[gmx-users] is it any serious error
hello all... when ever i run simulation i'm getting this kind of out put saying there is one warning as shown below Walking down the molecule graph to make shake-blocks initialising group options... processing index file... Analysing residue names: Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat There are: 4401 OTHER residues There are: 46 PROTEIN residues There are: 0 DNA residues Analysing Protein... Analysing Other... WARNING 1 [file aminoacids.dat, line 1]: T-Coupling group protein has fewer than 10% of the atoms (460 out of 13663) Maybe you want to try Protein and Non-Protein instead? Making dummy/rest group for Acceleration containing 13663 elements Making dummy/rest group for Freeze containing 13663 elements Making dummy/rest group for Energy Mon. containing 13663 elements Making dummy/rest group for VCM containing 13663 elements Number of degrees of freedom in T-Coupling group Protein is 912.90 Number of degrees of freedom in T-Coupling group Other is 26403.10 Making dummy/rest group for User1 containing 13663 elements Making dummy/rest group for User2 containing 13663 elements Making dummy/rest group for XTC containing 13663 elements Making dummy/rest group for Or. Res. Fit containing 13663 elements Making dummy/rest group for QMMM containing 13663 elements T-Coupling has 2 element(s): Protein Other Energy Mon. has 1 element(s): rest Acceleration has 1 element(s): rest Freeze has 1 element(s): rest User1 has 1 element(s): rest User2 has 1 element(s): rest VCM has 1 element(s): rest XTC has 1 element(s): rest Or. Res. Fit has 1 element(s): rest QMMM has 1 element(s): rest Checking consistency between energy and charge groups... Calculating fourier grid dimensions for X Y Z Using a fourier grid of 44x44x44, spacing 0.118 0.118 0.118 writing run input file... There was 1 warning gcq#100: Proceed, With Fingers Crossed (TeX) -- Bharath.K.Chakravarthi Ph:9535629260 -- 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] simulating the effect of Ph
hello all... i know simulating the effect of temperature and pressure on the protein is there any way to study the effect of Ph on the system -- Bharath.K.Chakravarthi Ph:9535629260 -- 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] is it any serious error
Bharath.K. Chakravarthi wrote: hello all... when ever i run simulation i'm getting this kind of out put saying there is one warning as shown below Walking down the molecule graph to make shake-blocks initialising group options... processing index file... Analysing residue names: Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat There are: 4401 OTHER residues There are: 46 PROTEIN residues There are: 0 DNA residues Analysing Protein... Analysing Other... WARNING 1 [file aminoacids.dat, line 1]: T-Coupling group protein has fewer than 10% of the atoms (460 out of 13663) Have you searched the list archive and Gromacs site for this error? Certainly you would have found this: http://www.gromacs.org/Documentation/Errors#T-Coupling_group_XXX_has_fewer_than_10.25_of_the_atoms As for whether or not that is appropriate, please read the Thermostats entry linked from the above page. -Justin Maybe you want to try Protein and Non-Protein instead? Making dummy/rest group for Acceleration containing 13663 elements Making dummy/rest group for Freeze containing 13663 elements Making dummy/rest group for Energy Mon. containing 13663 elements Making dummy/rest group for VCM containing 13663 elements Number of degrees of freedom in T-Coupling group Protein is 912.90 Number of degrees of freedom in T-Coupling group Other is 26403.10 Making dummy/rest group for User1 containing 13663 elements Making dummy/rest group for User2 containing 13663 elements Making dummy/rest group for XTC containing 13663 elements Making dummy/rest group for Or. Res. Fit containing 13663 elements Making dummy/rest group for QMMM containing 13663 elements T-Coupling has 2 element(s): Protein Other Energy Mon. has 1 element(s): rest Acceleration has 1 element(s): rest Freeze has 1 element(s): rest User1 has 1 element(s): rest User2 has 1 element(s): rest VCM has 1 element(s): rest XTC has 1 element(s): rest Or. Res. Fit has 1 element(s): rest QMMM has 1 element(s): rest Checking consistency between energy and charge groups... Calculating fourier grid dimensions for X Y Z Using a fourier grid of 44x44x44, spacing 0.118 0.118 0.118 writing run input file... There was 1 warning gcq#100: Proceed, With Fingers Crossed (TeX) -- Bharath.K.Chakravarthi Ph:9535629260 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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] simulating the effect of Ph
