Re: [gmx-users] Reduced Units
I don't understand what you are asking for. Mark On May 17, 2013 7:59 AM, Rasoul Nasiri nasiri1...@gmail.com wrote: Are you sure lattice cell set up in f.c.c structure has been explained there for the positions of molecules? On Thu, May 16, 2013 at 3:28 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Does manual 2.3 help? On Thu, May 16, 2013 at 2:51 PM, Rasoul Nasiri nasiri1...@gmail.com wrote: Hi All, Has anyone performed MD simulation on fluids in reduced units with GROMACS? I just wandering how the obtained density values through the box should be converted in the SI unit (Kg/m3). Thanks Rasoul -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Reduced Units
Hi All, Has anyone performed MD simulation on fluids in reduced units with GROMACS? I just wandering how the obtained density values through the box should be converted in the SI unit (Kg/m3). Thanks Rasoul -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Reduced Units
Does manual 2.3 help? On Thu, May 16, 2013 at 2:51 PM, Rasoul Nasiri nasiri1...@gmail.com wrote: Hi All, Has anyone performed MD simulation on fluids in reduced units with GROMACS? I just wandering how the obtained density values through the box should be converted in the SI unit (Kg/m3). Thanks Rasoul -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Reduced Units
Are you sure lattice cell set up in f.c.c structure has been explained there for the positions of molecules? On Thu, May 16, 2013 at 3:28 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Does manual 2.3 help? On Thu, May 16, 2013 at 2:51 PM, Rasoul Nasiri nasiri1...@gmail.com wrote: Hi All, Has anyone performed MD simulation on fluids in reduced units with GROMACS? I just wandering how the obtained density values through the box should be converted in the SI unit (Kg/m3). Thanks Rasoul -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] reduced units
Hello there, I'm a gromacs newbie. I am using gromacs function g_anaeig to do principle component analysis. I use coordinates (converted to be .trr files for gromacs) and topology from amber. I know that gromacs works with units like nm, kJ/mol etc, while amber with angstrom. Does anyone know that when gromacs read the coordinate files, whether it assumes the values are in nm or in angstrom (if so, gromacs converts them by itself to nm without telling us)? Thanks for any help. Sincerely, Pengzhi -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] reduced units
On 2/11/13 4:09 PM, Pengzhi Zhang wrote: Hello there, I'm a gromacs newbie. I am using gromacs function g_anaeig to do principle component analysis. I use coordinates (converted to be .trr files for gromacs) and topology from amber. I know that gromacs works with units like nm, kJ/mol etc, while amber with angstrom. Does anyone know that when gromacs read the coordinate files, whether it assumes the values are in nm or in angstrom (if so, gromacs converts them by itself to nm without telling us)? Gromacs uses nm for everything except when a .pdb file is specified for input or output, in which case Angstrom is used. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] reduced units
Thanks Justin. I do use a .pdb file as the topology file, which is also in Angstrom, not in full format of pdb though (basically atom index ,name and coordinates). So in my case, gromacs will read all the coordinates in angstrom? Thus I need to ignore the units nm in output .xvg files. Do I understand it correctly? Sincerely, Pengzhi On 2/11/13 4:09 PM, Pengzhi Zhang wrote: Hello there, I'm a gromacs newbie. I am using gromacs function g_anaeig to do principle component analysis. I use coordinates (converted to be .trr files for gromacs) and topology from amber. I know that gromacs works with units like nm, kJ/mol etc, while amber with angstrom. Does anyone know that when gromacs read the coordinate files, whether it assumes the values are in nm or in angstrom (if so, gromacs converts them by itself to nm without telling us)? Gromacs uses nm for everything except when a .pdb file is specified for input or output, in which case Angstrom is used. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] reduced units
On 2/11/13 5:02 PM, Pengzhi Zhang wrote: Thanks Justin. I do use a .pdb file as the topology file, which is also in Angstrom, not in full format of pdb though (basically atom index ,name and coordinates). So in my case, gromacs will read all the coordinates in angstrom? Thus I need to ignore the units nm in output .xvg files. Do I understand it correctly? No. There is no magic done here. If you provide a .pdb file as input or output to any Gromacs program, that program understands that .pdb files use Angstrom and it processes the coordinates appropriately. All Gromacs tools read and write nm by default, including trajectories (.trr and .xtc) as well as output files from analysis tools (.xvg and others). -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] reduced units
Justin, I'm a little confused again. Let me put it in a more general way. If
I used everything in .pdb and .trr files in reduced units {\sigma}, then
gromacs will assume them are in Angstroms, and output in nms (by dividing
the input values by 10). That means, the real unit for the output is
{\sigma}*10. Is it correct?
Sincerely,
Pengzhi
On 2/11/13 5:02 PM, Pengzhi Zhang wrote:
Thanks Justin.
I do use a .pdb file as the topology file, which is also in Angstrom,
not in full format of pdb though (basically atom index ,name and
coordinates). So in my case, gromacs will read all the coordinates in
angstrom? Thus I need to ignore the units nm in output .xvg files. Do I
understand it correctly?
No. There is no magic done here. If you provide a .pdb file as input or
output to any Gromacs program, that program understands that .pdb files use
Angstrom and it processes the coordinates appropriately. All Gromacs tools
read and write nm by default, including trajectories (.trr and .xtc) as well
as output files from analysis tools (.xvg and others).
-Justin
--
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
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Re: [gmx-users] reduced units
On 2/11/13 5:26 PM, Pengzhi Zhang wrote:
Justin, I'm a little confused again. Let me put it in a more general way. If
I used everything in .pdb and .trr files in reduced units {\sigma}, then
gromacs will assume them are in Angstroms, and output in nms (by dividing
the input values by 10). That means, the real unit for the output is
{\sigma}*10. Is it correct?
