[gmx-users] sep and tpo
Mehreen Jan
mehreen_jan1990 at yahoo.com
Thu Feb 4 15:16:35 CET 2016
i just make changes in gromacs 4.5.5>share>top>gromacs43a1.ff
step of command i performed :
> pdb2gmx -f protein.pdb -p protein.top -o protein.gro
>
> from list select the force field
> select 9 which is GROMOS96 43a1 force field
> select the water model:
> 1 SPC simple point charge
> then error message
> fatal error:
> residue SEP /TPO not found in residue topology database
--------------------------------------------
On Thu, 4/2/16, gromacs.org_gmx-users-request at maillist.sys.kth.se <gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
Subject: gromacs.org_gmx-users Digest, Vol 142, Issue 24
To: gromacs.org_gmx-users at maillist.sys.kth.se
Received: Thursday, 4 February, 2016, 5:53 PM
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Today's Topics:
1. Wall potential different results for
12-6 and table
(Sudharsan Pandiyan)
2. Re: Fwd: FW: PME settings in free
energy calculations
(Dries Van Rompaey)
3. Re: C_v and Temperature (Alexander
Alexander)
4. Re: trjconv options? (Justin Lemkul)
5. Re: $GMXLIB or the working directory
(Justin Lemkul)
----------------------------------------------------------------------
Message: 1
Date: Thu, 4 Feb 2016 11:34:43 +0000
From: Sudharsan Pandiyan <sudharsan.pandiyan at chem.kuleuven.be>
To: "gmx-users at gromacs.org"
<gmx-users at gromacs.org>
Subject: [gmx-users] Wall potential different results for
12-6 and
table
Message-ID:
<4A1AE85DA03CB144A9DE9FCDD245E17D218FC763 at ICTS-S-MBX7.luna.kuleuven.be>
Content-Type: text/plain; charset="iso-8859-1"
Dear Gmx users,
I am trying to simulate a wall potential using tabulated
potentials option. But it gives different potential values
when compared to the 12-6 option when I use same sigma and
epsilon values that are used to build the table. I intend to
modify my table potential later to more detailed form so I
have to make sure that it produces correct result. But my
check seems to show that there is a difference between using
12-6 and tabulated potentials for wall interaction. Could
any one of you what is the difference and how can I get the
correct potential for tabulated form?
PS: In the manual, its written that both 9-3 and 10-4 are
integrated over the surface area and 12-6 potential was
applied directly with the z-distance. But how the tabulated
potential is represented? (section 7.3.20)
Sincerely,
Sudharsan
------------------------------
Message: 2
Date: Thu, 4 Feb 2016 12:59:34 +0100
From: Dries Van Rompaey <dries.vanrompaey at gmail.com>
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] Fwd: FW: PME settings in free
energy
calculations
Message-ID:
<CAJefogcLAspn_6PHRiYdimcxXEDo4saQE2BQLFarcAmqopci+g at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi,
I'm using PME with the default Potential-Shift-Verlet
modifier. If I'm
interpreting the manual and comments on the mailinglist
correctly, the
settings for rcoulomb-switch shouldn't affect this and
PME-switching
shouldn't be necessary (although there seems to have been
some discussion
about this, https://gerrit.gromacs.org/#/c/2220/).
Has a consensus been
reached elsewhere?
Current nonbonded settings in my .mdp files are:
; Electrostatics
coulombtype
= PME
rcoulomb
= 1.0
; van der Waals
vdwtype
= cutoff
vdw-modifier =
Potential-switch
rvdw-switch
= 0.9
rvdw
= 1.0
; Apply long range dispersion corrections for Energy and
Pressure
DispCorr
= EnerPres
; Spacing for the PME/PPPM FFT grid
fourierspacing
= 0.08
; EWALD/PME/PPPM parameters
pme_order
= 6
ewald_rtol
= 1e-06
epsilon_surface = 0
Thanks in advance,
Dries
On 4 February 2016 at 00:56, Michael Shirts <mrshirts at gmail.com>
wrote:
> Hi, Dries-
>
> Questions like this are probably best answered on the
gmx-users list.
> I can't say too much for the Verlet scheme -- I know
that it was
> relatively recently adapted for free energies, and
there may be some
> combinations of settings that could give unanticipated
results.
>
> Pretty much all of our experience about nonbonded
calculations and
> free energies is collected in the following paper:
> http://pubs.acs.org/doi/abs/10.1021/ct4005068. We used
the group
> cutoff scheme since that was the only one that was
supported in
> GROMACS at the time.
>
> Since you haven't sent any files, it's hard to tell
what is actually
> going on. The one thing that has a tendency to happen
with the more
> recent update schemes is if you set a potential
modifier that is a
> switch, but don't set the distance the switch starts
at, then it is
> automatically set to zero. Check the mdout.mdp to
see if this is
> happening.