Bharath.K. Chakravarthi wrote: hello all... i know simulating the effect of temperature and pressure on the protein is there any way to study the effect of Ph on the system That is a complex question, but there are a number of useful discussions about this in the list archive. The short answer is not really, but you may be able to derive some useful information from altering the protonation state of certain residues in your protein structure using the interactive options of pdb2gmx. Some other useful information: http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation -Justin -- Bharath.K.Chakravarthi Ph:9535629260 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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] conversion of desmond trajectory files into gromacs
Really? This is really great! Is there any need to specify the location of the vmd libraries? If a tpr file is needed for the analysis (eg: trjconv -pbc mol) is this somehow still possible? On Apr 16, 2010, at 10:07 PM, Roland Schulz wrote: In case you use the GIT version of the analysis tools you don't need to convert the trajectories first. I've added that the analysis tools can read all vmd supported file formats if GROMACS finds the vmd libraries. Roland On Fri, Apr 16, 2010 at 11:33 AM, XAvier Periole x.peri...@rug.nl wrote: Well I guess you want to use gmx analysis tools so you'll have to build the gmx topology of your system when necessary! Often only a pdb file or a gro file is sufficient. On Apr 16, 2010, at 5:24 PM, ram bio wrote: Thanks Xavier, Could you make it more eloborate... Ram On Fri, Apr 16, 2010 at 4:38 PM, XAvier Periole x.peri...@rug.nl wrote: VMD reads Desmond trajectories and writes GMX format ... Rests the topology to deal with ... On Apr 16, 2010, at 4:15 PM, ram bio wrote: Dear All, I have run a dynamics of protein ligand complex in lipid bilayer dppc using desmond software and would like to convert the trajectory files files into gromacs format, is it possible?? if so, please let me know your suggestions. Thanks, Ram -- 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 thewww 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 -- 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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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
[gmx-users] How can I maintain a distance of at least 0.5 nm from each other of solutes
Dear All, Hello I understand one can adjust distance of between solvent molecules by genbox command and -vdwd but I don't know, how do it between the solutes? Thanks for helping! 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/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] How can I maintain a distance of at least 0.5 nm from each other of solutes
rasoul nasiri wrote: Dear All, Hello I understand one can adjust distance of between solvent molecules by genbox command and -vdwd but I don't know, how do it between the solutes? Position your solutes using editconf -center, then add solvent. -Justin Thanks for helping! Rasoul -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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] How can I maintain a distance of at least 0.5 nm from each other of solutes
Dear Justin, Hello again Thanks for the message. I want to increase the distance between solutes in simulation box before MD simulation. How can I do it? Rasoul On Sat, Apr 17, 2010 at 5:16 PM, Justin A. Lemkul jalem...@vt.edu wrote: rasoul nasiri wrote: Dear All, Hello I understand one can adjust distance of between solvent molecules by genbox command and -vdwd but I don't know, how do it between the solutes? Position your solutes using editconf -center, then add solvent. -Justin Thanks for helping! Rasoul -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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] How can I maintain a distance of at least 0.5 nm from each other of solutes
rasoul nasiri wrote: Dear Justin, Hello again Thanks for the message. I want to increase the distance between solutes in simulation box before MD simulation. How can I do it? You can't. If you know you need a certain distance, that should be part of your planning :) I suppose you could run a pulling simulation to separate your two species, but that requires substantially more work (and setup considerations) than the two or three quick editconf commands to properly build the system. -Justin Rasoul On Sat, Apr 17, 2010 at 5:16 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: rasoul nasiri wrote: Dear All, Hello I understand one can adjust distance of between solvent molecules by genbox command and -vdwd but I don't know, how do it between the solutes? Position your solutes using editconf -center, then add solvent. -Justin Thanks for helping! Rasoul -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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] How can I maintain a distance of at least 0.5 nm from each other of solutes
