Re: [gmx-users] mdrun on GROMACS 3.3.1

o use a mdrun from a different version of GROMACS it complains again as it is not the same as grompp. Do you have any tips for solving this problem? Thanks Francesca -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT T

Re: [gmx-users] problem with calculating SASA

by removing the unnecessary directives (see the wiki) 4. #include the new DNA .itp file in the existing system .top -Justin Cheers, Maryam *From:* Justin A. Lemkul *To:* Maryam Hamzehee ; Discussion list for GROMACS

Re: [gmx-users] umbrella curve

re to conduct a thorough error analysis to be sure the magnitudes of the minima and maxima are actually significant. -Justin -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksbur

Re: [gmx-users] mdrun on GROMACS 3.3.1

e ore 13.02, Justin A. Lemkul ha scritto: francesca vitalini wrote: Hallo GROMACS users! I'm trying to run a simple md script after running an energy minimization script on my system and I'm getting a wired error message Reading file dynamin_dimer_PR1.tpr, VERSION 3.3.1 (single precisi

Re: [gmx-users] mdrun on GROMACS 3.3.1

Segmentation fault I have checked with gmxcheck the .trr input file as it was suggested in another discussion, and apparently it is ok, so I really don't know what to do. Can you help me with that? Thanks Francesca Il giorno 31/gen/2012, alle

Re: [gmx-users] problem with make_ndx

se 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/Support/Mailing_Lists -- Justin A

Re: [gmx-users] g_dist

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/justin -- gmx-users mailing listgmx-

Re: [gmx-users] Pulling multiple groups

-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/Persona

Re: [gmx-users] g_analyze doubt

of), they come from the g_dist data, not what g_analyze is doing. Please provide a more clear description of what you are doing, including all relevant commands, and examples of the data files, if necessary. -Justin -- ==== Justin A. Lemkul Ph.D. Candi

Re: [gmx-users] the DNA md simulation

Banafsheh Mehrazma wrote: Dear all; Through the MD simulation for a DNA, I wonder whether we should change any options for the terminal bases or not. What is it that you think you should change? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS

Re: [gmx-users] g_analyze doubt

don't see how a distance greater than 0.8 nm is even possible in this case. -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] Pulling multiple groups

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

Re: [gmx-users] g_analyze doubt

Sorry, couldn't resist a bit of fun there... -Justin On 01-Feb-2012, at 6:48 PM, Justin A. Lemkul wrote: aiswarya pawar wrote: Dear Gromacs Users, i have data for the distance between the protein and water atoms within a cut off of 8A for 5ns using the g_dist option. Now i want to u

Re: [gmx-users] segmantation default

tter minimization or equilibration (or both), your .mdp settings are incorrect, or the free energy code is causing an instability (which is a symptom of the first two points, it does not suggest the free energy code is not working). -Justin -- ============ J

Re: [gmx-users] g_dist

group for calculation. That way you will get the distribution of headgroup distances from the COM of the micelle, thus approximately the radius of the micelle. -Justin -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Dep

Re: [gmx-users] g_dist

they used g_dist but it doesn't work me. Perhaps I am wrong about required program (command) for calculation of root-mean-square distance? Didn't Tsjerk already answer this? http://lists.gromacs.org/pipermail/gmx-users/2012-January/067984.html -Justin -- ======

Re: [gmx-users] segmantation default

r in the expansion of the constraint coupling matrix lincs-order = 12 1 Şubat 2012 19:41 tarihinde Justin A. Lemkul <mailto:jalem...@vt.edu>> yazdı: mehmet kıytak wrote: hi all... ı have a problem.. ı got segmentation fault when run nvt eq

Re: [gmx-users] g_dist

micelle)? Use g_gyrate, with a custom index group that contains the atoms of interest. If you're interested in the radius of the hydrocarbon atoms, make that an index group and perform the analysis on it. -Justin -- ==== Justin A. Lemkul Ph.D. Cand

Re: [gmx-users] g_dist

st Regards Dina ---- *From:* Justin A. Lemkul *To:* dina dusti ; Discussion list for GROMACS users *Sent:* Thursday, February 2, 2012 12:08 AM *Subject:* Re: [gmx-users] g_dist dina dusti wrote: > Dear Prof. > >

