Re: [gmx-users] MW particle type in TIP4Pew
Thanks for the clarification Dr. Justin and Prof. David van der Spoel. Regards, Mandar Kulkarni On Sun, Apr 14, 2019 at 1:37 PM David van der Spoel wrote: > Den 2019-04-14 kl. 12:17, skrev Mandar Kulkarni: > > Hi, > > I am simulating protein using amber14sb with TIP4Pew water. I found that > > particle type for dummy mass MW in TIP4Pew is D in gromacs force field > > files and type A in user contributed version of amber14sb. Even acpype > > converted topology gives type A for MW. > > > > My understanding is that type D is correct for MW atomtype. but, I just > > want to make sure that before proceeding to production runs. > > > Make that "V" for virtual site, but "D" for dummy is supported fro > backwards compatibility. "A" is wrong as atoms should have a mass. > > > Any suggestions will be helpful. Thanks in advance. > > > > Regards, > > Mandar Kulkarni > > > > > -- > David van der Spoel, Ph.D., Professor of Biology > Head of Department, Cell & Molecular Biology, Uppsala University. > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > http://www.icm.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 > 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! * 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.
[gmx-users] MW particle type in TIP4Pew
Hi, I am simulating protein using amber14sb with TIP4Pew water. I found that particle type for dummy mass MW in TIP4Pew is D in gromacs force field files and type A in user contributed version of amber14sb. Even acpype converted topology gives type A for MW. My understanding is that type D is correct for MW atomtype. but, I just want to make sure that before proceeding to production runs. Any suggestions will be helpful. Thanks in advance. Regards, Mandar Kulkarni -- 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] Osmotic Pressure Calculations and fixed reference values
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
jalem...@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
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] regarding calculation of intra-residue energy
Message-ID:
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
jalem...@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
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Osmotic Pressure Calculations and fixed
reference values of walls
Message-ID:
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
jalem...@vt.edu |
[gmx-users] Osmotic Pressure Calculations and fixed reference values of walls
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?
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?
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
--
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.
