the two lambda states that equation (14) is
referring to is the total mass (mass of solvent plus solute). My system is
1 solute (~40 atoms) infinitely diluted in solvent (23500). I wonder if I
am getting nonzero mass contributions (in my dhdl.xvg output) because of
finite-size effects? Would completely neglecting the mass contributions be
acceptable? Does doing this technically change the system to one that is 1
solute and an infinite number of solvent molecules where the mass
contributions limit is zero?

Best Regards,

Dan
-- 
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.

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

[Dan Gil]

I ran equilibrium simulations, and then a longer simulations with the
recommended sd integrator. Still, the mass_lambda dH/dL is nonzero and
sometimes it is the dominant contribution at certain lambdas. I don't think
it is a convergence issue because there aren't huge fluctuations in dH/dL
values seen in dhdl.xvg.

I also ran simulations where only the mass changed as a function of lambda.
Others (i.e. Electrostatic, Van der Waals, bonded, and restraints) were
kept constant. The mass still has an effect on the Helmholtz free energy
change. Is there possibly a mistake with how I've prepared the topology?

 [ moleculetype ]
HEPT 3

 [ atoms ]
 1   opls_135  1   HEPTCH3  1 -0.180 12.011
 opls_9610.36012.011
 2   opls_136  1   HEPTCH2  2 -0.120 12.011
 opls_9620.24012.011
 3   opls_136  1   HEPTCH2  3 -0.120 12.011
 opls_9620.24012.011
...
21   opls_140  1   HEPT  H  7  0.060  1.008
 opls_965   -0.12018.998
22   opls_140  1   HEPT  H  7  0.060  1.008
 opls_965   -0.12018.998
23   opls_140  1   HEPT  H  7  0.060  1.008
 opls_965   -0.12018.998

... [ bonds ] ... [ angles ] ... etc...

On Thu, May 11, 2017 at 11:33 AM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 5/11/17 9:49 AM, Dan Gil wrote:
>
>> Thank you Dr. Lemkul,
>>
>> The simulations ran, but I have some a question about the results.
>>
>> Is it natural to have a nonzero mass_lambda dH/dL? My intuition was that
>> the potential energy does not depend on mass, and my thinking was that the
>> mass contribution should be very small, if not zero.
>>
>>
> It should.  Maybe it's a convergence issue?
>
>
> -Justin
>
> Best Regards,
>>
>> Dan
>>
>> On Wed, May 3, 2017 at 10:46 AM, Justin Lemkul <jalem...@vt.edu> wrote:
>>
>>
>>>
>>> On 5/3/17 10:43 AM, Dan Gil wrote:
>>>
>>> Hi Dr. Kausar,
>>>>
>>>> If I want the molecule to have all of its nonbonded interactions with
>>>> the
>>>> rest of the system (solvent) at each lambda, don't I want to have vdwq
>>>> option ON for both couple-lambda0 and couple-lambda1?
>>>>
>>>> What I am attempting to do is mutate molecule A to molecule B through
>>>> the
>>>> simulation.
>>>>
>>>>
>>>> Relative free energy calculations are a little bit of a strange beast;
>>> you
>>> do need to set the B-state (couple-lambda1) to "none" and the B-state
>>> types
>>> and charges are read from [atoms].
>>>
>>>
>>> -Justin
>>>
>>> Best Regards,
>>>
>>>>
>>>> Dan
>>>>
>>>> On Wed, May 3, 2017 at 1:04 AM, Tasneem Kausar <
>>>> tasneemkausa...@gmail.com
>>>>
>>>>>
>>>>> wrote:
>>>>
>>>> In the last line of mdp file couple-lambda0 and couple-lambda1 have the
>>>>
>>>>> same vdwq variable. It indicates A and B state of system. So grompp is
>>>>> complaining about the identical states.
>>>>>
>>>>> You can also see the alchemistry.org for detail information about the
>>>>> free
>>>>> energy calculations.
>>>>>
>>>>> On Wed, May 3, 2017 at 2:14 AM, Dan Gil <dan.gil9...@gmail.com> wrote:
>>>>>
>>>>> Thank you Dr. Lemkul,
>>>>>
>>>>>>
>>>>>> Following your advice, I was able to calculate the solvation free
>>>>>> energy
>>>>>>
>>>>>> of
>>>>>
>>>>> two molecules that I am interested in. The results, unfortunately, were
>>>>>>
>>>>>> not
>>>>>
>>>>> what I expected. I want to try an alternative method, that is, the
>>>>>> alchemical thermodynamic integration method.
>>>>>>
>>>>>> If I understand this correctly, I should be able to calculate the free
>>>>>> energy difference between two systems A and B as I change the topology
>>>>>> of
>>>>>> the molecule from A to B in small steps.
>>>>>>
>>>>>> I wasn't able to find a tutorial online, but I attempted to try the
>>>>>>
>>>>>> method
>>>>>
>>>>> and I obtained this error from grompp:
&

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

[Dan Gil]

Thank you Dr. Lemkul,

The simulations ran, but I have some a question about the results.

Is it natural to have a nonzero mass_lambda dH/dL? My intuition was that
the potential energy does not depend on mass, and my thinking was that the
mass contribution should be very small, if not zero.

