[gmx-users] Osmotic Pressure Calculations and fixed reference values
Mandar Kulkarni
mandar.kulkarni.chem at gmail.com
Tue Jan 23 12:44:14 CET 2018
Dear Dr. Justin,
Thanks for the clarification and sorry for the delayed response from my
side.
I am calculating flat bottom potential along with osmotic pressure values
to verify my calculations. The flat bottom potential values calculated by
in-house code matches with g_energy values.
Thanks again.
On Dec 28, 2017 4:39 AM, <gromacs.org_gmx-users-request at maillist.sys.kth.se>
wrote:
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Today's Topics:
1. dielectric constant effect on protein, dna, water interface
(Sarath Chandra)
2. More dihedrals generated than provided in the force field &
"No default Proper Dih. types" as a result (Timofey Tyugashev)
3. Re: More dihedrals generated than provided in the force field
& "No default Proper Dih. types" as a result (Justin Lemkul)
4. Re: regarding calculation of intra-residue energy (Justin Lemkul)
5. Re: Osmotic Pressure Calculations and fixed reference values
of walls (Justin Lemkul)
6. Strange energy values with GMX 5.1, PME and Verlet (Diana Lousa)
----------------------------------------------------------------------
Message: 1
Date: Wed, 27 Dec 2017 18:00:36 +0530
From: Sarath Chandra <sarathchandradantu at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Subject: [gmx-users] dielectric constant effect on protein, dna,
water
interface
Message-ID:
<CAKi3H2XEvG0UxJpomMZM1xz4RydTguBhRBs=O-ddnMQVQ_3Teg at mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Fellow users,
I am working on a Protein-DNA complex and I have a question regarding the
electrostatic interaction energies calculated at the interface of protein,
DNA and water. I am using amber99sb+parambsc0 forcefield for my system
with TIP3P water simulated using gromacs4.6.4.
I understand that the additive forcefield does not capture polarizibility
well. I have already referred to articles on PME but it is not clear if the
PME takes into account the dielectric constant change at the protein, DNA,
water interface. During the electrostatic forces calculation is this
captured by calculation of local dipole moments on fly? This is critical to
understand the effect of protein on DNA structural properties.
I look forward to your reply.
Best regards,
Sarath
------------------------------
Message: 2
Date: Wed, 27 Dec 2017 21:39:41 +0700
From: Timofey Tyugashev <tyugashev at niboch.nsc.ru>
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] More dihedrals generated than provided in the
force field & "No default Proper Dih. types" as a result
Message-ID: <86c9cd94-8371-5abc-db05-d469d17aea23 at niboch.nsc.ru>
Content-Type: text/plain; charset=utf-8; format=flowed
I'm building a protein with a cubic [Fe4S4] cluster using parameters
from a published paper.
This parameters provide only two dihedral angles types (S-FE-SG-CB and
FE-S-FE-SG, where S and FE belong to the cluster and SG and CB belong to
the Cys residue).
GROMACS automatically generates far more dihedrals with types like
S-FE-S-FE (looks like all of them are inta-cluster) which are omitted in
the source paper and are explicitly stated to be redundant for MD.
However? grommp generates errors and stops:
ERROR 49 [file topol.top, line 32916]:
? No default Proper Dih. types
How to solve this problem?
------------------------------
Message: 3
Date: Wed, 27 Dec 2017 13:46:37 -0500
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] More dihedrals generated than provided in the
force field & "No default Proper Dih. types" as a result
Message-ID: <c76426b1-eb96-3043-dfe9-5ff6fb8004f7 at vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed
On 12/27/17 9:39 AM, Timofey Tyugashev wrote:
> I'm building a protein with a cubic [Fe4S4] cluster using parameters
> from a published paper.
> This parameters provide only two dihedral angles types (S-FE-SG-CB and
> FE-S-FE-SG, where S and FE belong to the cluster and SG and CB belong
> to the Cys residue).
> GROMACS automatically generates far more dihedrals with types like
> S-FE-S-FE (looks like all of them are inta-cluster) which are omitted
> in the source paper and are explicitly stated to be redundant for MD.
