[gmx-users] Re: Water models and diffusion coefficient
Thanks for all your answers. I tried collecting data more frequently (100 fs), used -trestart as the entire trajectory; however my diffusion coefficient for D2O is still in the range 1.4 - 1.5 e-5 cm^2/s. Surprisingly, the number of Hbonds, potential energy, density are all what would be expected for D2O at 300 K. This is mdrun followed by 1ns each of NVT and NPT equilibration. The way I made the D2O model is by overwriting the mass and charge of HW and OW in atomtypes.atp and the itp files for the model. I also updated this information in the aminoacids.rtp file. As a last ditch attempt, I am posting the mdp parameter file that I used for the MD run. I greatly appreciate all of your ideas and help. If there is anything that comes to mind, which could be the problem, please let me know. Thanks again. ; Run parameters integrator = md; leap-frog integrator nsteps = 500 ; 2 fs * 500 = 1000 fs = 10 ns dt = 0.002 ; 2 fs ; Output control nstxout = 50; save coordinates every 100 fs nstvout = 50; save velocities every 100 fs nstxtcout = 50; xtc compressed trajectory output every 100 fs nstenergy = 50; save energies every 100 fs nstlog = 50; update log file every 100 fs ; Bond parameters continuation= yes ; Restarting after NPT 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 ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals cutoff (in nm) ; 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 = V-rescale ; modified Berendsen thermostat tc-grps = System; only one component in the system tau_t = 0.1 ; time constant, in ps ref_t = 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 1.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.76e-5 ; isothermal compressibility of heavy water, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; Velocity generation is off -- View this message in context: http://gromacs.5086.n6.nabble.com/Water-models-and-diffusion-coefficient-tp5005377p5005409.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] 4.6 seems improved the efficiency
Indeed - that's about the order of improvement expected for just switching to 4.6 and proceeding as before on CPU-only hardware. Better use of SIMD instructions and calling force-only kernels when energies are not required are likely to be the code improvements leading to the performance improvement you note. (However, the new automated PME load balancing in mdrun may mean you don't need to use g_tune_pme for 4.6... see your log file.) Mark On Sat, Feb 9, 2013 at 9:38 AM, Albert mailmd2...@gmail.com wrote: Hello : I found the new released 4.6 probably improved very obviously for the efficiency. With the same system, I used 4.5.5 it can get 26 ns/day (144 CPU, 55,000 atoms, Amber FF) with g_tume_pme optimization. Now I used 4.6, even without g_tune_pme, the pme mesh/force can get 0.8-1.0 with efficiency 32 ns/day. That's really nice. I don't know whether other users have similar experiences for this new version. Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Re: Problem with dihedral restraint in gromacs 4.6
Last question (I hope). How can I choose the force constant? Indeed for the version 4.5, the force constant is defined by the option dihre_fc in the mdp input file. After this force is multiply by kfac contained in the dihedral_sections in the topology file Now this option is obsolete. The force constant is defined by kfac in gromacs4.6 ? If yes, kfac has now a unit. In kJ.mol-1.rad-2 ? Thank you -- View this message in context: http://gromacs.5086.n6.nabble.com/Problem-with-dihedral-restraint-in-gromacs-4-6-tp5005302p5005420.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Calculation of the Force on the center of bonds
Dear All, I need to define interaction sites on the center of C-H bonds instead of nuclei of each atom. The main reason was that non-bonding parameters (sigma and epsilon) have been parametrized in these centers and those are only available for the center of C-H. So, I just wanted to know how calculation of force can be implemented by GROMACS in this case. Best wishes 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] Calculation of the Force on the center of bonds
Try virtual sites constructions. On Feb 11, 2013, at 6:01 PM, Rasoul Nasiri wrote: Dear All, I need to define interaction sites on the center of C-H bonds instead of nuclei of each atom. The main reason was that non-bonding parameters (sigma and epsilon) have been parametrized in these centers and those are only available for the center of C-H. So, I just wanted to know how calculation of force can be implemented by GROMACS in this case. Best wishes 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] Calculation of the Force on the center of bonds