Best Regards,

Dan

On Wed, May 3, 2017 at 10:46 AM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 5/3/17 10:43 AM, Dan Gil wrote:
>
>> Hi Dr. Kausar,
>>
>> If I want the molecule to have all of its nonbonded interactions with the
>> rest of the system (solvent) at each lambda, don't I want to have vdwq
>> option ON for both couple-lambda0 and couple-lambda1?
>>
>> What I am attempting to do is mutate molecule A to molecule B through the
>> simulation.
>>
>>
> Relative free energy calculations are a little bit of a strange beast; you
> do need to set the B-state (couple-lambda1) to "none" and the B-state types
> and charges are read from [atoms].
>
>
> -Justin
>
> Best Regards,
>>
>> Dan
>>
>> On Wed, May 3, 2017 at 1:04 AM, Tasneem Kausar <tasneemkausa...@gmail.com
>> >
>> wrote:
>>
>> In the last line of mdp file couple-lambda0 and couple-lambda1 have the
>>> same vdwq variable. It indicates A and B state of system. So grompp is
>>> complaining about the identical states.
>>>
>>> You can also see the alchemistry.org for detail information about the
>>> free
>>> energy calculations.
>>>
>>> On Wed, May 3, 2017 at 2:14 AM, Dan Gil <dan.gil9...@gmail.com> wrote:
>>>
>>> Thank you Dr. Lemkul,
>>>>
>>>> Following your advice, I was able to calculate the solvation free energy
>>>>
>>> of
>>>
>>>> two molecules that I am interested in. The results, unfortunately, were
>>>>
>>> not
>>>
>>>> what I expected. I want to try an alternative method, that is, the
>>>> alchemical thermodynamic integration method.
>>>>
>>>> If I understand this correctly, I should be able to calculate the free
>>>> energy difference between two systems A and B as I change the topology
>>>> of
>>>> the molecule from A to B in small steps.
>>>>
>>>> I wasn't able to find a tutorial online, but I attempted to try the
>>>>
>>> method
>>>
>>>> and I obtained this error from grompp:
>>>>
>>>> WARNING 1 [file grompp.mdp, line 43]:
>>>>   The lambda=0 and lambda=1 states for coupling are identical
>>>>
>>>> I was hoping if you could help me understand what I am missing in my
>>>> topology or mdp file.
>>>>
>>>> Topology:
>>>>  [ moleculetype ]
>>>> HEPT 3
>>>>
>>>>  [ atoms ]
>>>>  1   opls_135  1   HEPTCH3  1 -0.180 12.011
>>>>  opls_9610.36012.011
>>>>  2   opls_136  1   HEPTCH2  2 -0.120 12.011
>>>>  opls_9620.24012.011
>>>>  3   opls_136  1   HEPTCH2  3 -0.120 12.011
>>>>  opls_9620.24012.011
>>>>  4   opls_136  1   HEPTCH2  4 -0.120 12.011
>>>>  opls_9620.24012.011
>>>>  5   opls_136  1   HEPTCH2  5 -0.120 12.011
>>>>  opls_9620.24012.011
>>>>  6   opls_136  1   HEPTCH2  6 -0.120 12.011
>>>>  opls_9620.24012.011
>>>>  7   opls_135  1   HEPTCH3  7 -0.180 12.011
>>>>  opls_9610.36012.011
>>>>  8   opls_140  1   HEPT  H  1  0.060  1.008
>>>>  opls_965   -0.12018.998
>>>>  9   opls_140  1   HEPT  H  1  0.060  1.008
>>>>  opls_965   -0.12018.998
>>>> 10   opls_140  1   HEPT  H  1  0.060  1.008
>>>>  opls_965   -0.12018.998
>>>> 11   opls_140  1   HEPT  H  2  0.060  1.008
>>>>  opls_965   -0.12018.998
>>>> 12   opls_140  1   HEPT  H  2  0.060  1.008
>>>>  opls_965   -0.12018.998
>>>> 13   opls_140  1   HEPT  H  3  0.060  1.008
>>>>  opls_965   -0.12018.998
>>>> 14   opls_140  1   HEPT  H  3  0.060  1.008
>>>>  opls

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

[Dan Gil]

Hi Dr. Kausar,

If I want the molecule to have all of its nonbonded interactions with the
rest of the system (solvent) at each lambda, don't I want to have vdwq
option ON for both couple-lambda0 and couple-lambda1?

What I am attempting to do is mutate molecule A to molecule B through the
simulation.

Best Regards,

Dan

On Wed, May 3, 2017 at 1:04 AM, Tasneem Kausar <tasneemkausa...@gmail.com>
wrote:

> In the last line of mdp file couple-lambda0 and couple-lambda1 have the
> same vdwq variable. It indicates A and B state of system. So grompp is
> complaining about the identical states.
>
> You can also see the alchemistry.org for detail information about the free
> energy calculations.
>
> On Wed, May 3, 2017 at 2:14 AM, Dan Gil <dan.gil9...@gmail.com> wrote:
>
> > Thank you Dr. Lemkul,
> >
> > Following your advice, I was able to calculate the solvation free energy
> of
> > two molecules that I am interested in. The results, unfortunately, were
> not
> > what I expected. I want to try an alternative method, that is, the
> > alchemical thermodynamic integration method.
> >
> > If I understand this correctly, I should be able to calculate the free
> > energy difference between two systems A and B as I change the topology of
> > the molecule from A to B in small steps.
> >
> > I wasn't able to find a tutorial online, but I attempted to try the
> method
> > and I obtained this error from grompp:
> >
> > WARNING 1 [file grompp.mdp, line 43]:
> >   The lambda=0 and lambda=1 states for coupling are identical
> >
> > I was hoping if you could help me understand what I am missing in my
> > topology or mdp file.
> >
> > Topology:
> >  [ moleculetype ]
> > HEPT 3
> >
> >  [ atoms ]
> >  1   opls_135  1   HEPTCH3  1 -0.180 12.011
> >  opls_9610.36012.011
> >  2   opls_136  1   HEPTCH2  2 -0.120 12.011
> >  opls_9620.24012.011
> >  3   opls_136  1   HEPTCH2  3 -0.120 12.011
> >  opls_9620.24012.011
> >  4   opls_136  1   HEPTCH2  4 -0.120 12.011
> >  opls_9620.24012.011
> >  5   opls_136  1   HEPTCH2  5 -0.120 12.011
> >  opls_9620.24012.011
> >  6   opls_136  1   HEPTCH2  6 -0.120 12.011
> >  opls_9620.24012.011
> >  7   opls_135  1   HEPTCH3  7 -0.180 12.011
> >  opls_9610.36012.011
> >  8   opls_140  1   HEPT  H  1  0.060  1.008
> >  opls_965   -0.12018.998
> >  9   opls_140  1   HEPT  H  1  0.060  1.008
> >  opls_965   -0.12018.998
> > 10   opls_140  1   HEPT  H  1  0.060  1.008
> >  opls_965   -0.12018.998
> > 11   opls_140  1   HEPT  H  2  0.060  1.008
> >  opls_965   -0.12018.998
> > 12   opls_140  1   HEPT  H  2  0.060  1.008
> >  opls_965   -0.12018.998
> > 13   opls_140  1   HEPT  H  3  0.060  1.008
> >  opls_965   -0.12018.998
> > 14   opls_140  1   HEPT  H  3  0.060  1.008
> >  opls_965   -0.12018.998
> > 15   opls_140  1   HEPT  H  4  0.060  1.008
> >  opls_965   -0.12018.998
> > 16   opls_140  1   HEPT  H  4  0.060  1.008
> >  opls_965   -0.12018.998
> > 17   opls_140  1   HEPT  H  5  0.060  1.008
> >  opls_965   -0.12018.998
> > 18   opls_140  1   HEPT  H  5  0.060  1.008
> >  opls_965   -0.12018.998
> > 19   opls_140  1   HEPT  H  6  0.060  1.008
> >  opls_965   -0.12018.998
> > 20   opls_140  1   HEPT  H  6  0.060  1.008
> >  opls_965   -0.12018.998
> > 21   opls_140  1   HEPT  H  7  0.060  1.008
> >  opls_965   -0.12018.998
> > 22   opls_140  1   HEPT  H  7  0.060  1.008
> >  opls_965   -0.12018.998
> > 23   opls_140  1   HEPT  H  7  0.060  1.008
> >  opls_965   -0.12018.998
> > ... And so on with the bonds, pairs, angles, and dihedrals directive.
> >
> > MDP File:
> >
> > ;Integration Method and Parameters
> > integrator   = md
> > nsteps   = 1
> > dt = 0.002
> > nstenergy

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

[Dan Gil]

Thank you Dr. Lemkul,

Following your advice, I was able to calculate the solvation free energy of
two molecules that I am interested in. The results, unfortunately, were not
what I expected. I want to try an alternative method, that is, the
alchemical thermodynamic integration method.

If I understand this correctly, I should be able to calculate the free
energy difference between two systems A and B as I change the topology of
the molecule from A to B in small steps.

I wasn't able to find a tutorial online, but I attempted to try the method
and I obtained this error from grompp:

WARNING 1 [file grompp.mdp, line 43]:
  The lambda=0 and lambda=1 states for coupling are identical

I was hoping if you could help me understand what I am missing in my
topology or mdp file.