> However? grommp generates errors and stops:
>
> ERROR 49 [file topol.top, line 32916]:
> ? No default Proper Dih. types
>
> How to solve this problem?
pdb2gmx automatically generates all possible dihedrals. If they are not
necessary in your force field description, either remove the offending
lines from your topology or assign them dihedral parameters with force
constants equal to zero so they impose no force.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==================================================
------------------------------
Message: 4
Date: Wed, 27 Dec 2017 13:47:26 -0500
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] regarding calculation of intra-residue energy
Message-ID: <e69c5489-4b81-d9d5-53ac-243753149e2d at vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed
On 12/26/17 1:34 PM, Saumyak Mukherjee wrote:
> Dear all,
>
> I have simulated myoglobin in water system. Now, I want to calculate the
> self interaction energy (Coulomb) of the protein. In that case shall I
> consider the interaction between the OE1 and OE2 atoms in glutamte, or
> other such pairs?
>
> Including all pairs, except the bonded pairs, the average self-energy of
> the protein is coming as 8108 kT from my program. Is this value plausible?
>
> Any comment/suggestion is appreciated.
First- and second-neighbor interactions are not included in standard
force fields, so if your calculation includes them, you're going to get
something that the force field is not designed to describe. Use the same
exclusions as the force field expects.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==================================================
------------------------------
Message: 5
Date: Wed, 27 Dec 2017 13:49:25 -0500
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Osmotic Pressure Calculations and fixed
reference values of walls
Message-ID: <baa3845e-2ca5-61af-078c-a1f5fc7adc72 at vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed
On 12/26/17 7:53 AM, Mandar Kulkarni wrote:
> Dear All,
> I am performing osmotic pressure simulations using 30 nucleoside molecules
> using 1D flat bottom restraints along Z-axis(Zmin and Zmax). I am using
> GROMACS 5.0.7 version and reference coordinates are provided using -r
> option in grompp.
> The osmotic pressure runs are performed under NPT conditions with
> semi-isotropic pressure coupling. I am calculating osmotic pressure using
> C-program which simply calculates forces on heavy atoms of nucleosides
> attempting to cross the Zmin and Zmax limits.
>
> I have searched archived posts, however, I am confused about possible
> implementation and post-processing in the present case. Any help will be
> really helpful to solve the following issues.
>
> 1. The upper and lower limits of the flat bottom restraints are defined
> while starting the simulations using static reference frame. Although
> |Zmax-Zmin|
> will be constant, is it correct to assume fixed minimum(Zmin) and
> maximum(Zmax) limits?
Such calculations are usually performed with a static z-dimension, e.g
incompressible along that axis. In that case, Zmin and Zmax are (and
should be) fixed.
> 2. During post-processing when one centers the trajectory and correct PBC
> for nucleoside molecules (trjconv -pbc mol -ur compact -center options),
is
> it appropriate to assume the same Zmin and Zmax values at t=0 throughout
> the analysis?
You shouldn't have to use any complex trjconv command. Just make
molecules whole and that should be correct. No additional centering is
required; your molecules stay in the central volume anyway, and you
don't want to shift coordinates when relying on fixed points in space
for computing your osmotic pressure forces.
-Justin
> 3. The GROMACS source code section below calculates flat-bottom restraint
> forces
>
> for (m = 0; (m < DIM); m++)
> {
> f[ai][m] += fm[m];
> /* Here we correct for the pbc_dx which included rdist */
> vir_diag[m] -= 0.5*(dx[m] + rdist[m])*fm[m];
>
> }
>
> How can we print force f[ai][m] at each time step to separate file? I
> assume it might be not straightforward to print these forces, but a short
> general guideline might help me to achieve the objective.
>
> Sorry for so many questions and Thanks in advance.
> Also, Wish you all happy new year in advance.
