Re: [gmx-users] Domain decomposition configuration

Denny Frost wrote: Is tpbconv with the "pbc" option the best way to make the molecules whole again? The only way, as far as I'm aware (aside from editconf's crude approach). Do this before you concatenate your systems. -Justin On Wed, Feb 9, 2011 at 2:06

Re: [gmx-users] g_hbond and 4.5.2 version

reported in 4.5.1: http://lists.gromacs.org/pipermail/gmx-users/2010-October/054905.html but not fixed until after 4.5.3 was released: http://lists.gromacs.org/pipermail/gmx-users/2010-December/056406.html -Justin Greetings Zuzana -- Justin A. Lemkul

Re: [gmx-users] Domain decomposition configuration

Mark Abraham wrote: On 10/02/2011 8:10 AM, Justin A. Lemkul wrote: Denny Frost wrote: Is tpbconv with the "pbc" option the best way to make the molecules whole again? The only way, as far as I'm aware (aside from editconf's crude approach). Do this before you conc

Re: [gmx-users] Domain decomposition configuration

Mark Abraham wrote: On 10/02/2011 12:45 PM, Justin A. Lemkul wrote: Mark Abraham wrote: On 10/02/2011 8:10 AM, Justin A. Lemkul wrote: Denny Frost wrote: Is tpbconv with the "pbc" option the best way to make the molecules whole again? The only way, as far as I'm aw

Re: [gmx-users] pull code

-equilibrium process. Please read the tutorial carefully. -Justin Kind regards, chetan From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: 09 February 2011 16:40 To: Discussion li

Re: [gmx-users] server_for_Gaussian

probably a violation of their license. -Justin Shahid Nayeem -- 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

Re: [gmx-users] PRODRG

ing. There are web servers and other software out there that can do this for you. Google is your friend. -Justin What do you think? On Wed, Feb 9, 2011 at 9:39 PM, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote: The OP's question is easily answered by referring to

Re: [gmx-users] ref_temp and gen_temp during simulated annealing

nks and regards /Bipin Singh/ / / / -- ============ 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/

Re: [gmx-users] rotamers during minimization

el = no -- ============ 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/P

Re: [gmx-users] localpressure.dat file not created

to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.e

Re: [gmx-users] PRODRG

don't use PRODRG. Gromos96 is a united-atom force field. -Justin Thanks in advance Mohsen On Thu, Feb 10, 2011 at 7:56 PM, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote: mohsen ramezanpour wrote: Dear Dr.Justin I have read this section before.

Re: [gmx-users] Re: crashed simulation: simulation of docked proteins in spc water crashes with LINCS warning (Mark Abraham)

or .mdp settings are being applied, breaking the force field model and causing the crash. Without seeing the .mdp and relevant topology(ies), it's impossible to say. -Justin -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Tr

Re: [gmx-users] Charges

ilitary Institute of Engineering Rio de Janeiro - RJ Brazil. -- ============ 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.

Re: [gmx-users] Re: Extending the simulation

l University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com <mailto:monu46...@yahoo.com> -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Traine

Re: [gmx-users] NVT run

tom of the output gro file? The one corresponding to that configuration, i.e. the last step. -Justin Regards, Thomas -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA j

Re: [gmx-users] extracting a structure from confout.gro file

trjconv and the index group created in step 3. -Justin Cordially DRICI nedjoua -- 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

Re: [gmx-users] rotamers and rings

will not be stable in MD. -Justin Sorry for bothering you again and thank you in advance for your help, Abdullah Ahmed -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksbur

Re: [gmx-users] Re: only one model is displayed

tions are welcomed. Regards, Joyce -- ============ 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 ==

Re: [gmx-users] Add custom residue to DNA index group

t; > 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-u

Re: [gmx-users] Add custom residue to DNA index group

gmx-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.

Re: [gmx-users] Terminus Atoms genrestr?

I would be very happy. Like the other Gromacs utilities, genrestr can make use of index files. -Justin Thank you, TJ Mustard -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia

Re: [gmx-users] Terminus Atoms genrestr?

abilities and syntax are not yet well-documented. -Justin Thank you, TJ Mustard On February 11, 2011 at 10:30 AM "Justin A. Lemkul" wrote: > > > TJ Mustard wrote: > > > > > > Hi all, > > > > > > Does anyone know how to ma

Re: [gmx-users] Terminus Atoms genrestr?