Re: [gmx-users] chitosan parameters?

simple. http://www.gromacs.org/Documentation/How-tos/Parameterization Putting the parameters in suitable format for use with Gromacs requires a thorough understanding of Chapter 5 of the manual. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral

Re: [gmx-users] g_dist

think of a way to make g_dist produce anything I would call a "root-mean-square distance." -Justin Thank you again because of your patient. Best Regards Dina -------- *From:* Justin A. Lemkul *To:* dina dusti ; Discuss

Re: [gmx-users] segmantation default

smallest allowed cell size (1.00) How can ı solve this problem...please help me... The error is still symptomatic of a crash. Your box is distorting too much and various algorithms (most notably DD) are crashing. -Justin 1 Şubat 2012 22:37 tarihinde Justin A. Lemkul <mailto:ja

Re: [gmx-users] System with 4 Hypericin Molecules in Water

her species) then they need to have different names (case sensitivity applies). -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_dist

ely, then average. This will require a large number of index groups (2 groups per molecule, multiplied by however many molecules you have to deal with) and will be very tedious, but it can be done in this manner. -Justin -- ============ Justin A. Lemkul Ph.D. Cand

Re: [gmx-users] Orders of the residues in gromacs

inate file is numbered from 1. If it is not, then what you think is residue 143 may not be interpreted that way by all external programs, depending on whether or not they respect the numbering of the .gro file. -Justin -- ======== Justin A. Lemkul Ph.D. Candidate I

Re: [gmx-users] trjconv select group

same number for the system. Any tips? http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts -Justin -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemk

Re: [Fwd: Re: [gmx-users] problems with KALP-15 IN DPPC tutorial]

on about how to manipulate such things can be found in the following tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/index.html -Justin -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Tra

Re: [gmx-users] trjconv select group

tp://www.gromacs.org/__Support/Mailing_Lists <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) 231-9

Re: [gmx-users] Reg error in dynamics

he 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/Perso

Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

box that was too diffuse condensing to adopt the density that the force field model will produce. It's probably best to start with a box that is more densely packed (closer to the target, to minimize shrinking). -Justin -- ======== Justin A. Lemkul Ph.D. Ca

Re: [gmx-users] problem with make_ndx

ion/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology -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/Page

Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

ch means your initial configuration is too diffuse and the application of NPT conditions is squishing it together to arrive at the density the force field model predicts. Build a system with an initial density closer to the target value. -Justin -- ========

Re: [gmx-users] problem with nvt equilibration

users-requ...@gromacs.org <mailto:gmx-users-requ...@gromacs.org>. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists <http://www.gromacs.org/Support/Mailing_Lists> -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral

Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

ields (which can be done in this case), we had to find a set of values that would reproduce the behavior of each parameter set. The value of 1.2 nm sufficiently reproduced the behavior of both, when combined. Without such justification, one should not alter cutoffs. -Justin -- =====

Re: [gmx-users] amber-lipid

d suitable parameters for you lipids, then the workflow is likely similar, though you may not have to create any sort of hybrid force field if the atom types, bonded parameters, etc are taken from an existing Amber force field. -Justin -- ==== Justin A. L

Re: [gmx-users] Index file

the entire protein group (1, by default) into its residues. -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] van der waals interaction

more specific about what you wish to measure. -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] umbrella-histogram-windows

tly. We can't tell. -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] g_dist

-- 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] Using groups in the mdp file

group. energy_grps = ACX This is an incorrect keyword that should have raised a fatal error. The proper keyword is "energygrps." -Justin -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Dep

Re: [gmx-users] Using groups in the mdp file

Ignacio Fernández Galván wrote: --- On Mon, 6/2/12, Justin A. Lemkul wrote: Perhaps the OP can provide the original grompp command and whether or not the -n flag was invoked. An incorrect index file can also give this error, I believe, if it does not contain the desired group. I'

