Re: [gmx-users] load imbalance

s 1101 University Ave, Rm. 8359 Madison, WI 53706 Phone: 608-265-3644 Email: kork...@wisc.edu <mailto:kork...@wisc.edu> -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg

[gmx-users] Re: doubt about your Umbrella Sampling tutorial

c Chemistry and Center for Research in Biological Chemistry and Molecular Materials Santiago de Compostela University E-15782 Santiago de Compostela (Spain) e-mail: rebeca.garcia.fand...@usc.es Phone: 34-981563100 ext 15760 -- ============ Justin A. Lemkul

Re: [gmx-users] minimum image violation

one's been able to diagnose the problem based on this (continually posted) information. If it's a useless trajectory, why bother? -Justin Thanking you With regards M. Kavyashree -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MI

Re: [gmx-users] error bars g_wham

-- 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: Error during executing the protein ligand tutorial

u're missing an exponent. But I'd echo what Mark has said - always provide real output directly copied from the screen, or else we're left to our suspicions and guesses, which ends up wasting everyone's time. -Justin -- ============ Justin A. Le

Re: [gmx-users] implicit solvent system set up

hone: 608-265-3644 Email: kork...@wisc.edu <mailto:kork...@wisc.edu> -- ============ 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 calculate RMSD per residue with Gromacs ?

Chih-Ying Lin wrote: Hi How to calculate RMSD per residue with Gromacs ? g_rmsf -od -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] PMF analysis and pull_dim (Step 6 of Justin's tutorial)

0 (which is the reference group), but pull_group1. Otherwise, yes. -Justin This came a bit longish, Thanks in advance, -Shay P.S. Using Gromacs 4.0.7 -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of B

Re: [gmx-users] query regarding g_ras command

ds, Rashi -- ==== 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 ma

Re: [gmx-users] query regarding g_ras command

ption. -Justin On Tue, Jun 21, 2011 at 6:53 PM, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote: rashi parihar wrote: I want to obtain solvent accessible surface area using g_sas command: g_sas -f *.xtc -s *.tpr -n *.ndx -o -or -oa.plz tell me the full

Re: [gmx-users] Questions about GB parameters

Can anyone comment further on either of these issues? -Justin Mark Abraham wrote: On 15/06/2011 4:24 AM, Justin A. Lemkul wrote: Hi All, I wanted to dig up an old discussion that hit the list a long time ago because I'm now encountering some problems understanding the GB settings m

Re: [gmx-users] How to set proper temperature and pressure coupling parameters, especially when using solvents other than water?

artificially relaxed. -Justin Thank you so much for your kind help, any suggestions or clues are very welcome. Yours xiaodong huang Research School of Chemistry ANU -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee

Re: [gmx-users] PMF and appending simulation: -pf and -px flags (gromacs 4.0.7)

in -px and -pf. Appending can be done, but without seeing your actual series of commands, no one can offer you any useful advice or insight as to why it isn't working in your case. -Justin -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Sc

Re: [gmx-users] DPPC temperatur setting

-- 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] Questions about GB parameters

r this one. I look forward to it :) -Justin Cheers /Per 21 jun 2011 kl. 18.42 skrev Justin A. Lemkul: Can anyone comment further on either of these issues? -Justin Mark Abraham wrote: On 15/06/2011 4:24 AM, Justin A. Lemkul wrote: Hi All, I wanted to dig up an old discussion that hit

Re: [gmx-users] restraints in PMF (Justin's tutorial)

Fandiño > > Department of Organic Chemistry and Center for Research in Biological > > Chemistry > > and Molecular Materials > > Santiago de Compostela University > > E-15782 Santiago de Compostela (Spain) > > e-mail: rebeca.garcia.fand...@usc.es &g

Re: [gmx-users] restraints in PMF (Justin's tutorial)

ot in advance for your help with this topic, and thank you > > > > very much also for publishing this interesting tutorial. There was > > > > nothing useful until that for Umbrella Sampling with Gromacs 4.0, so I > > > > think it is more than wellcome for all Gromacs u