Teemu Murtola wrote: Hi, On Fri, Feb 11, 2011 at 21:05, Justin A. Lemkul wrote: I don't know of any Gromacs tool (other than pdb2gmx) that is smart enough to determine terminal residues on its own. If you have multiple copies of the same molecule, then you know how many atoms are in

Re: [gmx-users] genbox error

4 exclusions Thanks and Regards, Rini Dr. Rini Gupta Postdoctoral Fellow University of British Columbia Vancouver <http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline.htm@Middle?> -- ============ Justin

Re: [gmx-users] Dangling phospholipids

then a gentle equilibration can bring everything together within a few ns. -Justin Cheers, Ramon Garduno El 09/02/2011 11:25 a.m., Justin A. Lemkul escribió: Dr. Ramón Garduño-Juárez wrote: Dear All, First of all I want to tank Justin Lemkul and Thomas Piggot for their useful comments

Re: [gmx-users] gromos96 charges

gromacs? It's simply the sum of the partial charges on all the constituent atoms. -Justin Cordially DRICI nedjoua -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksbur

Re: [gmx-users] Active site

that still converge. -Justin Thanks in advance for your guidances. Mohsen -- ==== 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

Re: [gmx-users] how to fixe distance

thing might be happening. -Justin cordially DRICI nedjoua -- ==== 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

Re: [gmx-users] Active site

relying on very old Gromacs versions. The fundamental principles still stand, though. Read in the manual about new .mdp options and new methods for calculating free energy. -Justin Thanks in advance for your guidance On Sat, Feb 12, 2011 at 4:50 PM, Justin A. Lemkul <mailto:jalem...@v

Re: [gmx-users] Re: Group LEU not found in index file

Regards, Adam -- ============ 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/

Re: [gmx-users] Active site

(maybe one that's already published) to validate your procedure. -Justin Thanks in advance for your reply On Sun, Feb 13, 2011 at 3:55 PM, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote: mohsen ramezanpour wrote: Dear Dr.Justin I couldn't find an

Re: [gmx-users] Output of Gromacs Demo

p://autos.yahoo.com/green_center/;_ylc=X3oDMTE4MGw4Z2hlBF9TAzk3MTA3MDc2BHNlYwNtYWlsdGFncwRzbGsDZ3JlZW5jZW50ZXI-> at Yahoo! Autos' Green Center. -- ======== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksbur

Re: Fw: [gmx-users] Output of Gromacs Demo

ight's Picks" <http://us.rd.yahoo.com/evt=49979/*http://tv.yahoo.com/> on Yahoo! TV. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksb

Re: [gmx-users] Output of Gromacs Demo

Justin Best, Majid -------- *From:* Justin A. Lemkul *To:* Discussion list for GROMACS users *Sent:* Sun, February 13, 2011 9:30:52 AM *Subject:* Re: [gmx-users] Output of Gromacs Demo majid hasan wrote: > I have attached the output of demo, and another Okay, I just ran the demo and kept pressing

Re: [gmx-users] CG to FG transformation error

numerous keywords that do not exist in normal Gromacs. -Justin Thanks, -Anirban -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemku

Re: [gmx-users] pull code

), and perhaps other options. There are examples in the list archive, if you spend some time searching. -Justin Kind regards, chetan From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu]

Re: [gmx-users] Gromacs Installation

-- Sucker-punch spam < http://us.rd.yahoo.com/evt=49981/*http://advision.webevents.yahoo.com/mailbeta/features_spam.html> with award-winning protection. Try the free Yahoo! Mail Beta. < http://us.rd.yahoo.com/evt=49981/*http://advision.webevents.yahoo

Re: [gmx-users] g_dipole

g. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ============ 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

Re: [gmx-users] NVE simulation

Thomas Koller wrote: Hello! Is it possible to run NVE simulations insteed of NVT or NPT in Gromacs? Yes. http://www.gromacs.org/Documentation/Terminology/NVE -Justin Thomas -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES

Re: [gmx-users] Umbrella sampling windows

u probably want either (1) a lower force constant or (2) more windows along your reaction coordinate. Option (2) seems to be more efficient, since you don't have to re-do your simulations, you can just run some more. -Justin Thank you in advance, Susana -- ====

Re: [gmx-users] top2psf.pl issue: trying to use vmd w/ MARTINI protein

). -Justin -j -- ======== 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-

Re: [gmx-users] Repulsion instead of adsorption

simulate long enough. 500 ps is an extremely short timeframe. -Justin any help will highly appreciated. -- ======== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[a

Re: [gmx-users] Protein-membrane system

: asegu...@ipn.mx <mailto:asegu...@ipn.mx>; aldoseg...@gmail.com <mailto:aldoseg...@gmail.com> == ===/* -- ======== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of

Re: [gmx-users] mpirun error?

? What does that line mean? See the manual and/or Gromacs 4 paper for an explanation of dynamic load balancing. This is a normal message. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of

Re: [gmx-users] zero atoms for FE P

ou didn't post it, so please do. -Justin Thanks moeed -- 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 ==

Re: [gmx-users] Protein-membrane system

rs@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

Re: [gmx-users] free energy blank dgdl

ntramol = no You didn't set "couple-moltype" so mdrun doesn't know which molecule to decouple. -Justin *********** Thank you in advance. Moeed -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Schola

Re: [gmx-users] domain decomposition error

-- 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

Re: [gmx-users] I need ligand topology file

ation procedure. http://www.gromacs.org/Downloads/User_contributions/Other_software http://www.gromacs.org/Documentation/How-tos/Parameterization -Justin -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochem

Re: [gmx-users] Weeks Chandler Andersen potential

ial> Is table option the only way to go ? Buckingham and LJ are the only default van der Waals functional forms available by default. So, yes, use tables. -Justin - Rohit -- ======== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Train

Re: [gmx-users] saving velocities and coordinates frequently

solvent might be an option, if appropriate for your system. -Justin Amit -- 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

Re: [gmx-users] RE: simulation of a metal binding sites

vision of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com <mailto:monu46...@yahoo.com> -- Justin

Re: [gmx-users] where to insert a new include DPOSRES in topology file?

cience - CNR Via Roma, 64 83100 Avellino Phone: +39 0825 299651 Fax: +39 0825 781585 E-mail: amarabo...@isa.cnr.it <mailto:amarabo...@isa.cnr.it> Skype account: annam1972 Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm "When a man with a gun meets a man with a pen, the man with t

Re: [gmx-users] Fwd: Adding small molecule parameters to charmm force field

o.com <mailto:monu46...@yahoo.com> -- ======== 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/Pers

Re: [gmx-users] SO4 ion

-Justin Thanks for your help. Simon Sham -- ============ 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.

Re: [gmx-users] unable to display MARTINI system with VMD

know where i am going wrong? any suggestions are very appreciated. There's a Tcl script from the same site where you (presumably) found my script, but I've never used it so I can't help you with that. -Justin -john -- ============ Justin A. L

Re: [gmx-users] unable to display MARTINI system with VMD

iate your help a lot. i am sort of isolated, lately, from anyone i can discuss anything regarding simulation issues. best, john -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Bla

Re: [gmx-users] Umbrella sampling for protein-drug system

.@gmail.com <mailto:aldoseg...@gmail.com> =/* -- ======== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (5

Re: [gmx-users] on force fields

it to gmx-users-requ...@gromacs.org <http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org>. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ======== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar

Re: [gmx-users] on force fields

r the resulting topology to be useful (or produced at all, for that matter). -Justin --- On *Mon, 2/21/11, Justin A. Lemkul //* wrote: From: Justin A. Lemkul Subject: Re: [gmx-users] on force fields To: "Discussion list for GROMACS users" Date: Monday, February 21,

Re: [gmx-users] how many contacts has a certain atom at MD

it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul

Re: [gmx-users] how many contacts has a certain atom at MD

-d. -Justin best, Olga 2011/2/21 Olga Ivchenko <mailto:olga.ivche...@gmail.com>> Thank you very much. best, Olga 2011/2/21 Justin A. Lemkul mailto:jalem...@vt.edu>> g_mindist -on (with suitable index groups) should also do the trick. -Jus

Re: [gmx-users] An argument about long range electrostatics

s. Thanks a lot Hassan -- ============ 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