Re: [gmx-users] harmonic distance restraints

selected groups. Note that the [distance_restraints] directive need not be contained within posre.itp; it can be anywhere within the [moleculetype] to which it applies. -Justin -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Traine

Re: [gmx-users] g_rdf

get an RDF out to 3x the box length. -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] Error energy minimization on protein with implicit water

rg/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision -Justin -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Bla

Re: [gmx-users] LINCS warning and segmentation fault for methane in 1-octanol simulation

this is a simple vdW transformation? -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/P

Re: [gmx-users] Energy minimization Error

Department of Mathematics and Informatics, FU-Berlin Arnimallee 6 14195 Berlin vital...@zedat.fu-berlin.de <mailto:vital...@zedat.fu-berlin.de> francesca.vital...@fu-berlin.de <mailto:francesca.vital...@fu-berlin.de> +49 3083875776 +49 3083875412 --

Re: [gmx-users] Energy minimization Error

strictly necessary for certain types of very sensitive calculations. For normal MD, convergence below 100-1000 kJ/mol-nm is typical. Other algorithms are listed in the manual. They may or may not be necessary. -Justin 2012/2/9 Justin A. Lemkul mailto:jalem...@vt.edu>> fra

Re: [gmx-users] Energy minimization Error

nology/Blowing_Up#Diagnosing_an_Unstable_System -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] Npt equilibration of the membrane-mimicking CCl4 layer

James Starlight wrote: Justin, 2012/2/6 Justin A. Lemkul mailto:jalem...@vt.edu>> Some simple calculations using the desired density and the box dimensions (to get the volume) will tell you exactly how many molecules you need. If you only "suppose" you

Re: [gmx-users] lipid tutorial problem

mx force field." The CA atom type is from ffgmx, and hence the error. -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] Umbrella Pulling

tters. -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] Number of windows in umbrella sampling

0.75 0 1 pull_start = yes pull_ngroups= 1 pull_group0 = Chain_B pull_group1 = Chain_A pull_rate1 = 0.01 pull_k1 = 1000 -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Dep

Re: [gmx-users] Number of windows in umbrella sampling

reason behind these phenomena, I cannot say, nor do I have time to sort through your data and try to work it out for you. Refer to the literature, find similar protocols, and proceed from there. -Justin Shahid Nayeem On Mon, Feb 13, 2012 at 7:15 PM, Justin A. Lemkul <mailto:jalem...@vt.

Re: [gmx-users] Umbrella Pulling

choosing a force constant. Guessing wildly at what's going on, I'd say you need longer simulations as it appears you have only just caused dissociation towards the end of the 500 ps. -Justin Steven On Mon, Feb 13, 2012 at 1:11 PM, Justin A. Lemkul <mailto:jalem...@v

Re: [gmx-users] bug for TIP4P water in GROMACS ?

@gromacs.org/msg18846.html It was a pretty significant bug, but did not affect 4.0.5 as the OP states, it was fixed for 4.0.4. It also affected only certain types of calculations, as the thread above suggests. -Justin -- Justin A. Lemkul Ph.D. Candidate

Re: [gmx-users] LJ parameter : geometric / arithmetic average

hat's taken as default ? Whatever is listed in the comb-rule column of the force field's [defaults] directive (described in manual section 5.7.1). -Justin -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department

Re: [gmx-users] Noise in a radial distribution function using g_rdf

generally expected. -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] GROMOS96 53a6 and PRODRG topologies

for the ligand was created employing the server PRODRG 2.5 Beta. How to change the charges? http://pubs.acs.org/doi/abs/10.1021/ci100335w -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry

Re: [gmx-users] Number of windows in umbrella sampling

vely quick literature searching will lead you to some suitable ideas. Spending a few hours doing some reading will save you months of wasted CPU time. -Justin Shahid nayeem On Mon, Feb 13, 2012 at 8:12 PM, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote: shahid nayeem wrote:

Re: [gmx-users] Number of windows in umbrella sampling

Justin A. Lemkul wrote: shahid nayeem wrote: Thanks Justin. I will try again. But please refer to some protocol if you know and one last question that before doing umbrella sampling simulation how can one be sure that the pulling is good and one should go ahead with selecting window and

