Re: [gmx-users] What is epsilon_r?

rs/2004-March/009650.html -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] Fe atom problems....in simulation

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.edu | (540) 231-

[gmx-users] Re: Questions

e Watkins stephan.ll...@students.unibe.ch University of Bern Insel Spital RIA Sahli Haüs II Freiburstrasse 21 Bern 3011 -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.

Re: [gmx-users] Re: Questions

lloyd riggs wrote: Original-Nachricht Datum: Tue, 17 Apr 2012 07:49:06 -0400 Von: "Justin A. Lemkul" An: lloyd riggs , Discussion list for GROMACS users Betreff: Re: Questions lloyd riggs wrote: Dear Justin, So I get no answere on the mail list so decided

Re: [gmx-users] Extending a simulation

not do a simple extension of the simulation. For production simulations that simply require more time, the steps listed on the Gromacs website are correct and there is no need to deal with .mdp files. -Justin -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctora

Re: [gmx-users] Fatal error: Bond atom type names can't be single digits

is pretty explicit that you have atom types that are not appropriately named; they are digits. Atom types can utilize numbers, but only as a part of the name. For instance, "CH3" is a valid atom type, but "3" is not. -Justin -- ======== Justin A

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

ed to existing files. -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] Error- Atom not found in residue seq nr while adding atom

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 -- Aiswarya B Pawar Project Assistant, Bioinformatics Dept, Indian Institute of Science Bangalore -- ====

Re: [gmx-users] g_wham problem with negative COM differences

Anni Kauko wrote: Anni Kauko wrote: > > > > Date: Wed, 11 Apr 2012 08:38:05 -0400 > > From: "Justin A. Lemkul" mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> > > Subje

Re: [gmx-users] Re: Questions WHAM

em is as far as what you're doing. If your creating Frankenstein files, there is always the possibility of some nefarious, subtle human error that you can't see ;) -Justin -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IG

Re: [gmx-users] Re: g_wham problem with negative COM differences

i Kauko Subject: Re: [gmx-users] g_wham problem with negative COM differences To: gmx-users@gromacs.org Message-ID: Content-Type: text/plain; charset="iso-8859-1" Anni Kauko wrote: Date: Wed, 11 Apr 2012 08:38:05 -0400 From: "Justin A. Lemkul"mailto:jalem...

Re: [gmx-users] Re:WHAM question

====== 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: Extending a simulation

-h you will see: -extend real 0 Extend runtime by this amount (ps) Alternatively, one can use -nsteps, which changes the *total* number of steps (not just adding on to the end). -Justin -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral S

Re: [gmx-users] Silly little question about PMF - g_wham

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

Re: [gmx-users] pdb2gmx error

tp://www.gromacs.org/Documentation/Errors On Tue, Apr 10, 2012 at 1:35 AM, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote: Bishwajit Das wrote: when i try to pdb2gmx -f *.pdb -o *_processed.gro -water spce command in my pdb file then i select AMBER99SB-ILDN for

Re: [gmx-users] Writing out individual coordinates

umber, which can then be parsed with something like awk or perl. -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] Re: Data 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 http://www.bevanlab.biochem.vt.edu/Pages/Perso

Re: [gmx-users] Re: Data Analysis

nge would coincide. -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] Error: No default angle/bond types

atoms and thus which types are not parameterized. At that point, you will either need to find/derive suitable parameters, or use a different force field that can address the system at hand. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral

Re: [gmx-users] fatal error: The solvent group non-Protein is not continuous

l material addresses such issues. -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] File editing - only one layer of water around a molecule

son you do not wish to use the default name. -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] File editing - only one layer of water around a molecule

thats to much for me. You should be passing your coordinate file to -f, not -s. -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

Re: [gmx-users] Radial distribution function (RDF) in cylindrical coordinates

puted from the x- and y-components only. -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] grompp 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] File editing - only one layer of water around a molecule

ginal command. -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] .top file for POPC membrane

tp://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.bev

Re: [gmx-users] g_dist explanation

te frames in between. You would need to do the run again, saving frames with greater frequency. Note that doing so will likely make your trajectory file quite a bit larger. -Justin -- ======== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT

Re: [gmx-users] File editing - only one layer of water around a molecule

e requires a .tpr file, as the error you got (below) indicates. If you want to make your life simple, be more specific in what you tell trjconv. Want a .pdb file? Tell it so: trjconv -n index.ndx -f my_molecule.pdb -o output.pdb -Justin -- ==== Justin

Re: [gmx-users] writing ff parameters as a text file

parameters, ffbonded.itp and ffnonbonded.itp. Both of these are also text files that can be viewed very simply. -Justin -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, V

Re: [gmx-users] About hydrogen bond ..