Re: [gmx-users] Can g_wham support using different temperature for different windows?

suggestions will be highly appreciated, thank you! A more straightforward approach is to (1) add more sampling windows or (2) increase the force constant in regions where there's poor sampling, or perhaps both. -Justin Cheers, Jianguo -- ==== Justin A. L

Re: [gmx-users] Can g_wham support using different temperature for different windows?

n best regards, Jianguo -------- *From:* Justin A. Lemkul *To:* Discussion list for GROMACS users *Sent:* Tuesday, 22 February 2011 09:35:37 *Subject:* Re: [gmx-users] Can g_wham support using different temperature for different windows? Jian

Re: [gmx-users] Can g_wham support using different temperature for different windows?

x27;ll have to introduce some kind of intramolecular restraints. -Justin Any Suggestions of dealing with the highly charged system? Cheers, Jianguo -------- *From:* Justin A. Lemkul *To:* Gromacs Users' List *Sent:* Tues

Re: [gmx-users] %exist hydrogen bond

s" statement on or around line 151 and the enclosing brace on line 161 (but leave the intervening content alone). -Justin -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia

Re: [gmx-users] Can g_wham support using different temperature for different windows?

o justify this procedure to a skeptical audience. -Justin Is there any other method to deal with the insufficient sampling? Any suggestions are welcome, thanks for your time reading this email! Cheers, Jianguo ------------ *From:* J

Re: [gmx-users] index file for interaction energies

gives what I need? You need to -rerun. g_energy does not take an index file, and it only analyzes existing groups, it cannot derive new ones. -Justin Thanks for your help Paniz -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-

Re: [gmx-users] index file for interaction energies

ergy gives what I need? You need to -rerun. g_energy does not take an index file, and it only analyzes existing groups, it cannot derive new ones. -Justin Thanks for your help Paniz -- ==== Justin A. Lemkul

Re: [gmx-users] index file for interaction energies

ou haven't set your energygrps properly and you don't want to completely run the simulation over again. -Justin On 22 February 2011 17:35, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote: Nick wrote: Dear Justin, Thanks for your reply and Sorry

Re: [gmx-users] Can g_wham support using different temperature for different windows?

This technique might work, provided you don't destabilize the membrane, but if the peptide is truly "stuck" in this orientation, I doubt that limited-range REMD would be very useful. -Justin Cheers Jianguo ----------

Re: [gmx-users] Re: Differences in rmsd with different force field

...@yahoo.com> -- ======== 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 =

Re: [gmx-users] Re: Differences in rmsd with different force field

orce field X is probably a bad choice, even if there is some element of precedent. -Justin On Tue, Feb 22, 2011 at 6:31 PM, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote: bharat gupta wrote: Hi I did a simulation of 3 ns with OPLS AA 2001 Force Field for

Re: [gmx-users] Re: Adding chromophore parameters to the charmm force field

National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com <mailto:monu46...@yahoo.com> -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES

Re: [gmx-users] Van der waals interaction between nanotubes

very helpful.Whether Any tutorials are available for such a kind of thing... Running a simulation while setting proper energygrps to decompose short-range nonbonded interactions sounds to be what you need to do. -Justin Thank you in advance guys -- ==== Jus

Re: [gmx-users] %exist hydrogen bond

ASN51 ND2 0.320 GLN23 OE111.191 . . . how to fix it? -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- =

Re: [gmx-users] Library file ffamber_tip3p.gro not found in current directory

-- -- SUNITA GUPTA -- ======== 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/Pag

Re: [gmx-users] how many contacts has a certain atom at MD

/2/21 Justin A. Lemkul mailto:jalem...@vt.edu>> Olga Ivchenko wrote: So I used mindist for a certain group of molecules which is surrounded by water. I got plot number of contacts versuc sumulation time. According to what I see in a distance < 0.6nm at

Re: [gmx-users] Van der waals interaction between nanotubes

sakthi kumaran wrote: On Wed, Feb 23, 2011 at 5:25 PM, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote: sakthi kumaran wrote: Dear all, Hi I am new to gromacs. I want to calculate the Van der waals interaction between two capped CNT facing e