>
> Best Regards,
> Mandar Kulkarni,
> Pusan National University, South Korea
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==================================================
------------------------------
Message: 6
Date: Wed, 27 Dec 2017 19:39:36 +0000
From: Diana Lousa <dlousa at itqb.unl.pt>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Subject: [gmx-users] Strange energy values with GMX 5.1, PME and
Verlet
Message-ID:
<CANqofoxi85ABTWPJG=HqAXKOmRrBLyD3Myncj6eqbiP9P=5qTg at mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Dear all,
For testing purposes, I performed a short simulation (10 ps) of a CL- and a
Na+ ion in vacuum with gmx 5.1.4 and compared the Group and Verlet cutoff
schemes. I ran gmx energy to monitor the interaction energy between the
ions and obtained the following results:
1) Verlet
Energy Average Err.Est. RMSD Tot-Drift
------------------------------------------------------------
-------------------
Pressure 0.128465 0.044 15.8209 -0.27251 (bar)
Coul-SR:NA-NA -244.832 0 -nan -4.68375e-14
(kJ/mol)
LJ-SR:NA-NA 0 0 0 0
(kJ/mol)
Coul-SR:NA-CL -153.193 7.4 32.7214 -43.0706
(kJ/mol)
LJ-SR:NA-CL 42.5252 1.7 20.9531 9.65428
(kJ/mol)
Coul-SR:CL-CL -244.832 0 -nan -4.68375e-14
(kJ/mol)
LJ-SR:CL-CL 0 0 0 0
(kJ/mol)
2) Group
Energy Average Err.Est. RMSD Tot-Drift
------------------------------------------------------------
-------------------
Pressure 0.0159313 0.039 17.1949 0.303503 (bar)
Coul-SR:NA-NA 0 0 0 0
(kJ/mol)
LJ-SR:NA-NA 0 0 0 0
(kJ/mol)
Coul-SR:NA-CL -152.361 8 33.2265 -46.2306
(kJ/mol)
LJ-SR:NA-CL 42.2222 1.9 22.5877 11.0263
(kJ/mol)
Coul-SR:CL-CL 0 0 0 0
(kJ/mol)
LJ-SR:CL-CL 0 0 0 0
(kJ/mol)
As you can see, the Coul-SR:NA-NA and Coul-SR:CL-CL have the value of
-244.832 when using Verlet, which is very strange. This does not happen
when using Group cutoff or when using Verlet in GMX 4.5 (the value is 0 in
these cases).
GMX 2016 gives similar results to GMX 5.1.4:
3) Verlet GMX 2016:
Energy Average Err.Est. RMSD Tot-Drift
------------------------------------------------------------
-------------------
Pressure -0.0106255 0.22 19.2119 0.756146 (bar)
Coul-SR:NA-NA -244.832 0 -nan -4.68375e-14
(kJ/mol)
LJ-SR:NA-NA 0 0 0 0
(kJ/mol)
Coul-SR:NA-CL -150.921 7.9 35.159 -45.7216
(kJ/mol)
LJ-SR:NA-CL 42.0629 2 25.1668 11.2282
(kJ/mol)
Coul-SR:CL-CL -244.832 0 -nan -4.68375e-14
(kJ/mol)
LJ-SR:CL-CL 0 0 0 0
(kJ/mol)
I am not using GPUs, since I know you cannot monitor energy groups when
using GPUs.
Does anyone have any idea why this happens and what consequences does it
have?
Here's the mdp:
****************************
define =
integrator = md
tinit = 0.0
dt = 0.002
nsteps = 5000
nstcomm = 1
nstxtcout = 500
xtc-precision = 1000
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 10
nstenergy = 1
nstlist = 20
ns_type = grid
;PME
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
fourierspacing = 0.16
pme_order = 4
vdwtype = cut-off
rvdw = 1.0
cutoff-scheme = Verlet ; or Group
; Energy monitoring
energygrps = NA CL
Tcoupl = v-rescale
tc-grps = Ion
tau_t = 0.10
ref_t = 300.0
; Isotropic pressure coupling is now of
; Pcoupl = berendsen
Pcoupl = No
; lincs_
constraint_algorithm=lincs
lincs_order = 8
constraints = none
lincs-warnangle = 90
?Thanks in advance
Best regards?
--
Diana Lousa
Post-doc
Protein Modeling Laboratory
ITQB/UNL
Oeiras, Portugal
------------------------------
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