Justin A. Lemkul wrote: rasoul nasiri wrote: Dear Justin, Hello again Thanks for the message. I want to increase the distance between solutes in simulation box before MD simulation. How can I do it? You can't. If you know you need a certain distance, that should be part of your planning :) I suppose you could run a pulling simulation to separate your two species, but that requires substantially more work (and setup considerations) than the two or three quick editconf commands to properly build the system. Correction: you can use editconf -translate with appropriate index groups to separate your solutes. This will also imply that you haven't added solvent, which is the same thing as positioning the two solutes appropriately in the first place (with editconf -center, as I posted before). -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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] How can I maintain a distance of at least 0.5 nm from each other of solutes
Hi, Thanks for the replies. Since I want to increase distance among co-solvents with themselves and with solutes, i must firstly fill the co-solvents along solutes and solvents after that i remove solvent, finally by edittconf -translate the co-solvents uniformally is distributed in the appropriate distances. Is it OK? Rasoul On Sat, Apr 17, 2010 at 5:43 PM, Justin A. Lemkul jalem...@vt.edu wrote: Justin A. Lemkul wrote: rasoul nasiri wrote: Dear Justin, Hello again Thanks for the message. I want to increase the distance between solutes in simulation box before MD simulation. How can I do it? You can't. If you know you need a certain distance, that should be part of your planning :) I suppose you could run a pulling simulation to separate your two species, but that requires substantially more work (and setup considerations) than the two or three quick editconf commands to properly build the system. Correction: you can use editconf -translate with appropriate index groups to separate your solutes. This will also imply that you haven't added solvent, which is the same thing as positioning the two solutes appropriately in the first place (with editconf -center, as I posted before). -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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] How can I maintain a distance of at least 0.5 nm from each other of solutes
rasoul nasiri wrote: Hi, Thanks for the replies. Since I want to increase distance among co-solvents with themselves and with solutes, i must firstly fill the co-solvents along solutes and solvents after that i remove solvent, finally by edittconf -translate the co-solvents uniformally is distributed in the appropriate distances. Is it OK? Why bother adding solvent if you're just going to remove it? Here's what I would do: 1. Position solutes in the box with editconf -center 2. Add co-solvents (with a large value of -vdwd, I suppose) 3. Add solvent I don't fully grasp why the initial position of the co-solvents matters so precisely; you may have a hard time satisfying all of the simultaneous distance requirements. Everything is just going to diffuse around anyway during MD. Maybe you have some reason I'm not thinking of, but it's a potentially complicated problem to build. -Justin Rasoul On Sat, Apr 17, 2010 at 5:43 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Justin A. Lemkul wrote: rasoul nasiri wrote: Dear Justin, Hello again Thanks for the message. I want to increase the distance between solutes in simulation box before MD simulation. How can I do it? You can't. If you know you need a certain distance, that should be part of your planning :) I suppose you could run a pulling simulation to separate your two species, but that requires substantially more work (and setup considerations) than the two or three quick editconf commands to properly build the system. Correction: you can use editconf -translate with appropriate index groups to separate your solutes. This will also imply that you haven't added solvent, which is the same thing as positioning the two solutes appropriately in the first place (with editconf -center, as I posted before). -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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] manual eq. 4.74-4.75 (dihedral restraints) head scratcher
Hello gmx-users, you rock and rollers,
Equations 4.74 and 4.75 in my copy of the manual have (please pardon
my pseudo-LaTeX):
(4.74)
\phi' = (\phi - \phi_0) MOD 2\pi
(4.75)
V(\phi') = \frac{1}{2}k ( \phi' - \phi_0 - \Delta \phi )^2 if \phi'
\Delta \phi
or
V(\phi') = 0 if \phi' \leq \Delta \phi
but should there be absolute values around all of the \phi-\phi_0?
Which way is it in the code -- with the absolute distance between \phi
and \phi_0 or the directed distance?
Also, as far as I can tell (and some mornings I definitely don't read
too good) neither the manual nor
http://wiki.gromacs.org/index.php/Dihedral_Restraints define the
fields in [ dihedral_restraints ], although the latter does name them.
There, I see
[ dihedral_restraints ]
; ai ajakal type label phi dphi kfac power
57 915 1 1 180 0 1 2
ai, aj, ak, al = atom numbers, obviously
type = ?, but I'm guessing there's only one type anyway
label = what is this one?
phi means phi0 ?
dphi means Delta phi, I guess
kfac is the force constant, probably
power = what is this one? Does 2 give me harmonic constraints?
I'd be happy to translate any answers given to the wiki, assuming I
get answered and that I'm allowed to edit the wiki.