>
> > From: Van Rompaey Dries <Dries.VanRompaey at uantwerpen.be>
> Date: Wednesday, February 3, 2016 at 12:34 PM
> To: Michael Shirts <michael.shirts at colorado.edu>
> Subject: PME settings in free energy calculations
>
> Dear prof. Shirts,
>
> I'm currently trying to figure out the PME settings for
a relative
> free binding energy simulation I'm working on. I took
the parameters
> from Matteo Aldeghi's
> paper(
> http://pubs.rsc.org/en/content/articlelanding/2015/sc/c5sc02678d#!divAbstract
> )
> as a starting point (adapted for the Verlet scheme by
scaling the
> fourierspacing to 0.08 and setting coulomb = rvdw =
1.0). I then tried
> to verify these settings by comparing a single point
energy
> calculation with these settings and one with very long
coulomb cutoffs
> as recommended on alchemistry.org.
>
> Unfortunately, I can't seem to get this quite right.
I'm getting
> differences in the hundreds of kj/mol, leading me to
suspect I'm doing
> something wrong. I'm calculating the energy values by
extracting
> CoulombSR and Coul-recip from the energy.xvg files.
I've tried
> calculating the energy with coulomb cutoffs at 3 nm and
10 nm, but
> agreement with the PME results remains rather poor.
David Mobley
> mentioned you performed extensive research on this
topic, and I'm
> hoping you could point me in the right direction.
>
> Thanks in advance,
>
> Dries
>
>
>
> ~~~~~~~~~~~~~~~~
> Michael Shirts
> Associate Professor
> michael.shirts at colorado.edu
> Phone: (303) 735-7860
> Office: JSCBB D317
> Department of Chemical and Biological Engineering
> University of Colorado Boulder
> --
> 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-request at gromacs.org.
>
------------------------------
Message: 3
Date: Thu, 4 Feb 2016 13:27:36 +0100
From: Alexander Alexander <alexanderwien2k at gmail.com>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] C_v and Temperature
Message-ID:
<CAEDv6u6oBgrFs7RHVHWkcSiS9D6xL-9FZ376uWSKOBp0KkXn_A at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Thank you for your response.
I am trying to calculate the heat capacity at constant
volume for a crystal
solid in different temperature; below are what "gmx energy
-fluct_props
..." gives me in 4 different temperatures:
T = 29.9 Cv = 24.4681 J/mol K
T = 99.9 Cv = 24.6643 J/mol K
T = 297.9 Cv = 24.4926 J/mol K
T = 799.9 Cv = 24.5054 J/mol K
And "gmx dos" gives something around "Heat capacity
0.000683396 (J/mol K)"
as quantum correction for all the simulation temperature I
have tried.
The result for the two last temperature is fascinating and
agree well with
my DFPT and phonon calculations as well as all the heat
capacity laws in
higher temperatures.
Also, I was expecting that the C_v reduces to around 2 or 3
J/mol K in
lower temperatures, but I do not know why the C_v in lower
temperature is
the same as higher temperature, although I had a well
prepared and
converged calculations. So, I would be so thankful if one
could comment on
this.
By the way, this is what I have in my dos.log file.
----------------------------
System = "A3B crystal Solid"
Nmol = 43904
Natom = 43904
dt = 0.2 ps
tmass = 2.05132e+06 amu
V = 415.228 nm^3
rho = 8203.43 g/l
T = 298.15 K
beta = 0.403395 mol/kJ
DoS parameters
Delta = 3.49303e-05
fluidicity = 0.00202656
hard sphere packing fraction = 441.911
hard sphere compressibility = 1.00454
ideal gas entropy = 0.0717008
hard sphere entropy = -0.762789
sigma_HS = 1.99851 nm
DoS0 = 2.3222
Dos2 = 627309
DoSTot = 6.19421
Diffusion coefficient from VACF 0.000169117 10^-5 cm^2/s
Diffusion coefficient from DoS 0.00023386 10^-5 cm^2/s
Heat capacity 0.000623269 J/mol K
------------------------------------------
Best regards,
Alex
On Thu, Feb 4, 2016 at 8:45 AM, David van der Spoel <spoel at xray.bmc.uu.se>
wrote:
> On 03/02/16 23:52, Alexander Alexander wrote:
>
>> Dear Gromacs user,
>>
>> Normally there is a "*ref-t" [K] *in .mdp
file as reference temperature
>> in
>> NVT calculation, in addition, yet another
Temperature must be indicated in
>> "gmx dos *-T* XXX ..." for example in heat capacity
(C_v) calculation with
>> quantum correction. So, I was wondering that which
of these two
>> temperatures is the one that the heat capacity
(C_v) has been calculated
>> in
>> to be reported later?
>>
> To get the simulation temperature run gmx energy
>
>
>> One more question:
>> In C_v calculation, would you please confirm me
that the "gmx dos" would
>> give only the quantum correction for C_v? Not the
total C_v including
>> quantum correction.