If your input is in reduced units, then so too is the output, per manual section
2.3. Perhaps you can provide an actual example of whatever is causing your
confusion.
-Justin
--
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
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RE: [gmx-users] reduced units
In my case, all the related units are about length, so I won't consider
temperature, charge etc.
Here is the confusion.
On one hand, from the above discussion: If the input is from the .pdb file,
which is in reduced units ( {\sigma}=3.8 Angstrom), as well as the
coordinate file, the program g_covar reads the coordinates in Anstroms and
convert them to nms, then gives an output of all the eigenvalues of the
covariance matrix, in units of nm^2, for example, the first eigenvalue given
is 5.5 nm^2. So mapping to the correct reduced units, I think I need to
change the nm^2 to ({\sigma}*10)^2=1444 Angstrom^2, thus the first
eigenvalue is 550 {\sigma}^2, i.e. 7942 Angstrom^2.
On the other hand, per to the manual, the output should be anyway 5.5
{\sigma}^2 although written in 5.5 nm^2 in the .xvg file, as if gromacs does
no unit-conversion here at all, even a .pdb file is given as input.
The latter gives values of better sense from my actual example.
Sincerely,
Pengzhi
On 2/11/13 5:26 PM, Pengzhi Zhang wrote:
Justin, I'm a little confused again. Let me put it in a more general
way. If I used everything in .pdb and .trr files in reduced units
{\sigma}, then gromacs will assume them are in Angstroms, and output
in nms (by dividing the input values by 10). That means, the real unit
for the output is {\sigma}*10. Is it correct?
If your input is in reduced units, then so too is the output, per manual
section 2.3. Perhaps you can provide an actual example of whatever is
causing your confusion.
-Justin
--
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] reduced units
On 2/11/13 6:15 PM, Pengzhi Zhang wrote:
In my case, all the related units are about length, so I won't consider
temperature, charge etc.
Here is the confusion.
On one hand, from the above discussion: If the input is from the .pdb file,
which is in reduced units ( {\sigma}=3.8 Angstrom), as well as the
coordinate file, the program g_covar reads the coordinates in Anstroms and
convert them to nms, then gives an output of all the eigenvalues of the
covariance matrix, in units of nm^2, for example, the first eigenvalue given
is 5.5 nm^2. So mapping to the correct reduced units, I think I need to
change the nm^2 to ({\sigma}*10)^2=1444 Angstrom^2, thus the first
eigenvalue is 550 {\sigma}^2, i.e. 7942 Angstrom^2.
On the other hand, per to the manual, the output should be anyway 5.5
{\sigma}^2 although written in 5.5 nm^2 in the .xvg file, as if gromacs does
no unit-conversion here at all, even a .pdb file is given as input.
The latter gives values of better sense from my actual example.
Using reduced units is far more straightforward from simple energy and
coordinate output; their interpretation in g_covar is less clear. I think the
latter case is right, but you would have to go into the code to be sure. The
former case represents huge values of covariance which do not make any sense to me.
-Justin
--
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
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[gmx-users] Reduced Units
Dear all I would like to do coarse-grained simulations using reduced LJ units. As I can see in the manual, this is possible, but I don't understand how... I use the Gromos96 53a6 force field. In the *ffG53a6nb.itp *the* σ* and *ε* are in *(nm*) and *(KJ/mol*) Also in the *ffG53a6.atp* the *mas*s is in* gr/mol*. Finally in the *mdp*file the *ref_t* is in *(K)* and the *time_step* in *(ps)* If I creat an atom A, and define *ε=σ=m=1*, how can I define that I want these numbers to be in reduced units? Also, how can I have reduced units in my *.mdp *file? Kind Regards, Chrysostomos -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Reduced Units
On Mon, Aug 9, 2010 at 9:58 AM, poj...@icp.uni-stuttgart.de wrote: Hi, I want to use the pme algorithm in GROMACS. Thge size of my box is 8.2x8.2x8.2 in reduced units. I am considering a collection of 1000 of CO2 molecules. If I am using reduced units, the values of the parameters rcoulomb=0.9 I think should be converted to reduced units rcoulomb=2.45 (my \sigma=0.366nm). But my question is how can one convert the value of fourierspacing=0.12 to reduced units? 'fourierspacing' is also in units of length and it's value is used to determine 'fourier_nx' etc., if the latter are set to zero. In that case, fourier_nx=(box length along x)/fourierspacing. So for same level of PME accuracy scale down 'fourierspacing' by sigma=0.366 also. (This script is in SI standard units) ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = pme rcoulomb-switch = 0 rcoulomb = 0.9 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r= 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no Thanks. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] reduced units
On Sat, Oct 17, 2009 at 06:10, lammps lammps lammp2fo...@gmail.com wrote: Dear, I want to do stochastic simulations in the framework of Langevin dynamics using Gromacs with the reduced units. The questions are: 1. How to turn on the reduced units? Is there any parameters for setting? I am not sure I understand. For Langevin dynamcis/thermostat use: integrator = SD bd-fric=0; Read the manual about the relations between dt tau-t, I use 5e-4 2, respectively. Hope I helped. Omer. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] reduced units
Dear, I want to do stochastic simulations in the framework of Langevin dynamics using Gromacs with the reduced units. The questions are: 1. How to turn on the reduced units? Is there any parameters for setting? 2. If I use the reduced temperature of 1, should the ref_t in the .mdp file be the 120.2717 ? Right? 3. I create the force field(.itp and .top) within the reduced units myself. Are there any suggestion for avoiding errors? Thanks in advance. -- wende ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