Dear Erik, Many thanks for your comment. The situation seems to be similar to TIP4P water model where the M site is located among the three other atoms. In my case, it's between the two C-H atoms. Could I ask you which parameters must be selected for these virtual sites? The interest molecule is n-alkane that have (2n+2) C-H bond. Is that make sense that I put the virtual sites there? Best Rasoul On Mon, Feb 11, 2013 at 5:33 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Try virtual sites constructions. On Feb 11, 2013, at 6:01 PM, Rasoul Nasiri wrote: Dear All, I need to define interaction sites on the center of C-H bonds instead of nuclei of each atom. The main reason was that non-bonding parameters (sigma and epsilon) have been parametrized in these centers and those are only available for the center of C-H. So, I just wanted to know how calculation of force can be implemented by GROMACS in this case. Best wishes 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 thewww 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
--
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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
--
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[gmx-users] Occupancy for a distance cut off
Dear Gromacs Users, I have a run a MD simulation on protein bound with ligand and ions using Gromacs 4.5.4. I am able to calculate the distances between ions and coordinating residues using g_dist. The output is in the form of xvg file, but I am looking for the occupancy for a cut off distance (3.5 Å) between ion and a particular residue atom during simulation. Please suggest. Thanks, Pramod -- 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] 4.6 seems improved the efficiency
Additionally to the new non-bonded SIMD kernels: - Bonded force calculation got some SIMD acceleration which should considerably improve performance; - There have been be major improvements in PME (courtesy of Berk Hess Roland Schulz), you should see anywhere between up to 1.5-2x performance improvement. OpenMP multi-threading is supported with separate PME nodes also with the group scheme which should reduce communication cost at high parallelization (turn it on with -npme N -ntomp_pme M). Note that g_tune_pme does not support tuning the number of OpenMP threads (yet). -- Szilárd On Mon, Feb 11, 2013 at 4:39 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Indeed - that's about the order of improvement expected for just switching to 4.6 and proceeding as before on CPU-only hardware. Better use of SIMD instructions and calling force-only kernels when energies are not required are likely to be the code improvements leading to the performance improvement you note. (However, the new automated PME load balancing in mdrun may mean you don't need to use g_tune_pme for 4.6... see your log file.) Mark On Sat, Feb 9, 2013 at 9:38 AM, Albert mailmd2...@gmail.com wrote: Hello : I found the new released 4.6 probably improved very obviously for the efficiency. With the same system, I used 4.5.5 it can get 26 ns/day (144 CPU, 55,000 atoms, Amber FF) with g_tume_pme optimization. Now I used 4.6, even without g_tune_pme, the pme mesh/force can get 0.8-1.0 with efficiency 32 ns/day. That's really nice. I don't know whether other users have similar experiences for this new version. Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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 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
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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Re: [gmx-users] Occupancy for a distance cut off
On 2/11/13 6:15 PM, ram bio wrote: Dear Gromacs Users, I have a run a MD simulation on protein bound with ligand and ions using Gromacs 4.5.4. I am able to calculate the distances between ions and coordinating residues using g_dist. The output is in the form of xvg file, but I am looking for the occupancy for a cut off distance (3.5 Å) between ion and a particular residue atom during simulation. Please suggest. g_dist -dist 0.35 -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] Occupancy for a distance cut off