Your g_hbond command is the correct approach. -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] Need help with tabulated non-bonding potential tablep file

and 1 or 2 values? 4) What's the meaning of the value/s at the right of the 2 indexes for a not LJ tabulated potential? 5) The pair interactions are scaled or set to zero when using tabulated non-bonding potentials? I need to set them zero... Thank you in advance. Johny. -- ==

Re: [gmx-users] File editing - only one layer of water around a molecule

it's necessary in this case, but it is. -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] File editing - only one layer of water around a molecule

what Gromacs expects as default input - that is why the error is coming up. Under most circumstances for trjconv operations, a .tpr file is passed to -s, but in your case, a .pdb will suffice. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral

Re: [gmx-users] Extending umbrella sampling window

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] error in starting/completing minimization

/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 | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal

Re: [gmx-users] -com switch in g_rdf

center of mass? If you select a system of pure benzene as the reference group, presumably the COM calculation will simply deduce the COM of the system and give you an RDF relative to this fixed point. -Justin -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS D

Re: [gmx-users] Simulation with nbutanol

idade Federal de Pernambuco 50740-540 Recife (PE) - Brazil Phone: +55 81 2126-8440 ext. 5007 Phone: +55 81 9197-9297. -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jal

Re: [gmx-users] Hypericin dimer affinity

able to determine the binding free energy. You could then back-calculate a Kd value from this free energy. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA

Re: [gmx-users] PBC treatment: need an explanation

distances (g_dist), contacts (g_mindist), etc. -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

Re: [gmx-users] why it is so slow in Blue gene?

ulations should give you a better idea on the setup for optimal performance. -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] Fatal error in popc simulation: Atomtype LC3 not found

oach is to append the contents of lipid.itp to the appropriate directives in ffnonbonded.itp and ffbonded.itp. See the approach in: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html -Justin -- ==== Justin A. Lemkul

Re: [gmx-users] Fatal error

Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database -Justin -- ======== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[a

Re: [gmx-users] a question about energygrps

for energygrps; it's just a decomposition of the nonbonded terms. The way your break it down depends on what you care to measure in the system. -Justin -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Departme

Re: [gmx-users] a question about energygrps

On 04/25/2012 04:13 PM, Justin A. Lemkul wrote: On 4/25/12 10:07 AM, Albert wrote: Hello: I am running a membrane simulation with gromacs and I wondering how to deal with energygrps? Should I put protein and lipids into one energygrps? Or I should leave the lipids stay with solvent and ions?

Re: [gmx-users] a question about energygrps

tively old) hardware. My rule of thumb is 1000 atoms/CPU, and then tweak from there if necessary. -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] Error in MD simulation

to allow the programs to do the bookkeeping for you eliminates the majority of the problems. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at

Re: [gmx-users] How to choose two atoms at the same time, using g_select selection.dat

g to make a simple group that consists of 2 atoms, make_ndx is easier, and using a plain text editor will be easiest, i.e.: [ my_group ] 1 2 -Justin -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemist

Re: [gmx-users] Atom types for phosphate group in OPLS-AA force field

P2 O4P P2 O5P P2 O6P O5P HO5P Thank you very much in advance! Antoine -- ============ 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] MD simulations of covalent bound protein-ligand complex by gromacs

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] double precision energy minimization show zero pressure in gromacs 4.5.5

-6.98604e+04 -5.12824e+02 -- ============ 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] Atom types for phosphate group in OPLS-AA force field

e will spend several months developing good parameters for a new residue or molecule. -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] Atom types for phosphate group in OPLS-AA force field

which have calculated for other molecules? There is a large database at http://virtualchemistry.org/index.php but I don't know if there will necessarily be anything similar to what you're looking for. -Justin Best regards, Antoine On 26/04/12 16:55, Justin A. Lemkul wrote:

Re: [gmx-users] double precision energy minimization show zero pressure in gromacs 4.5.5

then. There have been a vast amount of changes between 4.0.7 and 4.5.5 so hopefully someone who has been involved with such action will know more. It could be a sneaky bug, but I'm not stating that with 100% certainty. -Justin -- ==== Justin A. L