Topology:
 [ moleculetype ]
HEPT 3

 [ atoms ]
 1   opls_135  1   HEPTCH3  1 -0.180 12.011
 opls_9610.36012.011
 2   opls_136  1   HEPTCH2  2 -0.120 12.011
 opls_9620.24012.011
 3   opls_136  1   HEPTCH2  3 -0.120 12.011
 opls_9620.24012.011
 4   opls_136  1   HEPTCH2  4 -0.120 12.011
 opls_9620.24012.011
 5   opls_136  1   HEPTCH2  5 -0.120 12.011
 opls_9620.24012.011
 6   opls_136  1   HEPTCH2  6 -0.120 12.011
 opls_9620.24012.011
 7   opls_135  1   HEPTCH3  7 -0.180 12.011
 opls_9610.36012.011
 8   opls_140  1   HEPT  H  1  0.060  1.008
 opls_965   -0.12018.998
 9   opls_140  1   HEPT  H  1  0.060  1.008
 opls_965   -0.12018.998
10   opls_140  1   HEPT  H  1  0.060  1.008
 opls_965   -0.12018.998
11   opls_140  1   HEPT  H  2  0.060  1.008
 opls_965   -0.12018.998
12   opls_140  1   HEPT  H  2  0.060  1.008
 opls_965   -0.12018.998
13   opls_140  1   HEPT  H  3  0.060  1.008
 opls_965   -0.12018.998
14   opls_140  1   HEPT  H  3  0.060  1.008
 opls_965   -0.12018.998
15   opls_140  1   HEPT  H  4  0.060  1.008
 opls_965   -0.12018.998
16   opls_140  1   HEPT  H  4  0.060  1.008
 opls_965   -0.12018.998
17   opls_140  1   HEPT  H  5  0.060  1.008
 opls_965   -0.12018.998
18   opls_140  1   HEPT  H  5  0.060  1.008
 opls_965   -0.12018.998
19   opls_140  1   HEPT  H  6  0.060  1.008
 opls_965   -0.12018.998
20   opls_140  1   HEPT  H  6  0.060  1.008
 opls_965   -0.12018.998
21   opls_140  1   HEPT  H  7  0.060  1.008
 opls_965   -0.12018.998
22   opls_140  1   HEPT  H  7  0.060  1.008
 opls_965   -0.12018.998
23   opls_140  1   HEPT  H  7  0.060  1.008
 opls_965   -0.12018.998
... And so on with the bonds, pairs, angles, and dihedrals directive.

MDP File:

;Integration Method and Parameters
integrator   = md
nsteps   = 1
dt = 0.002
nstenergy= 1000
nstlog   = 5000

;Output Control
nstxout = 0
nstvout = 0

;Cutoff Schemes
cutoff-scheme= group
rlist= 1.0
vdw-type = cut-off
rvdw = 2.0

;Coulomb interactions
coulombtype  = pme
rcoulomb = 1.0
fourierspacing   = 0.4

;Constraints
constraints  = all-bonds

;Temperature coupling
tcoupl   = v-rescale
tc-grps  = system
tau-t= 0.1
ref-t= 300

;Pressure coupling
pcoupl = parrinello-rahman
ref-p = 1.01325
compressibility = 4.5e-5
tau-p = 5

;Free energy calculation
free-energy  = yes
init-lambda  = 0
delta-lambda = 0.1
couple-moltype   = HEPT
couple-lambda0   = vdwq
couple-lambda1   = vdwq

On Mon, Apr 3, 2017 at 2:05 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 4/3/17 2:01 PM, Dan Gil wrote:
>
>> Thank you Dr. Lemkul,
>>
>> I am trying to run grompp with the md integrator, but I am getting this
>> error:
>> "For proper sampling of the (nearly) decoupled state, stochastic dynamics
>> should be used"
>>
>> Should I ignore this warning with the -maxwarn option and try running it?
>> I
>> will see if I obtain comparable values for ethanol.
>>
>>
> People have already done such a comparison and that's why grompp is
> telling you this - it's better to use the Langevin integrator.  You'll get
> better sampling, particula

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

[Dan Gil]

Thank you Dr. Lemkul,

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

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

Best Regards,

Dan


On Mon, Mar 27, 2017 at 12:51 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 3/26/17 9:40 PM, Dan Gil wrote:
>
>> Hi,
>>
>> I am following Dr. Sander Pronk's and Dr. Justin Lemkul's tutorial on
>> calculating free energy of solvation. Is it possible and theoretically
>> sound to use the md integrator instead of the sd integrator for these
>> calculations?
>>
>>
> Langevin dynamics gives better sampling so it is frequently used for free
> energy calculations.  You may get comparable results with the leap-frog
> integrator, but I haven never done a side-by-side comparison.
>
> -Justin
>
> I have already done a considerable amount of work using md integration, and
>> I want to make sure that the free energy values I calculate are consistent
>> with my previous work.
>>
>> If using the md integrator is not sound, is there an alternative way of
>> calculating solvation energy that will be consistent?
>>
>> Best Regards,
>>
>> Dan
>>
>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
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[gmx-users] Using the md integrator for calculating free energy of solvation

[Dan Gil]

Hi,

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

I have already done a considerable amount of work using md integration, and
I want to make sure that the free energy values I calculate are consistent
with my previous work.

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

Best Regards,

Dan
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[gmx-users] Umbrella Sampling - LINCS error when pull group is in vapor phase

[Dan Gil]

Hi,

I am trying to calculate the adsorption free energy of a molecule onto
water. I want to use umbrella sampling to obtain the free energy profile as
a function of distance normal to a water surface.

I am getting LINCS error when my molecule is in the vapor phase. The error
messages indicate large deviations from the constraints only with the
molecule of interest, and nothing from the waters.

I am using all-bonds constraints.

How should I resolve this problem?

Best Regards,

Dan
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Re: [gmx-users] trr file

[Dan Gil]

Hi Rita,

How long did your simulation run? If it happens to be very long and you do
not want to run the simulation again, perhaps you can try analyzing it in
pieces.

Use trjconv with -b and -e options to extract small pieces of the .trr file
at a time. Analyze the small pieces, delete the .xtc file, and use trjconv
again to get the next piece from .trr.

