Re: [gmx-users] Viscosity in PE
From: David van der Spoel <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Viscosity in PE
Date: Thu, 07 Sep 2006 19:36:34 +0200
Esther Caballero-Manrique wrote:
You can calculate it from the velocity autocorrelation function, which can
be calculated using the g_velacc. The friction can be calculated from the
integral of the velocity autocorrelation function (friction=3KbT/(integral
of vacf)) and then the viscosity can be calculated using Stoke's equation
(friction=6 x PI x visc x radius). But you need to have saved the
velocities fairly often (say every 5 fs?). This came up recently in the
mailing lists, you can search the velocity autocorrelation function. This
method integrates the integral at time infinite (ie, see Morriss and
Evan's book /Statistical Mechanics of Nonequilibrium Liquids, /now on the
web @ http://rsc.anu.edu.au/~evans/evansmorrissbook.htm) which might or
might not be a good approximation for your system. Otherwise you can do
more sophisticated methods such as those outlined in chapter 6 of the
manual.
Hope it helps,
Esther
An alternative method that is implemented requires non-equibrium
simulations. Check out
@Article{Hess2002b,
author = {B. Hess},
title = {Determining the shear viscosity of model liquids from
molecular simulation},
journal = {J. Chem. Phys.},
year = 2002,
volume = 116,
pages ={209-217}
}
you have to set cos_acceleration in the mdp to e.g. 0.1 nm/ps^2
In Gromacs viscosity calculations can be done with several methods,
all of which are described in the paper mentioned above.
But for PE-1000 it is not that straightforward as for a simple liquid.
The system has very long relaxation times and the viscosity will be
very non-linear in the shear rate.
You should read some literature on viscosity calculations in polymer melts.
Berk.
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[gmx-users] Re: Simulation problem with extended membrane system!
Having actually looked back at my notes, here is what I did to extend pope.pdb into a larger system. However, the suggestion that I posted last time should work just as well. 1. Remove all waters 2. Duplicate the box until your heart's content. Make it larger than you actually want because the box will collapse to some extent. 3. MD with Z-only posre on lipid head groups (X and Y force components = zero). This step must be done with constant pressure (In this procedure, make sure to use isotropic pressure coupling so that the box max and min z don't come into contact with the membrane). NOTE for step 3: It is assumed that your edges line up with each other. Load the system into vmd and show periodic unit cells to make sure. If they line up poorly then I would find a new starting PDB. However, pope.pdb lines up well. 4. Adjust the z-dimension to what you want it to be, center your membrane in the z if you want to. 5. solvate the system. 6. Remove any waters that were placed within the membrane 7. energy minimize 8. posre run as before to allow the water to adjust to the membrane surfaces. However, during this run (and all the rest of the steps) I use semiisotropic Pcoupling. 9. equilibration phase without any position restraints 10. production run. If you are going to add protein, you could do that with the results of step 4 since most procedures involve stripping out any waters anyway. Again, the procedure that I outlined previously should work, but I have not tested that procedure, only this one. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Buckingham model for liquid of water
On Thursday 07 September 2006 23:18, Eudes Fileti wrote:
> Dear gmx-ers
> I have attemped to use the potential of Buckingham
> to simulate the water liquid. However I did not find
> papers that present the parameters of the potential.
> Actually I found a paper that mixed parameters LJ (O...O)
> and Buckingham (O-H, O-O and H...O).
> Can anyone let me know if there is a optmized set parameters
> for the water with this potential ?
The following article contains such a model:
@Article{Errington1998a,
author = {J. R. Errington and A. Z. Panagiotopoulos},
title ={A Fixed Point Charge Model for Water Optimized to the
Vapor-Liquid Coexistence Properties},
journal = BTjpcb,
year = 1998,
volume = 102,
pages ={7470-7475},
OPTabstract = {},
OPTnote = {},
doi = {http://dx.doi.org/}
}
--
Groeten,
Paul van Maaren
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[gmx-users] Buckingham model for liquid of water
Dear gmx-ersI have attemped to use the potential of Buckingham to simulate the water liquid. However I did not find papers that present the parameters of the potential. Actually I found a paper that mixed parameters LJ (O...O) and Buckingham (O-H, O-O and H...O). Can anyone let me know if there is a optmized set parameters for the water with this potential ?Thankseef-- __ Eudes Eterno Fileti Centro de Ciência Naturais e Humanas Universidade Federal do ABC Rua Santa Adélia, 166CEP 09210-170 skype: eefileti ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to exclude some atoms from coulomb interaction calculation?