Re: [gmx-users] Domain decomposition in FEP

e_of_x_nm The DD setup is based on a host of factors. Seeing a complete .mdp file would help. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jal

Re: [gmx-users] charmm27 in gromacs

) is required to understand any of the force fields implemented in Gromacs (or any other software, for that matter). -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg

Re: [gmx-users] in vacu simulation

uld in the case that no interactions would be calculated. -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

Re: [gmx-users] problems with pdb2gmx gromacs 3.3.1 version

e sorting atoms --- Any suggestions? Check the .rtp file - your atom is named in a way that is inconsistent with what the force field expects. -Justin -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Traine

Re: [gmx-users] problems with pdb2gmx gromacs 3.3.1 version

pdb2gmx -ter, if necessary. Otherwise, your version should work for what you need. -Justin 2012/2/16 Justin A. Lemkul : francesca vitalini wrote: Hi all! I'm trying to create a topology file from the pdb using the pdb2gmx command of gromacs 3.3.1 but I'm encountering some issues

Re: [gmx-users] Umbrella Pulling

u, Steven On Fri, Feb 17, 2012 at 10:41 AM, Steven Neumann mailto:s.neuman...@gmail.com>> wrote: On Mon, Feb 13, 2012 at 2:53 PM, Steven Neumann mailto:s.neuman...@gmail.com>> wrote: Thank you Justin! On Mon, F

Re: [gmx-users] running energy minimization error

does not conform to the required format. See Chapter 5 of the manual. -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] getting dssp executable

then I get the following error message: -bash: setenv: command not found You need to use "export" for bash; "setenv" is for csh. export DSSP=/opt/dssp/bin/dssp -Justin -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar

Re: [gmx-users] trajectory@vmd

-- 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] getting dssp executable

ing I have to do anything with the binary file to make it work? n the dssp website they don't write anything about it. What was your exact export command? -Justin Thanks again 2012/2/17 Justin A. Lemkul : francesca vitalini wrote: Dear all, In order to get the secondary structure of m

Re: [gmx-users] getting dssp executable

francesca vitalini wrote: export DSSP /home/cocktail/vitalini/gromacs_special/bin/dssp You forgot an '=' sign in the variable assignment. export DSSP=/home/... -Justin 2012/2/17 Justin A. Lemkul : francesca vitalini wrote: Thanks! However now I jet another error -bash: expo

Re: [gmx-users] Umbrella Pulling

Steven Neumann wrote: On Fri, Feb 17, 2012 at 2:12 PM, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote: Steven Neumann wrote: Hello Justin, As you recommended I run longer pulling of my ligand. I pull the ligand which is on the top of my protein s

Re: [gmx-users] Umbrella Pulling

Steven Neumann wrote: On Fri, Feb 17, 2012 at 2:52 PM, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote: Steven Neumann wrote: On Fri, Feb 17, 2012 at 2:12 PM, Justin A. Lemkul mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu <mailto:jalem.

Re: [gmx-users] The solvation free energy of a vdw ligand

x27;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 -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Tra

Re: [gmx-users] The solvation free energy of a vdw ligand

would recommend not using ffgmx for anything, though. The newer manual gives several reasons why it's a bad choice for just about any modern simulation. -Justin -- ======== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department

Re: [gmx-users] The solvation free energy of a vdw ligand

(which is, in itself, questionable) just because there is a convenient tool (PRODRG) that is also unreliable. Spending a few hours reading may save you months of effort that wind up being wasted. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS

Re: [gmx-users] Umbrella_pull_simulation

, that is not possible. -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] g_analyze -ee

thod. -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] Umbrella_pull_simulation

ll if you've ever posted your .mdp file, or at the very least, told us how much sampling you've done in each window. It may well be that your simulations are simply too short to observe adequate post-equilibration sampling. -Justin -- ============ Justin

Re: [gmx-users] problems with martinize.py

: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Se

Re: [gmx-users] Umbrella Pulling

^-2 -- ==== 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 list

Re: [gmx-users] Umbrella_pull_simulation

ude some amount of time at the beginning of each as equilibration (which you probably should do anyway, but without seeing your g_wham command, there's no way to know what you may or may not be considering). -Justin Shahid Nayeem On Mon, Feb 20, 2012 at 8:24 PM, Justin A. Lemkul <mailto