Re: [gmx-users] Re: Re:NVT equilibration of DMSO solvent (Charmm all-atom force field)

mble. -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

Re: [gmx-users] DPPC temperatur setting

e you should use. If you state the assumption that pure DPPC should be simulated at roughly 323 K and everything is relative to that, it's part of the interpretation of your results. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Schol

Re: [gmx-users] Relaxed frozen groups

desired freezegrps. -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

Re: [gmx-users]Question about reduced unit for coarse grain

e 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/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS D

Re: [gmx-users] How to set proper temperature and pressure coupling parameters, especially when using solvents other than water?

ry welcome. Yours xiaodong huang Research School of Chemistry ANU -- ==========__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Te

Re: [gmx-users]Question about reduced unit for coarse grain

who developed the web service you're trying to use, if this information is not otherwise documented somewhere (FAQ's, publication, etc). -Justin Thank you anyway. Ye 2011/6/22 Justin A. Lemkul mailto:jalem...@vt.edu>> Ye Yang wrote: Thank you very much, Mark.

[gmx-users] Re: Gromacs Query.

", line 226]: No default Proper Dih. types ERROR 0 [file "topol.top", line 227]: No default Proper Dih. types Please help me out in this issue.Thanks in advance... -- Justin A. Lemkul Ph.D. Candidate

Re: [gmx-users] DPPC temperatur setting

odel physiological reality, you likely shouldn't be using DPPC as your primary lipid. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul

Re: [gmx-users] Re: Relaxed frozen groups

ying a harmonic restraint to a group to keep it close to some reference location. You can set relative or absolute reference positions; see the manual. -Justin -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Bioche

Re: [gmx-users] pdb2gmx Could not find force field, when using -ff commandline parameter

a3.itp in /usr/share. No luck there either. Anything named ffG45a3.itp is retained only for compatibility in the newer version and should simply #include "gromos45a3.ff/forcefield.itp" and nothing more. -Justin -- Justin A. Lemkul Ph.D. C

Re: [gmx-users] Re: 1-4 cut off error during EM

ience 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 A. Lemkul Ph.D. Candidate ICTAS Doctoral S

Re: [gmx-users] Re: 1-4 cut off error during EM

EM of the protein and/or the modified residue itself would be a reasonable start to diagnosing the underlying problem. -Justin On Fri, Jun 24, 2011 at 11:23 AM, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote: bharat gupta wrote: Hi, I generated the top

Re: [gmx-users] Re: Box-dimensions -g_energy_output

able to figure out why only 1978700 data point are considered. Kindly give some suggestions. Thank you with regards M.Kavyashree -- ======== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry

Re: [gmx-users] lattice Coulomb energy between energy groups

me interactions between groups A and B. If there are no charges on groups A and B, you should be fine. -Justin -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jal

Re: [gmx-users] Re: Box-dimensions -g_energy_output

re the energy values go screwy. If you find a bunch of nonsensical information, then you have your answer. -Justin Thank you fro answering. With Regards M. Kavyashree On Fri, Jun 24, 2011 at 4:57 PM, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote: Kavyashree M wrote:

Re: [gmx-users] lattice Coulomb energy between energy groups

exclude the PME mesh term. -Justin Cheers Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi all I have set up a simulation with PBC using PME and specify an energy group enclusion involving some virtual sites and a hydrocarbon chain. i.e. hydrocarbon chain is one energy group and the virtual

Re: [gmx-users] Re: Box-dimensions -g_energy_output

ution. The only diagnostic I can suggest is gmxdump. It should be rather obvious what's going on - your reported averages are 0.04, but the actual values from the plot are clearly different. -Justin Thanks With regards M. Kavyashree On Fri, Jun 24, 2011 at 5:20 PM, Justin A. Lemkul <

Re: [gmx-users] Re: Box-dimensions -g_energy_output

file again. Thanks With regards M. Kavyashree On Fri, Jun 24, 2011 at 5:20 PM, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote: Kavyashree M wrote: Sir, I am sorry I did not get any mail for that query since I posted it.