Re: [gmx-users] %exist hydrogen bond

tical Physical Chemistry Group -- ======== 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

Re: [gmx-users] how many contacts has a certain atom at MD

on't see any problem with doing that. On what do you need advice? -Justin best, Olga 2011/2/21 Justin A. Lemkul mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> Olga Ivchenko wrote: S

Re: [gmx-users] Can g_wham support using different temperature for different windows?

ere involved. This might be a lot pessimistic but you should not get fooled by a CG model. Martini is really good for a lot of things but other things should really but be looked at carefully. XAvier. -- Justin A. Lemkul Ph.D. Candidate ICTAS Do

Re: [gmx-users] Residue 'DEF' not found in residue topology database

modify the force field properly. http://www.gromacs.org/Documentation/Tutorials#Membrane_Simulations -Justin I would be so glad if you can help me solve this problem. Thank you in advance, Deniz -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-I

[gmx-users] Website search broken

operators. Table './gromacs_wikidb/query_log' is marked as crashed and should be repaired tutorials I know that this search should work, so I figured it was a robust test. Anything else I search for gives me an analogous result. -Justin -- ============ J

Re: [gmx-users] Residue 'DEF' not found in residue topology database

erminology/Periodic_Boundary_Conditions -Justin Thank you in advance, Deniz On Wed, Feb 23, 2011 at 3:57 PM, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote: Emine Deniz Tekin wrote: Hi gromacs users, I am using the gromacs 4.5.3 version. I created a lipopetide

Re: [gmx-users] Minimisation restraints

my protein without moving (or minimizing) the backbone. Please has anyone done this before? Use genrestr to create a custom position restraint .itp file. -Justin Thank you. Carla -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGE

Re: [gmx-users] 9 particles communicated to PME node 5 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.

/Errors#X_particles_communicated_to_PME_node_Y_are_more_than_a_cell_length_out_of_the_domain_decomposition_cell_of_their_charge_group http://www.gromacs.org/Documentation/Terminology/Blowing_Up -Justin -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu

Re: [gmx-users] topology files for ligands in MD Simulation under OPLS AA force field

OPLS_AA force field and GROMACS package. Sincerely Yours Ruo-Xu Gu -- 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

Re: [gmx-users] CNT topology

this error again comes. please guide me. thank you so much Best Sara Azhari Phd Student -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (

Re: [gmx-users] How to countting hydrogen bond lifetime and donor--acceptor residue's atom ?

OW 0.160< BR>> ARG58NE SOL3595 OW 1.359 Can you give me some proposal? best regards -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemi

Re: [gmx-users] g_rms and g_cluster

r -h. -Justin Shahid Nayeem -- ============ 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/

Re: [gmx-users] How to countting Hbonds lifetime

t the case? Hydrogen bond lifetime can be computed with g_hbond, as Erik said before. -Justin Thank you very much. -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA j

Re: [gmx-users] %exist hydrogen bond - difference between number of lines in input and output files

tin best regards. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Bi

Re: [gmx-users] Re: How to countting Hbonds lifetime

nd and the donor-acceptor atoms. The g_hbond can do it? Sure, that's what hbond.ndx and hbmap.xpm are. -Justin Thank you very much. -- ======== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistr

Re: [gmx-users] water-medited hydrogen bonds - %exist hydrogen bonds

. -Justin any suggestion will highly appreciated. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee

Re: [gmx-users] g_dipole

anyone tell whats the problem. This is the expected behavior. See g_dipoles -h, especially the -acflen flag. -Justin I am using Gromacs VERSION 4.0.7 version. Thanks NIlesh -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT

Re: [gmx-users] g_dipole

Nilesh Dhumal wrote: How can I make prog. to read all frames. I already answered this. Use a proper setting for -acflen. -Justin On Thu, February 24, 2011 2:34 pm, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Hello, I am calculating dipole autocorrelation function for my system

Re: [gmx-users] em mdrun

happening? mdrun now uses thread-based parallelization by default, using all available nodes. To suppress this effect, use mdrun -nt 1. Otherwise, yes, it is a parallel calculation :) -Justin Thanks -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral

Re: [gmx-users] em mdrun

require such a large cell size. http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm The .log file may provide more useful diagnostic information. -Justin On 24 February 2011 16:21, J

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