Dan

On Sat, Oct 15, 2016 at 6:43 AM, Diana Lousa  wrote:

> Hi Rita,
>
> If none of this works, you can try a to do a rerun (run mdrun with the flag
> -rerun). You can provide a new mdp where you can tell gromacs to write an
> xtc with the frequency output that you want (using a lower frequency will
> generate a smaller xtc file)
>
> Good work!
>
> On Sat, Oct 15, 2016 at 6:37 AM, tasneem kausar  >
> wrote:
>
> > Hi
> > I think you can try analysis in more than one step by using -b and -e
> > option of trjconv.
> >
> > On Fri, Oct 14, 2016 at 5:59 PM, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > Prevention is the best medicine - ask google about reducing GROMACS
> > > trajectory storage volume :-)
> > >
> > > Mark
> > >
> > > On Fri, Oct 14, 2016 at 1:20 PM Nuno Azoia  wrote:
> > >
> > > > Have you tried the option -split?
> > > > I never tried, and I don't know if it will solve your problem, but
> give
> > > it
> > > > a try.
> > > >
> > > >
> > > > On Fri, Oct 14, 2016 at 11:34 AM, Rita Paiva Melo <
> > > > ritam...@ctn.tecnico.ulisboa.pt> wrote:
> > > >
> > > > > Hello,
> > > > >
> > > > > Thank you for your suggestions. I have already tried run trjconv
> but,
> > > as
> > > > > trajectory is heavy and server is full, out of memory error appears
> > and
> > > > > analysis tool crash.
> > > > >
> > > > > Best,
> > > > > Rita.
> > > > >
> > > > > -Original Message-
> > > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> > > > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of
> Nuno
> > > > Azoia
> > > > > Sent: 14 de outubro de 2016 11:19
> > > > > To: gmx-us...@gromacs.org
> > > > > Subject: Re: [gmx-users] trr file
> > > > >
> > > > > Hello Rita,
> > > > >
> > > > > I think the answer is trjconv. Try to convert it to xtc, reduce the
> > > > number
> > > > > of frames (with dt or skip), or reduce the components on the
> > > trajectory.
> > > > If
> > > > > you don't need solvent for the calculations you can create a
> > trajectory
> > > > > without it. Removing the solvent and convert it to xtc should have
> a
> > > > great
> > > > > impact in file size.
> > > > >
> > > > > Nuno Azoia
> > > > >
> > > > > On Fri, Oct 14, 2016 at 11:04 AM, Rita Paiva Melo <
> > > > > ritam...@ctn.tecnico.ulisboa.pt> wrote:
> > > > >
> > > > > > Dear all,
> > > > > >
> > > > > > Probably a rookie question but anyone knows how to reduce
> > trajectory
> > > > > > volume file to be analyzed (I have already tried trjconv)? I
> have a
> > > > > > trr file with  167 GB and analysis tools crash.
> > > > > >
> > > > > > Thanks,
> > > > > > Rita.
> > > > > >
> > > > > > --
> > > > > > 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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> > > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_
> gmx-users
> > > or
> > > > > > send a mail to gmx-users-requ...@gromacs.org.
> > > > > >
> > > > > --
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> > > > > --
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> > > > >
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Re: [gmx-users] How to make a program run on the trajectory

[Dan Gil]

Hi Prasun,

Does your question have to do with reading the .trr format?

If you want, you could convert it into a friendlier format such as .gro.
Use gromacs trjconv to convert from .trr to .gro format.

Best Regards,

Dan

On Saturday, September 17, 2016, João Henriques <
joao.henriques.32...@gmail.com> wrote:

> Dear Prasun,
>
> I am genuinely puzzled by your email. If taken literally, I'd have to
> assume that you are stating that you don't know how to feed the trajectory
> file as an argument to your programs, but that doesn't make any sense,
> given that you explicitly say that you coded the programs yourself. If you
> can code tools to run over binary files, such trivial matter can't be the
> problem here...
>
> Therefore, could you please state more specifically what is it that you
> can't accomplish? Please be more verbose as well, it should help.
>
> Thank you,
> João
>
> On Fri, Sep 16, 2016 at 8:23 PM, prasun kumar  > wrote:
>
> > Hello
> >
> > I have written some programs in Fortran and PERL.
> > Now I want to make them run on a trajectory file (.trr).
> > Can some body guide me for the same. I believe that it must be available
> on
> > net. However, I was not able to find so.
> >
> > Thanx in advance.
> >
> > Regards
> > Prasun
> >
> > PRASUN (ASHOKA)
> > Desire + stability = Resolution
> > Resolution + Hard work = Success
> > --
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[gmx-users] Force-Field for Ketals

[Dan Gil]

Hi,

I want to model a linear compound that has a ketal component.

While building the OPLSAA topology (.itp) file for this molecule I ran into
not having the C-C-C angle parameterized in -O-(CH3)2C-O-. I have spent
some time looking for a different force field that may have this entire
molecule, without success. Does anyone know of a force field that does? Or
does OPLSAA actually contain one, and I miss interpreted something?

Best Regards,

Dan
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Re: [gmx-users] Help with MD of water

[Dan Gil]

Hi,

There is a method in gromacs to insert water molecules into a box of size
defined by you. Depending on the version of gromacs you have, it will be
something like gmx insert-molecules.

Dan

On Tuesday, August 9, 2016, Omamuyovwi Akemu 
wrote:

> Dear Gromacs Users,
> I will like to do a molecular dynamics simulation of water in gromacs.
> Thereafter obtain thermodynamics observable like potential energy and well
> as structural and dynamics properties of the system.
>
> However, I kindly request for help with the topology file (.top) and
> molecular structure file (.gro) or a guide to kick off the simulation.
> I will really appreciate any comment.Thank you.
> Jolayemi Omamuyovwi RitaResearch Student,University of Benin,Nigeria.
> Sent from Yahoo Mail on Android
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Re: [gmx-users] (no subject)

[Dan Gil]

Hi,

On gromacs 4.6, the use of g_dist explicitly states "the molecule in the
input trajectory should be whole (e.g. by preprocessing with trjconv
 -pbc) or a
matching topology should be provided."
If you want to calculate the distance between the center of mass (COM) of
two groups of residues, you need to have the mass of the residues. I
imagine that you are having issues because your trajectory isn't whole. Do
you at least have the masses of the groups you are interested in? Writing
your own code to calculate the distance might be an easy solution.

On Tue, Aug 16, 2016 at 7:08 AM, Shubham Sehrawet <
shubham.cristia...@gmail.com> wrote:

> Dear users
>
> I have been trying to find distance between the centroids of two groups of
> residues. I have a trajectory file that was created on some other
> simulating platform. Therefore, I do not have the run input file (tpr) and
> I am not able to perform the analysis.
> Can you please suggest me some way to tackle the problem.
>
> Thank you
> Shubham
> --
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Re: [gmx-users] umbrella sampling for determining interfacial energy

[Dan Gil]

Hi, this is a good coincidence, but I think I do something very similar to
what you just described.

I use umbrella sampling to estimate the free energy profile as a function
of distance from a liquid-vapor interface. Then, the free energy cost of
adsorption to the interface can be approximated. I can imagine that it
should work just as well with liquid-solid interfaces.

I found these references helpful.

A. M. Ferrenberg and R. H. Swendsen, Phys. Rev. Lett. 63, 1195 (1989).
 http://dx.doi.org/10.1103/PhysRevLett.63.1195
- P.-C. Li and D. E. Makarov, J. Phys. Chem. B 108, 745 (2004).
 http://dx.doi.org/10.1021/jp0363895

On Thu, Aug 11, 2016 at 2:58 PM, Ray Chao  wrote:

> Hi, gmx users,
>
> I am doing research on liquid-solid interface. I see that the umbrella
> sampling can be used to calculate the binding energy, so I am wondering if
> the umbrella sampling can be used to calculate the interfacial free energy
> between different liquids and solids by pulling the liquid towards the
> solid surface. If not, is there any other way to do this in Gromacs?
>
> Thank you very much.
> --
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Re: [gmx-users] radial-density profile and radial distribution curve for water-CNT system

[Dan Gil]

The manual for version 4.6 is available online. The analysis command you
want is g_rdf, for version 4.6. g_rdf plots the radial distribution
function, which is what I think you are calling radial distribution curve.
The manual has a nice explanation of it so please check it out. The radial
density profile, must mean the distribution function that is not normalized
by dividing by the local density (the limit as r approaches infinity is not
unity).