Re: [gmx-users] g_analyze -ee

y for thank from you. Best Regards Dina *From:* Justin A. Lemkul *To:* dina dusti ; Discussion list for GROMACS users *Sent:* Saturday, February 18, 2012 5:29 PM *Subject:* Re: [gmx-users] g_analyze -ee dina dusti

Re: [gmx-users] Umbrella Pulling

Steven Neumann wrote: On Mon, Feb 20, 2012 at 7:32 PM, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote: Steven Neumann wrote: Dear Justin and Gmx Users, I run a pulling of my ligand away from my protein with the same mdp file and I obtained two

Re: [gmx-users] Umbrella Pulling

Steven Neumann wrote: On Mon, Feb 20, 2012 at 7:55 PM, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote: Steven Neumann wrote: On Mon, Feb 20, 2012 at 7:32 PM, Justin A. Lemkul mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu <mailto:jalem.

Re: [gmx-users] Umbrella Pulling

Steven Neumann wrote: On Mon, Feb 20, 2012 at 8:07 PM, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote: Steven Neumann wrote: On Mon, Feb 20, 2012 at 7:55 PM, Justin A. Lemkul mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu <mailto:jalem.

Re: [gmx-users] T-coupling problem?

section. All elements of the system have to be under the control of a thermostat. Do not confusing the "freezing" method with something related to temperature; they are separate concepts. If you need further help, post your full .mdp file. -Justin -- =========

Re: [gmx-users] Umbrella_pull_simulation

n Shahid Nayeem On Tue, Feb 21, 2012 at 1:04 AM, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote: shahid nayeem wrote: I am attaching a profile.xvg and histo.xvg. In each window 10ns sampling was done. The umbrella pullcode used is as follows. ; Pul

Re: [gmx-users] how to extract the x y z

lina wrote: Hi, I don't know how to extract the position like the x y z with t or r with t. g_traj prints coordinates from a trajectory. -Justin -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Departme

Re: [gmx-users] several questions about g_hbond -contact

l question is, obviously: what is the correct command to provide to obtain what I want, i.e. the number of contacts between the protein and the ligand within a cutoff radius of 0.5 nm? Don't use g_hbond at all. g_mindist -d 0.5 -on -Justin --

Re: [gmx-users] Pressure coupling and membrane-type simulations

of the fluid layer is largely irrelevant, isn't it? Then again, if the walls are not rigid, then they become a liability under pressure coupling as they may buckle. Seems to me this should be the principal concern. -Justin -- ============ Justin A. Le

Re: [gmx-users] Protonation state of the ionisable residues

prone. You'd have to add in the new atoms, renumber *all* subsequent bonded and nonbonded interactions. The better approach is to re-create the topology with pdb2gmx -asp -glu. -Justin -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar M

Re: [gmx-users] Protonation state of the ionisable residues

-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] Umbrella Sampling - spacing

-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] NPT - umbrella sampling

what makes sense in your case. Typically, position restraints are applied during equilibration. -Justin -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]v

Re: [gmx-users] Umbrella Sampling - gen_temp

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] NPT - umbrella sampling

Steven Neumann wrote: On Thu, Feb 23, 2012 at 12:00 PM, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote: Steven Neumann wrote: Dear Justin and Gmx Users, I extracted 42 frames from my trajctory of pulling ligand away from my protein (no position r

Re: [gmx-users] Error note

and how it should be fixed. Charge groups should be small. You have one that is very large. -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] what restraint can I use to prevent membrane diffusion along the Z-axis?

COM motion removal should take care of this. I do not see how the bilayer would be the only species that moves; the water molecules are not static. They too are moving in z along with the membrane. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS

Re: [gmx-users] Error note

ghbor searching. If the group is large, then short-range forces may not be calculated accurately. The warning from grompp was a recent addition to the code; if you're using an older version you may not have triggered it. -Justin -- ==== Justin A. L

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