Hi Justin, Thanks for the suggestion. I executed the following command: g_dist -f n101c2naclprod2-12nsvrpr.trr -s n101c2naclpose2prod2nsvrpr.tpr -n index.ndx -dist 0.35 -o N101Cbest2NACL606S336HG1.xvg and the output was distance calculated for every 10 frames in nm as under: t: 11870 336 SER 4166 HG1 0.239086 (nm) t: 11880 336 SER 4166 HG1 0.248868 (nm) t: 11890 336 SER 4166 HG1 0.231819 (nm) t: 11900 336 SER 4166 HG1 0.218495 (nm) t: 11910 336 SER 4166 HG1 0.233166 (nm) t: 11920 336 SER 4166 HG1 0.283512 (nm) t: 11930 336 SER 4166 HG1 0.239512 (nm) t: 11940 336 SER 4166 HG1 0.216938 (nm) t: 11950 336 SER 4166 HG1 0.220066 (nm) t: 11960 336 SER 4166 HG1 0.227595 (nm) t: 11970 336 SER 4166 HG1 0.247895 (nm) t: 11980 336 SER 4166 HG1 0.259074 (nm) t: 11990 336 SER 4166 HG1 0.228319 (nm) t: 12000 336 SER 4166 HG1 0.264722 (nm) So, my question is that now do maths and find percent frames that were above the 3.5 Å and expresses it relation to unity for occupancy. That is if i have 30 frames above 3.5Å out of 100, then the occupancy would be 0.7. Please advice if there is any other ways to do it.. Thanks, Pramod On Mon, Feb 11, 2013 at 7:19 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/11/13 6:15 PM, ram bio wrote: Dear Gromacs Users, I have a run a MD simulation on protein bound with ligand and ions using Gromacs 4.5.4. I am able to calculate the distances between ions and coordinating residues using g_dist. The output is in the form of xvg file, but I am looking for the occupancy for a cut off distance (3.5 Å) between ion and a particular residue atom during simulation. Please suggest. g_dist -dist 0.35 -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 -- 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] Occupancy for a distance cut off
On 2/11/13 9:16 PM, ram bio wrote: Hi Justin, Thanks for the suggestion. I executed the following command: g_dist -f n101c2naclprod2-12nsvrpr.trr -s n101c2naclpose2prod2nsvrpr.tpr -n index.ndx -dist 0.35 -o N101Cbest2NACL606S336HG1.xvg and the output was distance calculated for every 10 frames in nm as under: t: 11870 336 SER 4166 HG1 0.239086 (nm) t: 11880 336 SER 4166 HG1 0.248868 (nm) t: 11890 336 SER 4166 HG1 0.231819 (nm) t: 11900 336 SER 4166 HG1 0.218495 (nm) t: 11910 336 SER 4166 HG1 0.233166 (nm) t: 11920 336 SER 4166 HG1 0.283512 (nm) t: 11930 336 SER 4166 HG1 0.239512 (nm) t: 11940 336 SER 4166 HG1 0.216938 (nm) t: 11950 336 SER 4166 HG1 0.220066 (nm) t: 11960 336 SER 4166 HG1 0.227595 (nm) t: 11970 336 SER 4166 HG1 0.247895 (nm) t: 11980 336 SER 4166 HG1 0.259074 (nm) t: 11990 336 SER 4166 HG1 0.228319 (nm) t: 12000 336 SER 4166 HG1 0.264722 (nm) So, my question is that now do maths and find percent frames that were above the 3.5 Å and expresses it relation to unity for occupancy. That is if i have 30 frames above 3.5Å out of 100, then the occupancy would be 0.7. Please advice if there is any other ways to do it.. Redirect the output into a file, count the number of lines in the file with wc -l and you have the answer. -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] Occupancy for a distance cut off
Thank you!! On Mon, Feb 11, 2013 at 8:29 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/11/13 9:16 PM, ram bio wrote: Hi Justin, Thanks for the suggestion. I executed the following command: g_dist -f n101c2naclprod2-12nsvrpr.trr -s n101c2naclpose2prod2nsvrpr.tpr -n index.ndx -dist 0.35 -o N101Cbest2NACL606S336HG1.xvg and the output was distance calculated for every 10 frames in nm as under: t: 11870 336 SER 4166 HG1 0.239086 (nm) t: 11880 336 SER 4166 HG1 0.248868 (nm) t: 11890 336 SER 4166 HG1 0.231819 (nm) t: 11900 336 SER 4166 HG1 0.218495 (nm) t: 11910 336 SER 4166 HG1 0.233166 (nm) t: 11920 336 SER 4166 HG1 0.283512 (nm) t: 11930 336 SER 4166 HG1 0.239512 (nm) t: 11940 336 SER 4166 HG1 0.216938 (nm) t: 11950 336 SER 4166 HG1 0.220066 (nm) t: 11960 336 SER 4166 HG1 0.227595 (nm) t: 11970 336 SER 4166 HG1 0.247895 (nm) t: 11980 336 SER 4166 HG1 0.259074 (nm) t: 11990 336 SER 4166 HG1 0.228319 (nm) t: 12000 336 SER 4166 HG1 0.264722 (nm) So, my question is that now do maths and find percent frames that were above the 3.5 Å and expresses it relation to unity for occupancy. That is if i have 30 frames above 3.5Å out of 100, then the occupancy would be 0.7. Please advice if there is any other ways to do it.. Redirect the output into a file, count the number of lines in the file with wc -l and you have the answer. -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 -- 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