Dan

On Thu, Aug 11, 2016 at 1:20 AM, Ankita Joshi 
wrote:

> Dear Gromacs Users,
>
> I am working on a water- double walled carbon nanotube system. After the
> completion of simulation using Gromacs 4.6.5, it was found that the water
> molecules are present inside the double walled carbon nanotube as well as
> in the bulk of the system. I want to plot the radial density profile and
> the radial distribution curve. Can anyone tell me how to plot these curves
> and the difference between them?
>
>
> Thanks,
> Ankita
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Re: [gmx-users] Upgrading to Gromacs/5.1 - Problems with Umbrella Sampling

[Dan Gil]

I see. Now I understand what "pull-start" option means. Changing that
option made it work! Thank you Justin.

On Mon, Aug 8, 2016 at 6:04 AM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 8/7/16 1:21 PM, Dan Gil wrote:
>
>> In Gromacs/4.6, I used init to define the distance from the solvent COM
>> that the solute should be pulled to. Has it changed for Gromacs/5.1?
>>
>>
> Nothing has changed except (1) syntax and (2) the ability to now apply
> multiple restraints simultaneously.  Everything with respect to setting
> references distances, etc. is functionally the same.
>
> What should I do if I want to pull the solute to [0, 1, 2, 3] nm away from
>> the solvent COM?
>>
>>
> You can do that with "pull-coord1-init = X" and "pull-start = no" but this
> is setting the reference distance to X, so if the initial coordinates are
> far from that value, you're imparting a large force to start, which may not
> be stable. It may work, but those initial steps are going to be dicey.
>
> -Justin
>
>
> Here is the section I think you are talking about also:
>> Pull group 1 'a_Cooh' has 1 atoms
>> Pull group 2 'SOL' has 5715 atoms
>> Number of degrees of freedom in T-Coupling group System is 44530.00
>> Pull group  natoms  pbc atom  distance at start  reference at t=0
>>1 1 0
>>    2      5715 18540   3.011 nm  3.011 nm
>>
>> On Sun, Aug 7, 2016 at 1:15 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>>
>>
>>>
>>> On 8/7/16 1:13 PM, Dan Gil wrote:
>>>
>>> Hi,
>>>>
>>>> I've made the change you suggested. The output file pullx.xvg has
>>>> changed
>>>> from something like:
>>>>
>>>> @ s0 legend "1"
>>>> @ s1 legend "1 dZ"
>>>> 0. 3.01072 3.01072
>>>> 0.2000 2.98101 2.98101
>>>> 0.4000 2.94186 2.94186
>>>> 0.6000 2.95316 2.95316
>>>>
>>>> to this:
>>>>
>>>> @ s0 legend "1"
>>>> @ s1 legend "1 dZ"
>>>> 0. 3.01072 -3.01072
>>>> 0.2000 2.98101 -2.98101
>>>> 0.4000 2.94186 -2.94186
>>>> 0.6000 2.95316 -2.95316
>>>>
>>>> The second column should the COM of the solvent, the third column should
>>>> be
>>>> the position of a_Cooh. I am still wondering what is going on, since
>>>> init
>>>> =
>>>> 0.
>>>>
>>>>
>>>>
>>>> pull-coord1-start= yes
>>>
>>> grompp tells you what the reference distance is at the start; check to
>>> make sure this is what you want it to be.  pull-coord1-init = 0 means
>>> "don't add anything extra to what is already there."
>>>
>>>
>>> -Justin
>>>
>>>
>>> On Sun, Aug 7, 2016 at 11:37 AM, Justin Lemkul <jalem...@vt.edu> wrote:
>>>>
>>>>
>>>>
>>>>> On 8/7/16 11:35 AM, Dan Gil wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>>>
>>>>>> The pullx.xvg file is returning the coordinates of the solvent, and
>>>>>> not
>>>>>> the
>>>>>> solute (a_Cooh) as I want.
>>>>>> The solute is being pulled in a coordinate other than Z, although I
>>>>>> specify:
>>>>>>  pull-coord1-dim =N N Y
>>>>>> What is going on here?
>>>>>>
>>>>>>
>>>>>> Swap
>>>>>>
>>>>> pull-coord1-groups = 1 2
>>>>> for
>>>>> pull-coord1-groups = 2 1
>>>>>
>>>>> to do what you had been doing in the previous version.  You've inverted
>>>>> the pull vector relative to the 4.6 settings.
>>>>>
>>>>> -Justin
>>>>>
>>>>>
>>>>> On Sun, Aug 7, 2016 at 7:20 AM, Billy Williams-Noonan <
>>>>>
>>>>> billy.williams-noo...@monash.edu> wrote:
>>>>>>
>>>>>> Hi All,
>>>>>>
>>>>>>
>>>>>>> I'm having a similar problem and wouldn't mind some advice either.  I
>>>>>>> am
>>>>>>> getting LINCS warnings on one cluster that I run my sampling on, but
>>>>>>> the
>>>>>>> pull-code works 

Re: [gmx-users] Upgrading to Gromacs/5.1 - Problems with Umbrella Sampling

[Dan Gil]

In Gromacs/4.6, I used init to define the distance from the solvent COM
that the solute should be pulled to. Has it changed for Gromacs/5.1?

What should I do if I want to pull the solute to [0, 1, 2, 3] nm away from
the solvent COM?

Here is the section I think you are talking about also:
Pull group 1 'a_Cooh' has 1 atoms
Pull group 2 'SOL' has 5715 atoms
Number of degrees of freedom in T-Coupling group System is 44530.00
Pull group  natoms  pbc atom  distance at start  reference at t=0
   1 1 0
   2  5715 18540   3.011 nm  3.011 nm