Re: [gmx-users] Re: Box-dimensions -g_energy_output

7;ve done have given normal results. In that case, re-run the simulation that's causing problems (or at least a short part of it, to test) and see if you get usable output. -Justin Thanks With Regards M. Kavyashree On Fri, Jun 24, 2011 at 6:32 PM, Justin A. Lemkul <mailto:jalem...

Re: [gmx-users] Regarding g_dist -dist option

bipin singh wrote: Hello, I just want to ask that in g_dist module, -dist option expect distance as a real argument, so the distance should be in nm or A for that... Please read the manual, Chapter 2. -Justin -- Justin A. Lemkul Ph.D. Candidate

Re: [gmx-users] About the %SS values in the output of do_dssp

idues, but since chain separators count as residues, the calculations are all done out of 47 residues instead. You'll have to either modify the code to account for this problem or simply re-calculate the averages yourself. -Justin Thank you in advance for your help SA -- ==

Re: [gmx-users] Simulation of Primed DNA

/Documentation/File_Formats/specbond.dat -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

Re: [gmx-users] (no subject)

group you've selected is not suitable for the analysis. -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

Re: [gmx-users] print inter and intra energy

the .edr file with g_energy. -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

Re: [gmx-users] Periodic Images - clarification

ting the same (or tangentially related) questions with no answer, time that could have been spent running a proper simulation to recover what you lost. -Justin -- ======== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department

Re: [gmx-users] Periodic Images - clarification

've done just one simulation. -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 =

Re: [gmx-users] missing topology file adn creating a new one

n only, then manually add the missing water and ions to the topology. If you're system is something more complex than that, then hopefully you've documented your procedure well such that you can reproduce it. And don't let files go "missing" :) -Justin -- ====

Re: [gmx-users] Comparing MD ensembles with exp. NOE restraints --> bus error

(the latest), please try again with this version. If you are using 4.5.4 or the error persists, please file an issue report on redmine.gromacs.org and include your .tpr and .pdb files necessary to reproduce the problem. -Justin -- ============ Justin A. Lemkul

Re: [gmx-users] minimization problem (Martini simulation)

licate any unit cell in any dimension using genconf -nbox. -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.be

Re: [gmx-users] g_covar : segmentation fault

files to reproduce the problem. -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

Re: [gmx-users] The RMSD of a metal ion

with trjconv and issue g_rms -nofit to calculate the RMSD of the metal ion. -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)

Re: [gmx-users] minimization problem (Martini simulation)

stable. You should set "gen_vel = yes" to start a reasonable equilibration period. -Justin -- ======== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg,

Re: [gmx-users] pull direction of steered MD in Gromacs

://www.gromacs.org/Documentation/Tutorials?highlight=tutorials#Pull_Code_and_Umbrella_Sampling -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] about periodic image violations

the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- =

Re: [gmx-users] Broken protein chain.

structure to create a reasonable topology and run any sort of simulation. Missing termini may not be significant, but any atoms or residues missing within the chain have to be reconstructed. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral

Re: [gmx-users] reg ionic strngth

function, please post it, otherwise do not expect the users of this list to do your thinking for you. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul

Re: [gmx-users] Iusses while converting a POPE pdb with pdb2gmx and ff charmm27

-5.459 1.932 1.00 0.00 11 -- ======== 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.bioche

Re: [gmx-users] How to protonate a gmx trajectory?

e .pdb files of each of your trajectory frames, then re-concatenate them as a new .xtc file. That would be somewhat tedious, but should work. -Justin -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Bioche

Re: [gmx-users] building a new molecule which does not exist in gmx data base

ustin -- ==== 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/j

Re: [gmx-users] trjorder and index

ing a single trajectory impossible. -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/

Re: [gmx-users] converting psf file to gromacs .itp file

top2psf.pl that is available from the User Contributions page on the Gromacs site that does the opposite (.itp to .psf) that you may be able to reverse engineer for your purpose. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT

Re: [gmx-users] Re: Running Lyz in water

9686933963* -- ==== 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] Iusses while converting a POPE pdb with pdb2gmx and ff charmm27