May the Force be with you (as long as it's calculated in hand-tuned
assembly loops),
Dan
--
Quas Exact Comprehendere et ponderare Dei est non hominum. - Juan de Salas
--
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Re: [gmx-users] How can I maintain a distance of at least 0.5 nm from each other of solutes
Thanks for the information. Because of haven't satisfactory model from my co-solvent and I have to add it randomly along with the solvent by genbox -ci -nmol. the reason of this criteria relate to crash of system (solute+co-solvent+solvent) in the first step of simulation, because small distance between solute and co-solvents and co-solvents with themselves cause to rise of pressure. Rasoul . On Sat, Apr 17, 2010 at 6:03 PM, Justin A. Lemkul jalem...@vt.edu wrote: rasoul nasiri wrote: Hi, Thanks for the replies. Since I want to increase distance among co-solvents with themselves and with solutes, i must firstly fill the co-solvents along solutes and solvents after that i remove solvent, finally by edittconf -translate the co-solvents uniformally is distributed in the appropriate distances. Is it OK? Why bother adding solvent if you're just going to remove it? Here's what I would do: 1. Position solutes in the box with editconf -center 2. Add co-solvents (with a large value of -vdwd, I suppose) 3. Add solvent I don't fully grasp why the initial position of the co-solvents matters so precisely; you may have a hard time satisfying all of the simultaneous distance requirements. Everything is just going to diffuse around anyway during MD. Maybe you have some reason I'm not thinking of, but it's a potentially complicated problem to build. -Justin Rasoul On Sat, Apr 17, 2010 at 5:43 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Justin A. Lemkul wrote: rasoul nasiri wrote: Dear Justin, Hello again Thanks for the message. I want to increase the distance between solutes in simulation box before MD simulation. How can I do it? You can't. If you know you need a certain distance, that should be part of your planning :) I suppose you could run a pulling simulation to separate your two species, but that requires substantially more work (and setup considerations) than the two or three quick editconf commands to properly build the system. Correction: you can use editconf -translate with appropriate index groups to separate your solutes. This will also imply that you haven't added solvent, which is the same thing as positioning the two solutes appropriately in the first place (with editconf -center, as I posted before). -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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] conversion of desmond trajectory files into gromacs
On Sat, Apr 17, 2010 at 7:54 AM, XAvier Periole x.peri...@rug.nl wrote: Really? This is really great! Is there any need to specify the location of the vmd libraries? By default it tries to find them at /usr/local/lib/vmd/plugins/*/molfile If you have them installed somewhere else you can specify it by setting the VMD_PLUGIN_PATH environment variable. If a tpr file is needed for the analysis (eg: trjconv -pbc mol) is this somehow still possible? It would be pretty simple to add, that one can read this molecule information also from pdb or from psf. But I didn't have time to do it. In case you are interested to do that, I can give you help doing it. Until someone implements it, one still needs the tpr file. For cases where it is difficult to generate a top file we have a version of psfgen which generates a top file from a psf. But we don't have solved the license issue so far (NAMD license) and thus can't provide this version yet. Roland On Apr 16, 2010, at 10:07 PM, Roland Schulz wrote: In case you use the GIT version of the analysis tools you don't need to convert the trajectories first. I've added that the analysis tools can read all vmd supported file formats if GROMACS finds the vmd libraries. Roland On Fri, Apr 16, 2010 at 11:33 AM, XAvier Periole x.peri...@rug.nl wrote: Well I guess you want to use gmx analysis tools so you'll have to build the gmx topology of your system when necessary! Often only a pdb file or a gro file is sufficient. On Apr 16, 2010, at 5:24 PM, ram bio wrote: Thanks Xavier, Could you make it more eloborate... Ram On Fri, Apr 16, 2010 at 4:38 PM, XAvier Periole x.peri...@rug.nl wrote: VMD reads Desmond trajectories and writes GMX format ... Rests the topology to deal with ... On Apr 16, 2010, at 4:15 PM, ram bio wrote: Dear All, I have run a dynamics of protein ligand complex in lipid bilayer dppc using desmond software and would like to convert the trajectory files files into gromacs format, is it possible?? if so, please let me know your suggestions. Thanks, Ram -- 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 thewww 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 -- 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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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 -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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