On Sun, Aug 7, 2016 at 1:15 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 8/7/16 1:13 PM, Dan Gil wrote:
>
>> Hi,
>>
>> I've made the change you suggested. The output file pullx.xvg has changed
>> from something like:
>>
>> @ s0 legend "1"
>> @ s1 legend "1 dZ"
>> 0. 3.01072 3.01072
>> 0.2000 2.98101 2.98101
>> 0.4000 2.94186 2.94186
>> 0.6000 2.95316 2.95316
>>
>> to this:
>>
>> @ s0 legend "1"
>> @ s1 legend "1 dZ"
>> 0. 3.01072 -3.01072
>> 0.2000 2.98101 -2.98101
>> 0.4000 2.94186 -2.94186
>> 0.6000 2.95316 -2.95316
>>
>> The second column should the COM of the solvent, the third column should
>> be
>> the position of a_Cooh. I am still wondering what is going on, since init
>> =
>> 0.
>>
>>
>>
> pull-coord1-start= yes
>
> grompp tells you what the reference distance is at the start; check to
> make sure this is what you want it to be.  pull-coord1-init = 0 means
> "don't add anything extra to what is already there."
>
>
> -Justin
>
>
>> On Sun, Aug 7, 2016 at 11:37 AM, Justin Lemkul <jalem...@vt.edu> wrote:
>>
>>
>>>
>>> On 8/7/16 11:35 AM, Dan Gil wrote:
>>>
>>> Hi,
>>>>
>>>> The pullx.xvg file is returning the coordinates of the solvent, and not
>>>> the
>>>> solute (a_Cooh) as I want.
>>>> The solute is being pulled in a coordinate other than Z, although I
>>>> specify:
>>>>  pull-coord1-dim =N N Y
>>>> What is going on here?
>>>>
>>>>
>>>> Swap
>>> pull-coord1-groups = 1 2
>>> for
>>> pull-coord1-groups = 2 1
>>>
>>> to do what you had been doing in the previous version.  You've inverted
>>> the pull vector relative to the 4.6 settings.
>>>
>>> -Justin
>>>
>>>
>>> On Sun, Aug 7, 2016 at 7:20 AM, Billy Williams-Noonan <
>>>
>>>> billy.williams-noo...@monash.edu> wrote:
>>>>
>>>> Hi All,
>>>>
>>>>>
>>>>> I'm having a similar problem and wouldn't mind some advice either.  I
>>>>> am
>>>>> getting LINCS warnings on one cluster that I run my sampling on, but
>>>>> the
>>>>> pull-code works fine on other clusters we have access to, which is
>>>>> making
>>>>> me doubt the entire process.
>>>>>
>>>>> Best regards,
>>>>>
>>>>> Billy
>>>>>
>>>>> On 7 August 2016 at 03:34, Dan Gil <dgil...@gmail.com> wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>>>
>>>>>> I am changing from Gromacs/4.6 to Gromacs/5.1, and I have a piece of
>>>>>> .mdp
>>>>>> file that I am confused with.
>>>>>>
>>>>>> I am pulling an atom of solute, indexed a_Cooh, towards the COM of
>>>>>>
>>>>>> solvent.
>>>>>
>>>>> This is a slab geometry, with the plane normal to the z-axis direction.
>>>>>>
>>>>>> My
>>>>>
>>>>> output (pullx.xvg) should contain the deltaZ value between the solute Z
>>>>>> coordinate and solvent COM z coordinate. With my current Gromacs/5.1
>>>>>> attempt, I don't think I am getting the correct results.
>>>>>>
>>>>>> On Gromacs/4.6:
>>>>>> pull =umbrella
>>>>>> pull_geometry =distance
>>>>>> pull_dim =N N Y
>>>>>> pull_init1 =0
>>>>>> pull_k1 =100
>>>>>> pull_nstxout =100
>>>>>> pull_group0 =SOL
>>>>>> pull_group1 =a_Cooh
>>>>>>
>>>>>> My attempt with Gromacs/5.1:
>&

Re: [gmx-users] Upgrading to Gromacs/5.1 - Problems with Umbrella Sampling

[Dan Gil]

Hi,

I've made the change you suggested. The output file pullx.xvg has changed
from something like:

@ s0 legend "1"
@ s1 legend "1 dZ"
0. 3.01072 3.01072
0.2000 2.98101 2.98101
0.4000 2.94186 2.94186
0.6000 2.95316 2.95316

to this:

@ s0 legend "1"
@ s1 legend "1 dZ"
0. 3.01072 -3.01072
0.2000 2.98101 -2.98101
0.4000 2.94186 -2.94186
0.6000 2.95316 -2.95316

The second column should the COM of the solvent, the third column should be
the position of a_Cooh. I am still wondering what is going on, since init =
0.



On Sun, Aug 7, 2016 at 11:37 AM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 8/7/16 11:35 AM, Dan Gil wrote:
>
>> Hi,
>>
>> The pullx.xvg file is returning the coordinates of the solvent, and not
>> the
>> solute (a_Cooh) as I want.
>> The solute is being pulled in a coordinate other than Z, although I
>> specify:
>>  pull-coord1-dim =N N Y
>> What is going on here?
>>
>>
> Swap
> pull-coord1-groups = 1 2
> for
> pull-coord1-groups = 2 1
>
> to do what you had been doing in the previous version.  You've inverted
> the pull vector relative to the 4.6 settings.
>
> -Justin
>
>
> On Sun, Aug 7, 2016 at 7:20 AM, Billy Williams-Noonan <
>> billy.williams-noo...@monash.edu> wrote:
>>
>> Hi All,
>>>
>>> I'm having a similar problem and wouldn't mind some advice either.  I am
>>> getting LINCS warnings on one cluster that I run my sampling on, but the
>>> pull-code works fine on other clusters we have access to, which is making
>>> me doubt the entire process.
>>>
>>> Best regards,
>>>
>>> Billy
>>>
>>> On 7 August 2016 at 03:34, Dan Gil <dgil...@gmail.com> wrote:
>>>
>>> Hi,
>>>>
>>>> I am changing from Gromacs/4.6 to Gromacs/5.1, and I have a piece of
>>>> .mdp
>>>> file that I am confused with.
>>>>
>>>> I am pulling an atom of solute, indexed a_Cooh, towards the COM of
>>>>
>>> solvent.
>>>
>>>> This is a slab geometry, with the plane normal to the z-axis direction.
>>>>
>>> My
>>>
>>>> output (pullx.xvg) should contain the deltaZ value between the solute Z
>>>> coordinate and solvent COM z coordinate. With my current Gromacs/5.1
>>>> attempt, I don't think I am getting the correct results.
>>>>
>>>> On Gromacs/4.6:
>>>> pull =umbrella
>>>> pull_geometry =distance
>>>> pull_dim =N N Y
>>>> pull_init1 =0
>>>> pull_k1 =100
>>>> pull_nstxout =100
>>>> pull_group0 =SOL
>>>> pull_group1 =a_Cooh
>>>>
>>>> My attempt with Gromacs/5.1:
>>>> pull =yes
>>>> pull-ngroups= 2
>>>> pull-ncoords= 1
>>>> pull-group1-name = a_Cooh
>>>> pull-group2-name = SOL
>>>> pull-coord1-type  = umbrella
>>>> pull-coord1-geometry =distance
>>>> pull-coord1-groups = 1 2
>>>> pull-coord1-dim =N N Y
>>>> pull-coord1-start= yes
>>>> pull-coord1-init  =0
>>>> pull-coord1-k=1000
>>>> pull-print-components = yes
>>>> pull_nstxout =100
>>>>
>>>> Best Regards,
>>>>
>>>> Dan
>>>> --
>>>> 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.
>>>>
>>>>
>>>
>>>
>>> --
>>> Billy Noonan*|*PhD Student*|*Bsci ( *Adv* ), IA Hon
>>>
>>> *LinkedIn Profile
>>> <http://www.linkedin.com/profile/preview?locale=en_US;
>>> trk=prof-0-sb-preview-primary-button>
>>> **|*   +61420 382 557
>>>
>>> Monash Institute for Pharmaceutical Sciences ( *MIPS* )
>>> Royal Parade, Parkville, 3052
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>>> * Please search the archive at http://www.gromacs.org/
>>> Support/Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs

Re: [gmx-users] Upgrading to Gromacs/5.1 - Problems with Umbrella Sampling

[Dan Gil]

Hi,

The pullx.xvg file is returning the coordinates of the solvent, and not the
solute (a_Cooh) as I want.
The solute is being pulled in a coordinate other than Z, although I specify:
 pull-coord1-dim =N N Y
What is going on here?