Dear all,I did a massive MD simulation of nanostructure. In my calculation, over 80% atoms have zero charge and the main CPU time is devoted to Coulomb interaction. I wonder if anyone knows how to exclude these neutral atoms from Coublomb interaction so that a lot of CPU time will be saved.Many thanks,Cherry __Do You Yahoo!?Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Viscosity in PE
Esther Caballero-Manrique wrote:
You can calculate it from the velocity autocorrelation function, which
can be calculated using the g_velacc. The friction can be calculated
from the integral of the velocity autocorrelation function
(friction=3KbT/(integral of vacf)) and then the viscosity can be
calculated using Stoke's equation (friction=6 x PI x visc x radius). But
you need to have saved the velocities fairly often (say every 5 fs?).
This came up recently in the mailing lists, you can search the velocity
autocorrelation function. This method integrates the integral at time
infinite (ie, see Morriss and Evan's book /Statistical Mechanics of
Nonequilibrium Liquids, /now on the web @
http://rsc.anu.edu.au/~evans/evansmorrissbook.htm) which might or might
not be a good approximation for your system. Otherwise you can do more
sophisticated methods such as those outlined in chapter 6 of the manual.
Hope it helps,
Esther
An alternative method that is implemented requires non-equibrium
simulations. Check out
@Article{Hess2002b,
author = {B. Hess},
title = {Determining the shear viscosity of model liquids from
molecular simulation},
journal = {J. Chem. Phys.},
year = 2002,
volume = 116,
pages ={209-217}
}
you have to set cos_acceleration in the mdp to e.g. 0.1 nm/ps^2
Esther Caballero-Manrique
Guenza Group
University of Oregon
Eugene, OR
usa
541-346-2485
Alessandro Mattozzi wrote:
Dear Gromacs-users
I have already run some MD, both in NVT and NPT, of Polyethylene (1000
atoms-backbone).
I would like to estimate the viscosity of my systems. Is it possible
even if it is a rubbery solid? Which method is the most suitable?
Regards
Alessandro Mattozzi
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--
David.
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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[gmx-users] Re: Simulation problem with extended membrane system!
Hello Chris So you mean to do a constrained MDS to let the lipids "fill the gaps" between the box edges and lipids, after that do a unconstrained MDS, then we'll get a fine structure, am I right? Thank you very much, I'll try that Xin Liu On 9/7/06, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote: If you can't write a script, then do the minimization and equilibration with water frozen in the z dimension (freeze_groups = water; freeze_dim = n n y) or use constraints in the z dimension (posre.itp force constant 1000 along z and 0 along x and y). This will stop it from going into the membrane. Before you start, sort the initial PDB according to z (you could do this in excel), remove any waters that you don't want, resort according to original order, and run pdb2gmx. Note that pope.pdb does have a small cluster of waters in the membrane. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Continue run
Dňa Št 7. September 2006 15:27 Navratna Vajpai napísal: > Dear All.. > to continue the run, as i understood, I modified the md.mdp and then > use the .tpr and .trr for the further run. Can anyone suggest that it > is the right way or not? actually in one of the tutorials note i have > just found to change the options as -time $value -until $value. > I was wondering whether my way is also OK or not. Nearly right, but you don't need to modify the .mdb file. If your simulation crashed, simply execute 'tpbconv -s your_file.tpr -f your_file.trr -o your_new_file.tpr' (or you can add -e your_file.edr for energy) - this will generate new .tpr, which you use by running mdrun - that will generate something like your_new_file.trr and you can join then by 'trjcat -f your_file.trr your_new_file.trr -o your_full_file.trr, which will contain the whole simulation. The -time $value generates .tpr, which will start simulation from $value time (normally it starts from the last possible positions, so this is in the most cases not necessary). -until and -extend parameters you can use for continuing finished simulation until the given time/for the given time. The parameters of the simulation is allways the same. I hope it will help. Milan ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Continue run