>> IF so, then, the Total C_v would be:
>> Total C_v = "gmx energy -nmol -fluct_props" + "gmx
dos -T ..."
>>
> Have you checked the output from gxm dos?
> It describes everything in quite some detail.
>
>
>> Thank you so much.
>>
>> Cheers,
>>
>> Alex
>>
>>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:
+46184714205.
> spoel at xray.bmc.uu.se
http://folding.bmc.uu.se
> --
> 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
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or
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>
------------------------------
Message: 4
Date: Thu, 4 Feb 2016 07:51:27 -0500
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] trjconv options?
Message-ID: <56B3494F.4070703 at vt.edu>
Content-Type: text/plain; charset=windows-1252;
format=flowed
On 2/4/16 4:27 AM, Timofey Tyugashev wrote:
>
>
>> Message: 2
>> Date: Wed, 3 Feb 2016 07:37:42 -0500
>> From: Justin Lemkul<jalemkul at vt.edu>
>> To:gmx-users at gromacs.org
>> Subject: Re: [gmx-users] trjconv options?
>> Message-ID:<56B1F496.5090604 at vt.edu>
>> Content-Type: text/plain; charset=windows-1252;
format=flowed
>>
>>
>>
>> On 2/3/16 6:34 AM, Timofey Tyugashev wrote:
>>> >Thank you for replies on my previous
questions.
>>> >And now I have another one dealing with
trjconv.
>>> >
>>> >I have a simulation of a three-chain
protein/nucleic acid complex. Naturally,
>>> >it gets broken in three separate strands by
PBC.
>>> >After trying several, I settled on using
options '-pbc mol' with '-ur compact'
>>> >which makes the complex look decent again
and it looks like that does the job.
>>> >But I'm worried about a possibility of
something getting unrepaired by this
>>> >option and getting unnoticed by me. What is
the way to check for it?
>> Any molecules that appear to fly away suddenly will
be a pretty dead giveaway.
>>
>> In general, for multimeric complexes, you need to
do a lot more work, e.g.
>> centering on a single chain after making molecules
whole and removing jumps. If
>> a simple -pbc mol -ur compact does the trick,
probably nothing has actually
>> crossed a periodic boundary yet.
>>
>>> >Also it keeps tumbling around the cell
during the trajectory. It's annoying. Is
>>> >there a way to pin down the cluster and
stop it from rotating?
>> This is what trjconv -fit is for.
>>
>> -Justin
> Well, both vmd and pymol render .gro file (and
trajectory files) with DNA
> strands and protein positioned in different corners of
the box.
> Also, editconf -pbc has no effect on .gro file with the
broken complex. How it's
> supposed to behave?
>
> So in this case I should at first run trjconv with
'-pbc whole', make second run
> with '-pbc nojump', then make third run with '-pbc mol'
to properly repair the
> trajectory?
> I guess for -fit I should pick 'progressive' option?
Complex systems require complex operations. Start with
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow
because that order of operations generally works well.
Then see posts in the
archive, because this comes up frequently. Typically,
after making molecules
whole and removing jumps, you can center on a custom index
group that defines
some useful center. Then you can do whatever fitting
you like.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu
| (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
------------------------------
Message: 5
Date: Thu, 4 Feb 2016 07:53:06 -0500
From: Justin Lemkul <jalemkul at vt.edu>
To: Mehreen Jan <mehreen_jan1990 at yahoo.com>
Cc: Discussion list for GROMACS users <gmx-users at gromacs.org>
Subject: Re: [gmx-users] $GMXLIB or the working directory
Message-ID: <56B349B2.80808 at vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed
Please continue this discussion on the gmx-users mailing
list. I am not a
private help service.
On 2/4/16 12:13 AM, Mehreen Jan wrote:
> respected sir!
> thank so much for reply and time
> respected sir i have no idea about whic kind of
changes are required for $GMXLIB or the working directory
>
> i just make changes in gromacs
4.5.5>share>top>gromacs43a1.ff . i have done no
changes in $GMXLIB and i dont know what type of changes are
/ i required for $GMXLIB.
> snapshots are attached of all steps kindly find the
attachment.
>
> step of command i performed :
> pdb2gmx -f protein.pdb -p protein.top -o protein.gro
>
> from list select the force field
> select 9 which is GROMOS96 32a1 force
field
> select the water model:
> 1 SPC simple point charge
> then error message
> fatal error:
> residue SEP /TPO not found in residue topology
database
>
Stop trying to modify 43A1; you likely aren't familiar
enough with the structure
and file formats.
Use the 43A1p files directly. They work. I
verified it yesterday. Download
the force field archive, put it in your working directory or
GMXLIB and use it.
Don't use 43A1 because it simply won't work.
This much should be clear based
on the repetition of the exact same error message every time
you do anything.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu
| (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
------------------------------
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