00 0.998 1.00 0.00 11 ATOM250 H16Z POPE2 -15.893 -5.459 1.932 1.00 0.00 11 -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA

Re: [gmx-users] error in running pdb2gmx command

in Because Of Another Smile . . . ." Regards, Rashi -- ============ 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.bioch

Re: [gmx-users] Question about g_bar output

a bug. Proper output is discussed in the BAR tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/07_analysis.html -Justin -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Departme

Re: [gmx-users] Question about g_bar output

never version 4.5.5 is released. -Justin Warren Gallin On 2011-06-29, at 12:48 PM, Justin A. Lemkul wrote: Warren Gallin wrote: Hi, I've just run g_bar on data from a simulation, and I am having trouble reconciling the graphical output with the numerical output. The units s

Re: [gmx-users] the effect of the ligand on each residue

that is most meaningful to you, based on the behavior observed in the trajectory. You can analyze backbone, sidechain, or all protein atoms separately. Several iterations may be informative, using several different groups. -Justin -- Justin A. Lemkul

Re: [gmx-users] the effect of the ligand on each residue

n 30 Haziran 2011 14:43 tarihinde Justin A. Lemkul <mailto:jalem...@vt.edu>> yazdı: ahmet yıldırım wrote: Dear users, I want to see the effect of the ligand on each residue using the following command: g_rmsf -s run.tpr -f run.xtc -o

Re: [gmx-users] Regarding PDB file

I have to delete some other things also. The only lines you absolutely must remove are the coordinate entries. REMARK and CONECT lines are ignored by pdb2gmx and most other Gromacs programs. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral

Re: [gmx-users] Calculate distance between two atoms

create the necessary groups with a text editor. (2) What is the exact format of g_dist that should be applied on the command line? Please read g_dist -h. -Justin -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Dep

Re: [gmx-users] terminal_fixing

). If you choose the zwitterion forms, your topology will be broken. -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

Re: [gmx-users] 3rd neighbor

taken from Table 7 (Oostenbring et al. JCC 2004, 53A6) and the [ nonbond_params ] contain the hard coded parameter of Table 8. So, where are the parameter of table 9 written? These are in [pairtypes]. See manual section 5.3.4. -Justin -- Justin A

Re: [gmx-users] solvent_protein interaction energy

terms. -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/j

Re: [gmx-users] energygrps long-range interaction

group contributions, but the usefulness of this information is debatable. -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

Re: [gmx-users] interaction energy

sely based on what you actually need to analyze. -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.bioc

Re: [gmx-users] interaction energy

> "Select the terms you want from the following list by > selecting either (part of) the name or the number or a combination. > End your selection with an empty line or a zero." > > Writing all terms to the same output file will result in nothing but an > incoherent mess.

Re: [gmx-users] interaction energy

gt; > > > > --- > > > > > > > > how one can write this all to a file ! > > > > > > > > > > As prompted by g_energy: > > > > > > "Select the terms you want from the following list by > > &g

Re: [gmx-users] how is dVpot/dlambda calculated

manual, section 4.5. -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

Re: [gmx-users] energygrps long-range interaction

do we? Presumably, since the effect of the reaction field is uniform beyond rcoulomb. The problem with RF is the discontinuity present at the cutoff. -Justin Gyorgy Citando "Justin A. Lemkul" : gyorgy.han...@fc.up.pt wrote: Dear Users, I'm wondering if it is possible to extract

Re: [gmx-users] reg g_morph

-ninterm 10 what should i do to get 10 intermediate structure You should expect only one output file. It should have 10 intermediate frames. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry

Re: [gmx-users] Water-Mediated Hydrogen Bonds

Eagerly waiting for your reply. Thanking You Faithfully Raja -- ==== 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

Re: [gmx-users] Water-Mediated Hydrogen Bonds

meone else does. -Justin On Sat, Jul 2, 2011 at 5:24 PM, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote: Raja Pandian wrote: Dear All, I’m doing research in the field of Protein-DNA interaction. I have gone through these papers,