On Sun, Aug 7, 2016 at 7:20 AM, Billy Williams-Noonan <
billy.williams-noo...@monash.edu> wrote:

> Hi All,
>
> I'm having a similar problem and wouldn't mind some advice either.  I am
> getting LINCS warnings on one cluster that I run my sampling on, but the
> pull-code works fine on other clusters we have access to, which is making
> me doubt the entire process.
>
> Best regards,
>
> Billy
>
> On 7 August 2016 at 03:34, Dan Gil <dgil...@gmail.com> wrote:
>
> > Hi,
> >
> > I am changing from Gromacs/4.6 to Gromacs/5.1, and I have a piece of .mdp
> > file that I am confused with.
> >
> > I am pulling an atom of solute, indexed a_Cooh, towards the COM of
> solvent.
> > This is a slab geometry, with the plane normal to the z-axis direction.
> My
> > output (pullx.xvg) should contain the deltaZ value between the solute Z
> > coordinate and solvent COM z coordinate. With my current Gromacs/5.1
> > attempt, I don't think I am getting the correct results.
> >
> > On Gromacs/4.6:
> > pull =umbrella
> > pull_geometry =distance
> > pull_dim =N N Y
> > pull_init1 =0
> > pull_k1 =100
> > pull_nstxout =100
> > pull_group0 =SOL
> > pull_group1 =a_Cooh
> >
> > My attempt with Gromacs/5.1:
> > pull =yes
> > pull-ngroups= 2
> > pull-ncoords= 1
> > pull-group1-name = a_Cooh
> > pull-group2-name = SOL
> > pull-coord1-type  = umbrella
> > pull-coord1-geometry =distance
> > pull-coord1-groups = 1 2
> > pull-coord1-dim =N N Y
> > pull-coord1-start= yes
> > pull-coord1-init  =0
> > pull-coord1-k=1000
> > pull-print-components = yes
> > pull_nstxout =100
> >
> > Best Regards,
> >
> > Dan
> > --
> > 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.
> >
>
>
>
> --
> Billy Noonan*|*PhD Student*|*Bsci ( *Adv* ), IA Hon
>
> *LinkedIn Profile
> <http://www.linkedin.com/profile/preview?locale=en_US;
> trk=prof-0-sb-preview-primary-button>
> **|*   +61420 382 557
>
> Monash Institute for Pharmaceutical Sciences ( *MIPS* )
> Royal Parade, Parkville, 3052
> --
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> Support/Mailing_Lists/GMX-Users_List before posting!
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>
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> send a mail to gmx-users-requ...@gromacs.org.
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[gmx-users] Upgrading to Gromacs/5.1 - Problems with Umbrella Sampling

[Dan Gil]

Hi,

I am changing from Gromacs/4.6 to Gromacs/5.1, and I have a piece of .mdp
file that I am confused with.

I am pulling an atom of solute, indexed a_Cooh, towards the COM of solvent.
This is a slab geometry, with the plane normal to the z-axis direction. My
output (pullx.xvg) should contain the deltaZ value between the solute Z
coordinate and solvent COM z coordinate. With my current Gromacs/5.1
attempt, I don't think I am getting the correct results.

On Gromacs/4.6:
pull =umbrella
pull_geometry =distance
pull_dim =N N Y
pull_init1 =0
pull_k1 =100
pull_nstxout =100
pull_group0 =SOL
pull_group1 =a_Cooh

My attempt with Gromacs/5.1:
pull =yes
pull-ngroups= 2
pull-ncoords= 1
pull-group1-name = a_Cooh
pull-group2-name = SOL
pull-coord1-type  = umbrella
pull-coord1-geometry =distance
pull-coord1-groups = 1 2
pull-coord1-dim =N N Y
pull-coord1-start= yes
pull-coord1-init  =0
pull-coord1-k=1000
pull-print-components = yes
pull_nstxout =100

Best Regards,

Dan
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[gmx-users] Questions about OPLS force fields

[Dan Gil]

Hi,

I am creating a topology for a molecule that is not defined by OPLS. I have
some questions that I want to ask:

1. What is bondtype and ptype in ffnonbonded.itp?

2. If I use the Buckingham potential to define nonbonded interactions
between atom A and atom B, does this potential apply to all A and B atoms
in the system? For example, I have a molecule that has oxygen atoms. I
define the Buckingham potential of oxygen atoms with various other atoms in
an .itp file of this molecule. If I have water molecules as the solvent,
how will the .itp file affect the interactions between water molecules?

2. When do I need [ pairs ] directive, and when do I not? If I use the
buckingham potential, do I not need it?

Best Regards,

Dan
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Re: [gmx-users] Radial Distribution Function - is there symmetry?

[Dan Gil]

Thanks for the great explanation!

On Wed, Jun 22, 2016 at 5:14 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> In general it won't be. Take a  pure NaCL cubic crystal - G(r)_NaCl is the
> same as G(r)_ClNa by symmetry. Now take an identical crystal with any
> single Cl replaced by Br (or half of them, or whatever) and assume all the
> lattice dimensions remain the same. G(r)_ClNa is the same as before, but
> G_(r)_NaCl cannot be the same as before. Or try it on your favourite
> simulation trajectory :-)
>
> Mark
>
> On Wed, Jun 22, 2016 at 11:06 PM Dan Gil <dgil...@gmail.com> wrote:
>
> > Hi,
> >
> > I am calculating the radial distribution function, and I am wondering if
> > G(r)_jk = G(r)_kj. I always assumed that it was, and when I looked at the
> > equation it seemed to be the case. But I am having trouble finding
> sources
> > that state G(r)_jk = G(r)_kj, therefore I wanted to ask for your opinion.
> >
> > Best Regards,
> >
> > Dan
> > --
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[gmx-users] Radial Distribution Function - is there symmetry?

[Dan Gil]

Hi,

I am calculating the radial distribution function, and I am wondering if
G(r)_jk = G(r)_kj. I always assumed that it was, and when I looked at the
equation it seemed to be the case. But I am having trouble finding sources
that state G(r)_jk = G(r)_kj, therefore I wanted to ask for your opinion.

Best Regards,

Dan
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Re: [gmx-users] Gromacs 5.1 insert-molecules - Generating bad contacts?

[Dan Gil]

You are right!

Thank you.

On Mon, Jun 20, 2016 at 1:00 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 6/20/16 12:04 PM, Dan Gil wrote:
>
>> Hi Mark,
>>
>> I thought about your said, and tried to manage the VDW radi of atoms with
>> the "-radius" option.
>> I believe it scales the known VDW radi values by the number specified by
>> me. So I try:
>> "gmx insert-molecules ... ... -radius 1.2"
>>
>>  The result is still the same, I get segmentation errors because rms goes
>> to nan. I try again with "-radius 1.5" and I am still getting lucky.
>>
>>
> Your interpretation is incorrect.  See the help information, which
> explains:
>
> "A database (vdwradii.dat) of van der Waals
> radii is read by the program, and the resulting radii scaled by -scale. If
> radii are not found in the database, thoseatoms are assigned the
> (pre-scaled)
> distance -radius."
>
> Setting radii that large (over 1 nm) will probably make it hard for
> anything but the first few molecules to be inserted at all.
>
> -Justin
>
> Also, excuse me for creating a new question again. I was subscribed to
>> receive batch emails from the users-list, and I did not know how to
>> respond
>> questions in that mode.
>>
>> Thanks,
>>
>> Dan
>>
>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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Re: [gmx-users] Gromacs 5.1 insert-molecules - Generating bad contacts?