Re: [gmx-users] Position Restraints

said. -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] Re: GPCR MD Tutorial Using GROMACS (URL)

s the criteria is selecting it, for instance popc, dopc or dppc? The choice of lipid depends on what you need to model. -Justin -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksbur

Re: [gmx-users] Position Restraints

what the problem is. You'll have to describe what you're doing in greater detail. -Justin Regards, Dariush On Thu, Apr 26, 2012 at 1:38 PM, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote: On 4/26/12 1:35 PM, Dariush Mohammadyani wrote: Dear All, I

Re: [gmx-users] help about "Inconsistent DD boundary staggering limits"

8,21: Exited with exit code 255 srun: error: cu09n191: tasks 66,69: Exited with exit code 255 srun: error: cu11n188: tasks 114,117: Exited with exit code 255 srun: error: cu11n185: tasks 90,93: Exited with exit code 255 srun: error: cu09n141: tasks 42,45: Exited with exit

Re: [gmx-users] help about "Inconsistent DD boundary staggering limits"

ures. -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] Re: GPCR MD Tutorial Using GROMACS (URL)

/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.bevanlab.biochem.vt.edu/Pages/Personal/justin ===

Re: [gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

ns. As far as I can tell, you shouldn't be doing 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 | (540) 231-9080 http://www.beva

Re: [gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

xactly following the tutorial with same KALP peptide. I am ending up with 'Area per lipid: 3.73355898918962 nm^2' within 10 iterations which is far lower than Justin's. Why? 3.73 nm^2 is 373 A^2 - mind the fact that the units have a square term. -Justin -- ============

Re: [gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

ll gap is normal and will close when doing equilibration as the solvent fills in around the lipid headgroups. -Justin -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, V

Re: [gmx-users] TRR file with nstxout= 0

, so you're likely getting very frequent output of velocities into the .trr file. -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] TRR file with nstxout= 0

On 4/27/12 11:34 AM, Steven Neumann wrote: On Fri, Apr 27, 2012 at 4:28 PM, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote: On 4/27/12 11:22 AM, Steven Neumann wrote: Dear Gmx Users, I am running 2 us simulation in implicit solvent model:

Re: [gmx-users] TRR file with nstxout= 0

On 4/27/12 12:09 PM, Steven Neumann wrote: On Fri, Apr 27, 2012 at 4:38 PM, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote: On 4/27/12 11:34 AM, Steven Neumann wrote: On Fri, Apr 27, 2012 at 4:28 PM, Justin A. Lemkul mailto:jalem...@vt.edu> <mailto:jal

Re: [gmx-users] calculation of the mean B factor of a PDB file

-- 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] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder

m is. What is the initial distance between the drug and membrane, as measured by g_dist? What is the length of your unit cell along the z-axis? -Justin -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Bioche

Re: [gmx-users] Making Disulfide Bonds

macs.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 Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia

Re: [gmx-users] Making Disulfide Bonds

s of in vacuo MD to see if the structure adjusts. -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.bevan

Re: [gmx-users] Make an index file

't': atom type | 'keep' nr 'splitat' nr 'h': help 'r': residue 'res' nr 'chain' char "name": group 'case': case sensitive 'q': save and quit 'ri': residue index Now, what i

Re: [gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder

catom0 = 0 > > pull_ngroups = 1 > > pull_group0 = DPPC > > pull_group1 = drug > > > > Have not decided the radii of the cylinder yet, but that is besides the point here. > > > > I run with the 4.5.5 version and cannot figure what the problem is. &g

Re: [gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder

t you are trying to do and see. -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] File editing - only one layer of water around a molecule

where. Order of arguments is irrelevant to all Gromacs commands. -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] File editing - only one layer of water around a molecule

formation. -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 maili

Re: [gmx-users] Umbrella Sampling Hypericin Dimer

two molecules in water, there is no need for position restraints at all. The only biasing potential you need is the one maintaining a distance between the two molecules. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT

Re: [gmx-users] New Gromacs Release

thus far I see no major changes to existing content. -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] Box of water

is. Use the -maxsol option when invoking genbox. -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] disre and posres together?