Re: [gmx-users] reg g_morph

elative to whatever group you told g_morph to use. -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

Re: [gmx-users] g_mindist

ormation about hydrophobic and hydrophilic contacts, you need to use special index groups that tell g_mindist (or any other tool) which atoms to consider. In this way, you can count how many of each type of contact evolve over time. -Justin -- ======== Justin A. Lemkul

Re: [gmx-users] g_mindist

of such interactions, a basic biochemistry textbook should cover it. -Justin 03 Temmuz 2011 00:24 tarihinde Justin A. Lemkul <mailto:jalem...@vt.edu>> yazdı: ahmet yıldırım wrote: Dear Justin, You said before "you can obtain some idea by usin

Re: [gmx-users] Mu-X

-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 ma

Re: [gmx-users] g_sas calculation

in each case the calculation group should always be the protein-ligand merged group. -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

Re: [gmx-users] reg electrostatic potential

stiffness. Without some applied deformation, I don't know how you'd quantify this. -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] g_sas calculation

ed in method #2 previously. That way, you can get the interior cavity surface area, not the exterior components as I was thinking. -Justin Thanks 2011/7/3 Justin A. Lemkul mailto:jalem...@vt.edu>> ahmet yıldırım wrote: Dear users, I want to compute SASA between

Re: [gmx-users] g_sas calculation

Justin A. Lemkul wrote: ahmet yıldırım wrote: Dear Justin, Firstly thanks for your valuable information. Now, is there any error? Please see the following commands: protein and ligand are merged by make_ndx g_sas -f run.xtc -s run.tpr -o area_protein.xvg -n protein_ligand.ndx Select a

Re: [gmx-users] Cytochrom C

Dariush Mohammadyani wrote: Hi all, Has anybody made initial configuration for Cytochrom C? Can it be shared with me? There are several in the PDB. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee

Re: [gmx-users] another question about performance

.4ns/hour. I am very confused about this output. How could this happen? Is there only two hours something each day? I don't understand the problem. 7.095 ns/day * 3.383 hr/ns = 24.002385 hr/day. -Justin -- ============ Justin A. Lemkul Ph.D. Candidate IC

Re: [gmx-users] Running_crashed_run

option but it does not works in my case. Thanks for any help. If it's not working, surely there is an error printed somewhere. Without that, it's impossible to help. -Justin -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGE

Re: [gmx-users] Re: Re: nodes 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 -- gmx-users maili

Re: [gmx-users] regarding NVT equilibration

-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/Perso

Re: [gmx-users] RDF(PMF) and Umbrella sampling

out = 150 Cheers Gavin -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department

Re: [gmx-users] Removing Water Molecules

tin -- ==== 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/jus

Re: [gmx-users] Removing Water Molecules

Steven Neumann wrote: On Fri, Jan 6, 2012 at 3:48 PM, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote: Steven Neumann wrote: Dear Gmx Users, I am setting up the simulation of a protein attached to the half of a nanotube. I set up my system and form

Re: [gmx-users] RDF(PMF) and Umbrella sampling

tin By free I mean. The absolute distance between the COG of the ref group and that of the pull group. Cheers Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Dear all I have a query regarding umbrella sampling simulations that I have carried out to study a dynamical process of a guest i

Re: [gmx-users] RDF(PMF) and Umbrella sampling

-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 l

Re: [gmx-users] RDF(PMF) and Umbrella sampling

, in a direction where the COM distance never changes sign (always increasing or always decreasing). It is the simplest case of pulling. -Justin -- ======== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virgini

Re: [gmx-users] Removing Water Molecules

Steven Neumann wrote: On Fri, Jan 6, 2012 at 4:04 PM, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote: Steven Neumann wrote: On Fri, Jan 6, 2012 at 3:48 PM, Justin A. Lemkul mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu <mailto:jalem.

Re: [gmx-users] RDF(PMF) and Umbrella sampling

what did you mean about by "straight pull" ? Cheers Gavin Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> Hi Justin >> >> Thanks for the reply. I wanted my "pulling" to be free in all >> directions,

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