[Dan Gil]

Hi Mark,

I thought about your said, and tried to manage the VDW radi of atoms with
the "-radius" option.
I believe it scales the known VDW radi values by the number specified by
me. So I try:
"gmx insert-molecules ... ... -radius 1.2"

 The result is still the same, I get segmentation errors because rms goes
to nan. I try again with "-radius 1.5" and I am still getting lucky.

Also, excuse me for creating a new question again. I was subscribed to
receive batch emails from the users-list, and I did not know how to respond
questions in that mode.

Thanks,

Dan
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[gmx-users] Gromacs 5.1 - trouble with insert-molecules

[Dan Gil]

Hi,

I am upgrading from gromacs 4.6 to gromacs 5.1. Gromacs 4.6 had "genbox,"
which I was able to use without a problem.

With gromacs 5.1, I am using insert-molecules to generate my initial
configuration containing water, ethanol, and a lennard-jones particle which
I defined. When I attempt to minimize the energy using "steep", the program
crashes, apparently due to clashes.

Even an initial configuration containing only ethanol atoms will crash as
well.

As an additional side note, I was able to run the program on a personal
computer using single-precision. When I run it with double-precision, it
crashes.

I think that perhaps I am not using insert-molecules correctly, so I will
show you the commands I used.

---
Preconditions: I begin with solute.gro file containing 1 atom. There is
ethanol.gro and water.gro which contains the coordinates of 1 molecules of
ethanol and water, respectively.

First I insert a number of ethanol molecules.
gmx insert-molecules -f solute.gro -ci ethanol.gro -box 6 6 6 -nmol
numberOfEthanols -o out.gro

Then I insert a number of water molecules.
gmx insert-molecules -f out.gro -ci water.gro -box 8 8 8 -nmol
numberOfWaters -o + out2.gro
---

Best Regards,

Dan
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[gmx-users] Gromacs 5.1 insert-molecules - Generating bad contacts?

[Dan Gil]

Hi,

I am upgrading from gromacs 4.6 to gromacs 5.1. Gromacs 4.6 had "genbox,"
which I was able to use without a problem.

With gromacs 5.1, I am using insert-molecules to generate my initial
configuration containing water, ethanol, and a lennard-jones particle which
I defined. When I attempt to minimize the energy using "steep", the program
crashes, apparently due to clashes.

Here is an excerpt of the error right before the program crashes:

Step 19, time 0.038 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms nan, max 0.005299 (between atoms 9321 and 9317)

-

Also another side note, I was able to run the program on a personal
computer using single-precision. When I run it with double-precision, it
crashes.

Best Regards,

Dan
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Re: [gmx-users] Calculating hydrogen bonding density - issues with g_sas?

[Dan Gil]

Is g_sas applicable to more than one molecule at a time?

I have 4500 water molecules in the liquid state. I am using the command:
g_sas -f traj.trr -s topol.tpr -tv volume.xvg


On Tue, Jul 7, 2015 at 10:31 AM, Dan Gil dan.gil9...@gmail.com wrote:

 I am using the default radius of 0.14 nm. In this case, I believe that it
 is consistent. Nevertheless, I have tried using a probe much larger with no
 significant difference in the results.
 The way I am using g_sas is: I have 4500 water molecules. I specified that
 I want the volume of all of them.

 On Tue, Jul 7, 2015 at 10:11 AM, Mark Abraham mark.j.abra...@gmail.com
 wrote:

 Hi,

 Is the radius being used consistent with your assumption?

 Mark

 On Tue, Jul 7, 2015 at 3:58 PM Dan Gil dan.gil9...@gmail.com wrote:

  Hi,
 
  I am using g_hbond to count the number of h-bonds and then g_sas to
  calculate the volume. I want to get the number of hydrogen bonds per
  volume. But I am having issues with g_sas - the volume calculated is
 about
  one half of the expected value. For instance, in a pure water system
 (NVT,
  SPCE, T=300K) periodic in the x and y directions, volume was found to be
  about 60nm^3, whereas I expected 130nm^3.
 
  I would appreciate any advice!
 
  Best,
 
  --
  Dan Gil
  Case Western Reserve University | Class of 2016
  Researcher, Department of Chemical Engineering
  dan.gil9...@gmail.com
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 --
 Dan Gil
 Case Western Reserve University | Class of 2016
 Researcher, Department of Chemical Engineering
 dan.gil9...@gmail.com




-- 
Dan Gil
Case Western Reserve University | Class of 2016
Researcher, Department of Chemical Engineering
dan.gil9...@gmail.com
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[gmx-users] Calculating hydrogen bonding density - issues with g_sas?

[Dan Gil]

Hi,

I am using g_hbond to count the number of h-bonds and then g_sas to
calculate the volume. I want to get the number of hydrogen bonds per
volume. But I am having issues with g_sas - the volume calculated is about
one half of the expected value. For instance, in a pure water system (NVT,
SPCE, T=300K) periodic in the x and y directions, volume was found to be
about 60nm^3, whereas I expected 130nm^3.

I would appreciate any advice!

Best,

-- 
Dan Gil
Case Western Reserve University | Class of 2016
Researcher, Department of Chemical Engineering
dan.gil9...@gmail.com
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Re: [gmx-users] Calculating hydrogen bonding density - issues with g_sas?

[Dan Gil]

I am using the default radius of 0.14 nm. In this case, I believe that it
is consistent. Nevertheless, I have tried using a probe much larger with no
significant difference in the results.
The way I am using g_sas is: I have 4500 water molecules. I specified that
I want the volume of all of them.

On Tue, Jul 7, 2015 at 10:11 AM, Mark Abraham mark.j.abra...@gmail.com
wrote:

 Hi,

 Is the radius being used consistent with your assumption?

 Mark

 On Tue, Jul 7, 2015 at 3:58 PM Dan Gil dan.gil9...@gmail.com wrote:

  Hi,
 
  I am using g_hbond to count the number of h-bonds and then g_sas to
  calculate the volume. I want to get the number of hydrogen bonds per
  volume. But I am having issues with g_sas - the volume calculated is
 about
  one half of the expected value. For instance, in a pure water system
 (NVT,
  SPCE, T=300K) periodic in the x and y directions, volume was found to be
  about 60nm^3, whereas I expected 130nm^3.
 
  I would appreciate any advice!
 
  Best,
 
  --
  Dan Gil
  Case Western Reserve University | Class of 2016
  Researcher, Department of Chemical Engineering
  dan.gil9...@gmail.com
  --
  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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-- 
Dan Gil
Case Western Reserve University | Class of 2016
Researcher, Department of Chemical Engineering
dan.gil9...@gmail.com
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