. Thank you for your time B.Mehrazma -- 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] POPC: ff53a6 and CHARMM36 formats

ace or send it togmx-users-requ...@gromacs.org <mailto:gmx-users-requ...@gromacs.org>. Can't post? Readhttp://www.gromacs.org/Support/Mailing_Lists -- ======== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of

Re: [gmx-users] segmentation fault during equilibration

ong. -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/jus

Re: Fw: [gmx-users] GROMOS87 and CHARMM27

ers@gromacs.org <mailto: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. Use the www interface or send it to gmx-

Re: [gmx-users] segmentation fault during equilibration

st a guess since I don't know. Otherwise: http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System -Justin -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistr

Re: [gmx-users] File editing - only one layer of water around a molecule

e to ISO" group. So, for instance, if ISO is group 1 and "Close to ISO" is group 5, you would type: 1 | 5 at the make_ndx prompt, which will create a group called Close_to_ISO_ISO, thus a merged group of all atoms in "Close to ISO" and ISO. -Justin -- ==

Re: [gmx-users] segmentation fault during 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/Personal/justin -- g

Re: [gmx-users] File editing - only one layer of water around a molecule

l.ndx will have the merged 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/Personal/justin

Re: [gmx-users] GROMOS87 and CHARMM27

under the new parameters. -Justin Thanks, Shima *From:* Justin A. Lemkul *To:* Shima Arasteh ; Discussion list for GROMACS users *Sent:* Tuesday, May 1, 2012 9:44 PM *Subject:* Re: Fw: [gmx-users] GROMOS8

Re: [gmx-users] Re: Re: g_wham problem with negative COM differences

>>>>> >>>>> Your problem stems from the use of "distance" geometry. This >>> method >>>>> assumes the >>>>> sign along the reaction coordinate does not change, i.e. always >>>&

Re: [gmx-users] How to remove H atom from residue in gro file?

ou to create a properly merged molecule that can form the intermolecular disulfide because the two molecules will be considered as one [moleculetype], as Gromacs requires. -Justin -- ======== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trai

Re: [gmx-users] Number of coordinate in topol.top and solv.gro not matching

ur coordinate file. Note that you're off by 15 atoms, which is exactly how many are in the ligand described in the tutorial. Go back and read the instructions closely, as appending the ligand to the protein coordinate file is discussed in detail. -Justin -- ============

Re: [gmx-users] GROMOS87 and CHARMM27

ial at all, because the parameters are different for sure. Having little idea what you're doing, I'll tend to agree. -Justin Cheers, Shima -------- *From:* Justin A. Lemkul *To:* Shima Arasteh ; Discussion li

Re: [gmx-users] Number of cooredinate in topol.top and solv.gro not matching

0 0.0 0.0 Have you correctly incremented the second line of conf.gro to indicate that more atoms have been added? Without it, editconf will read the wrong number of lines and exclude the ligand. -Justin -- ============ Justin A. Lemkul Ph.D. Can

Re: [gmx-users] trjconv correct the pbc before analysis

g the -center option of trjconv. You can do it all in one shot for simple systems of a couple peptides with trjconv -center -pbc mol -ur compact. Note that these "corrections" for PBC are only necessary for visualization, not the analysis itself. -Justin -- ===

Re: [gmx-users] missing gbsa parameters

ypes you need based on chemical similarity to existing atom types/functional groups. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg,

Re: [gmx-users] membrane simulation

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] Lamb-Protein

contribution displayed by g_energy; Most are fairly obvious, others are discussed on gromacs.org. In the case of "Lamb-" terms, these are the lambda values when the free energy code is being utilized. -Justin -- ==== Justin A. Lemkul Ph.D. Candi

Re: [gmx-users] Lamb-Protein

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] how to extract trajectories into individual pdb file?

:gmx-users-requ...@gromacs.org>. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- ======== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry

Re: [gmx-users] Error: 1 atoms are not part of any of the T-Coupling groups

es gen_temp= 300 gen_seed= -1 I am not clear how i can add MG2+ while creating index.ndx file. Please help me out. Three approaches: 1. Create a group that replaces "Water_and_ions" with one that contains the MG2+ ion within the solvent 2. Add MG2+ to residuetypes.dat so

Re: [gmx-users] missing gbsa parameters

're seeing. For any missing atom type, you need to add appropriate parameters for it into gbsa.itp. This may be trivial (redundancy in some atom types) or it may be difficult (deriving new parameters that are compatible with the parent force field). -Justin -- =

Re: [gmx-users] missing gbsa parameters

line, maybe something is not being parsed properly. -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.b

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