Dear All..to continue the run, as i understood, I modified the md.mdp and then use the .tpr and .trr for the further run. Can anyone suggest that it is the right way or not? actually in one of the tutorials note i have just found to change the options as -time $value -until $value. I was wondering whether my way is also OK or not.ThanksNav ***Navratna VajpaiPh. D student in Prof. Grzesiek's laboratoryDepartment of Structural BiologyBiozentrum, University of BaselKlingelbergstrasse 70,CH-4056Basel, Switzerland.Phone- +41 61 267 2080(O) +41 78 744 0810(M)[EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Viscosity in PE
You can calculate it from the velocity autocorrelation function, which can be calculated using the g_velacc. The friction can be calculated from the integral of the velocity autocorrelation function (friction=3KbT/(integral of vacf)) and then the viscosity can be calculated using Stoke's equation (friction=6 x PI x visc x radius). But you need to have saved the velocities fairly often (say every 5 fs?). This came up recently in the mailing lists, you can search the velocity autocorrelation function. This method integrates the integral at time infinite (ie, see Morriss and Evan's book /Statistical Mechanics of Nonequilibrium Liquids, /now on the web @ http://rsc.anu.edu.au/~evans/evansmorrissbook.htm) which might or might not be a good approximation for your system. Otherwise you can do more sophisticated methods such as those outlined in chapter 6 of the manual. Hope it helps, Esther Esther Caballero-Manrique Guenza Group University of Oregon Eugene, OR usa 541-346-2485 Alessandro Mattozzi wrote: Dear Gromacs-users I have already run some MD, both in NVT and NPT, of Polyethylene (1000 atoms-backbone). I would like to estimate the viscosity of my systems. Is it possible even if it is a rubbery solid? Which method is the most suitable? Regards Alessandro Mattozzi ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Simulation problem with extended membrane system!
If you can't write a script, then do the minimization and equilibration with water frozen in the z dimension (freeze_groups = water; freeze_dim = n n y) or use constraints in the z dimension (posre.itp force constant 1000 along z and 0 along x and y). This will stop it from going into the membrane. Before you start, sort the initial PDB according to z (you could do this in excel), remove any waters that you don't want, resort according to original order, and run pdb2gmx. Note that pope.pdb does have a small cluster of waters in the membrane. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Viscosity in PE
Title: Viscosity in PE Dear Gromacs-users I have already run some MD, both in NVT and NPT, of Polyethylene (1000 atoms-backbone). I would like to estimate the viscosity of my systems. Is it possible even if it is a rubbery solid? Which method is the most suitable? Regards Alessandro Mattozzi ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Charge calculation in Gromacs
> Dear All who may concern, > I have some questions for the charge calculation in Gromacs, I used > the > forcefied ffG43a1 for the protein and inhibitors. Does the charge for the > protein is the charge per residue? The charge on a residue is the sum of the charges on the (united) atoms that make it up. The charge on a protein is the sum of the charges on the residues that make it up (or all of the atoms, obviously). The charge per residue is almost never considered, as it normally doesn't aid anybody understanding physical behaviour. Hope that answers your question, because I can't understand it. > This forcefield is just for the polar > H, > right? For the nonpolar H, it will merge the H into the Heavy atom, right? Don't know in this specific case, but there are such forcefields. > I > would like to know that does this force field also calculate the charge > for > the nonpolar H and then sum the charge with the heavy atom which it > connects > to or it doesn't calculate the charge for the nonpolar H? The charge on a united atom is just a number - as is the charge on a polar H, or any H in a non-united-atom force field. You can think of it as the sum of the charges on the multiple atoms it models if it helps. > Does the charge > of > the Heavy atom is its own charge without sum together with the nonpolar H > which connect to it? Moreover, I would like to know that if I would like > to > use quantum mechanics (qm) to calculate the charge for my inhibitor, what > should be the method and the basis set to use to calculate for the charge > to > make it compiles with the ffG43a1 force fields? Sounds like you should find the documentation (journal article?) for this force field and read it. Also some introductory material on how force fields work sounds like it might be worthwhile :-) Wanting to extend a force field you don't understand yet is a recipe for disaster... Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Charge calculation in Gromacs
Dear All who may concern, I have some questions for the charge calculation in Gromacs, I used the forcefied ffG43a1 for the protein and inhibitors. Does the charge for the protein is the charge per residue? This forcefield is just for the polar H, right? For the nonpolar H, it will merge the H into the Heavy atom, right? I would like to know that does this force field also calculate the charge for the nonpolar H and then sum the charge with the heavy atom which it connects to or it doesn't calculate the charge for the nonpolar H? Does the charge of the Heavy atom is its own charge without sum together with the nonpolar H which connect to it? Moreover, I would like to know that if I would like to use quantum mechanics (qm) to calculate the charge for my inhibitor, what should be the method and the basis set to use to calculate for the charge to make it compiles with the ffG43a1 force fields? Thank you in advance for all of your help. Hope to hear from you soonWith Best all regardKanin Wichapong ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: invacuo minimization
[EMAIL PROTECTED] wrote: Hi David, I have checked the mdout.mdp and as you said it has pbc = xyz. What do I do now. I havent run editconf, but why it is taking pbc conditions? How do I remove these?? pbc=no thanks Anwar -- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational Biology and Bioinformatics Center for DNA Fingerprinting and Diagnostics(CDFD) Nacharam Hyderabad-500 076 INDIA. Tel: +91-8413-235467,68,69,70 ext 2019 [EMAIL PROTECTED] --- -REPLY TO- Date:Thu Sep 07 18:00:08 GMT+08:00 2006 FROM: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: gmx-users Digest, Vol 29, Issue 14 Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://www.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to [EMAIL PROTECTED] You can reach the person managing the list at [EMAIL PROTECTED] When replying, please edit your Subject line so it is more specific than "Re: Contents of gmx-users digest..." Today's Topics: 1. Re: invacuo minimization (David van der Spoel) 2. LIE energy calculation! (Mikko Hellgren) -- Message: 1 Date: Thu, 07 Sep 2006 10:44:52 +0200 From: David van der Spoel <[EMAIL PROTECTED]> Subject: Re: [gmx-users] invacuo minimization To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed [EMAIL PROTECTED] wrote: Dear gmx users, When I am minimizing a trimer protein in vacuum by SD as well as CG methods, one of the monomer gets apart from the rest of the protein and places itself away from the other two monomers, which are intact. No periodic box is assigned. But when I am running editconf and assigning a box, then the structures are intact. What is the reason for the above behaviour? I am pasting the em.mdp below: chekc your mdout.dmp, the default pbc = xyz cpp = /lib/cpp define = -DFLEX_SPC constraints = none ;integrator = CG integrator = steep nsteps = 1000 ; ; Energy minimizing stuff ; emtol = 100 ;for SD emstep = 0.1 ;for CG ;emstep = 0.001 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb= 1.0 rvdw= 1.0 Tcoupl = no Pcoupl = no gen_vel = no Anwar -- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational Biology and Bioinformatics Center for DNA Fingerprinting and Diagnostics(CDFD) Nacharam Hyderabad-500 076 INDIA. Tel: +91-8413-235467,68,69,70 ext 2019 [EMAIL PROTECTED] --- - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: invacuo minimization
the protein. Should I put restraints (c-alpha, all atoms) on both protein and ligand or only protein or ligand or neither of them? My initial thought would be to put restraint on c-alpha of the protein and let the rest of the system be "free". Mikko One cannot avoid making mistakes if one tries to produce a set of words, or of mathematical formulae, to describe nature. Nature is more complicated than language or mathematics. Nevertheless, one must do one's best to produce a set of symbols which are not to discordant with the facts. J.B.S. Haldane, preface to "What is Life?", Lindsay Drummond, 1949 -- next part -- A non-text attachment was scrubbed... Name: mikhel.vcf Type: text/x-vcard Size: 343 bytes Desc: Card for Mikko Hellgren <[EMAIL PROTECTED]> Url : http://www.gromacs.org/pipermail/gmx-users/attachments/20060907/9db7c71d/mikhel-0001.vcf -- ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users End of gmx-users Digest, Vol 29, Issue 14 * - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] LIE energy calculation!
Hi Dear users, I have started to do calculations of the binding between a protein and different ligands. I have read articles on the LIE method and one tutorial. But still I have some quite general questions. I am using Cut-off and NVT ensamble. 1. When I run my ligands in a water solution without the protein, should I add counterions (Cl and Na) at physiological concentrations (about 10mM to 100mM) or make the system neutral with one or two ions or can I ignore any ions the simulation. 2. Should I put any restraints on the ligand in the simulation without the protein? 3. When I run my ligand bound to the protein. Should I put restraints (c-alpha, all atoms) on both protein and ligand or only protein or ligand or neither of them? My initial thought would be to put restraint on c-alpha of the protein and let the rest of the system be "free". Mikko One cannot avoid making mistakes if one tries to produce a set of words, or of mathematical formulae, to describe nature. Nature is more complicated than language or mathematics. Nevertheless, one must do one's best to produce a set of symbols which are not to discordant with the facts. J.B.S. Haldane, preface to "What is Life?", Lindsay Drummond, 1949 begin:vcard n:Hellgren;Mikko fn:Mikko Hellgren tel;cell:+46-737280550 tel;fax:+46-8-338453 tel;work:+46-8-52487747 org:Karolinska Institutet;Department of Medical Biochemistry and Biophysics adr:;;Scheeles väg 2 Scheelelaboratoriet;Stockholm;;SE-171 77 ;Sweden version:2.1 email;internet:[EMAIL PROTECTED] title:Graduate Student end:vcard ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] invacuo minimization
[EMAIL PROTECTED] wrote: Dear gmx users, When I am minimizing a trimer protein in vacuum by SD as well as CG methods, one of the monomer gets apart from the rest of the protein and places itself away from the other two monomers, which are intact. No periodic box is assigned. But when I am running editconf and assigning a box, then the structures are intact. What is the reason for the above behaviour? I am pasting the em.mdp below: chekc your mdout.dmp, the default pbc = xyz cpp = /lib/cpp define = -DFLEX_SPC constraints = none ;integrator = CG integrator = steep nsteps = 1000 ; ; Energy minimizing stuff ; emtol = 100 ;for SD emstep = 0.1 ;for CG ;emstep = 0.001 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb= 1.0 rvdw= 1.0 Tcoupl = no Pcoupl = no gen_vel = no Anwar -- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational Biology and Bioinformatics Center for DNA Fingerprinting and Diagnostics(CDFD) Nacharam Hyderabad-500 076 INDIA. Tel: +91-8413-235467,68,69,70 ext 2019 [EMAIL PROTECTED] --- - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] invacuo minimization
Dear gmx users, When I am minimizing a trimer protein in vacuum by SD as well as CG methods, one of the monomer gets apart from the rest of the protein and places itself away from the other two monomers, which are intact. No periodic box is assigned. But when I am running editconf and assigning a box, then the structures are intact. What is the reason for the above behaviour? I am pasting the em.mdp below: cpp = /lib/cpp define = -DFLEX_SPC constraints = none ;integrator = CG integrator = steep nsteps = 1000 ; ; Energy minimizing stuff ; emtol = 100 ;for SD emstep = 0.1 ;for CG ;emstep = 0.001 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb= 1.0 rvdw= 1.0 Tcoupl = no Pcoupl = no gen_vel = no Anwar -- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational Biology and Bioinformatics Center for DNA Fingerprinting and Diagnostics(CDFD) Nacharam Hyderabad-500 076 INDIA. Tel: +91-8413-235467,68,69,70 ext 2019 [EMAIL PROTECTED] --- - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] about gromacs
代振宇 wrote: Hello, everyone: Would you please tell me that whether Gromacs can be used to do Molecular Dynamics studies for Polymer like PVC or PET? Thanks a lot. yes if you provide the input files. gromacs does not have many tools to deal with preparing input files for such systems, but have a look at genbox. dai0601 2006-09-07 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
