Re: [gmx-users] how to obtain binding energy?

reliable. -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] how to obtain binding energy?

with "Is there a tutorial for..." then the answer is always: http://www.gromacs.org/Documentation/Tutorials I suspect you'll find something useful there :) -Justin -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Tra

Re: [gmx-users] mirroring a trajectorie

g times in the .xvg file? The coordinates are all the same, just in a different (but still sequential) order. -Justin Greetings Thomas -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia

Re: [gmx-users] Request to solve this fatal error-reg

-- 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_order output is mirrored

Igor Marques -- ============ 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] g_order output is mirrored

I'd suspect the index file(s) and/or g_order commands rather than convergence issues, in this case. -Justin thanks! -Justin best regards and thanks in advance! Igor Marques -- Justin A. Lemkul Ph.D

Re: [gmx-users] how to obtain binding energy?

ain delta delta G by PMF method again? I would suggest you consult my paper that is associated with the umbrella sampling tutorial. -Justin -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Vir

Re: [gmx-users] surface tension of monolayer

ence Khon Kaen University, Thailand Tel. (Mobile) 081-2630095 -- ==== 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] g_order output is mirrored

sing -Justin (this applies also to the DMPC chains of my colleague) best regards! igor Igor Marques On Tue, May 17, 2011 at 9:47 PM, Igor Marques <mailto:igor.drago...@gmail.com>> wrote: Igor Marques On Tue, May 17, 2011 at 9:42 PM, Justin A. Lemkul mailto:jale

Re: [gmx-users] P-LINCS and nstlist

w.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.b

Re: [gmx-users] RHEL OS, g_mdrun

-disable-threads. -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] lipids per area charmm36 popc

f course discarded as 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.b

Re: [gmx-users] reg centre of mass in SMD

None of this is necessary. Gromacs does all COM calculations internally. -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] About -pbc option of trjconv

use -pbc whole? http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech

Re: [gmx-users] average trajectory

-- 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] Manually aborting a simulation

: mpirun -machinefile cp -np 8 mdrun -s nvt-pr.tpr -o nvt-pr.trr -c water.pdb -e nvt-pr.edr -g nvt-pr.log & Use 'ps' to locate the process ID and kill it in the terminal. -Justin -- ======== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Schol

Re: [gmx-users] Re: water dimer is gas phase

m -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] Re: water dimer is gas phase

healthy? I agree with this. The system should be going absolutely haywire :) -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] issue with newest version of martini model

there? You're better off contacting the MARTINI developers, since this is not actually a Gromacs problem. -Justin -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksbur

Re: [gmx-users] problem during energy minimization

pbc=xyz; ; Energy minimizing stuff emtol = 1000.0 emstep = 0.01 regards, sree -- ==== 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] NPT and NVT ensembles

was stable. -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] segmentation fault.

ostats#What_Not_To_Do -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] Re: water dimer is gas phase

rm to proper spacing. Presumably there are usable frames in your .trr/.xtc file that you can watch to see what's happening in the simulation, but I suspect that you'll find the water molecules are simply drifting apart. -Justin -- ======== Justin A. Lemkul

Re: [gmx-users] extract histograms of phi and psi

D of the manual. You'll be able to find your answer there. -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] Fluorescence Anisotropy

is of dihedral angles and/or transitions can be done by g_angle and/or g_dih. -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] re: ciis peptide linkage

only metastable - it runs but produces strange output. -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] problem during Energy minimization

14 - Thanks, Parul -- ============ 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_sdf

inflexible; it was designed (it appears) around calculations involving water. g_spatial is much more flexible, and I believe it was for this reason that g_sdf has been removed from newer Gromacs versions. Try g_spatial instead. -Justin -- Justin A. Lemkul

Re: [gmx-users] NPT for compressing

and_Restraints You said you were using position restraints (presumably that's what "PR" means). If this is not the case, please provide an accurate description of what you're doing. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doct

Re: [gmx-users] NPT for compressing

Elisabeth wrote: On 21 May 2011 19:02, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote: Elisabeth wrote: On 20 May 2011 23:04, Mark Abraham mailto:mark.abra...@anu.edu.au> <mailto:mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>>

Re: [gmx-users] -ci option

here a way to randomly generate various configurations of ions each time on using -ci? Set a different value of -seed. -Justin Thanks, SN -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Vir

Re: [gmx-users] Error in energy group exclusion

Coulombic terms) are excluded in the mechanism above. -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] Error in energy group exclusion

ical behavior, which you're now ignoring. If this is not your intent, then please explain further. -Justin On Mon, May 23, 2011 at 21:28, Justin A. Lemkul wrote: bipin singh wrote: Hello users, I am getting the following

Re: [gmx-users] Velocity autocorrelation function of water using g_velacc

uilibrated, or at the very least, the original frames are messing with the VACF calculation. -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] Gromacs Installation Error on Powerbook G$ Running OS 10.5.8

unction ‘tMPI_Atomic_cas’: ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h:57: warning: implicit declaration of function ‘__sync_bool_compare_and_swap’ If anyone has any suggestions, they would be greatly appreciated. Thanks. Matthew Bick Rockefeller University -- ==

Re: [gmx-users] Gromacs Installation Error on Powerbook G$ Running OS 10.5.8

gcc45, +gsl, +no_x11 [avoids openmotif] and +optimize [for gsl]) Once you do get it working, watchout for overheating on that thing :) -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemi

Re: [gmx-users] Rg

obule that doesn't resemble the native state? If the latter, then Rg can be misleading. At extremely high temperature, though, I would expect just about any protein to be very elongated, unless it has lots of disulfides to keep it compact. -Justin -- =======

Re: [gmx-users] Error in energy group exclusion

ly accounts for a (very) large fraction of the total Coulombic interactions in the simulated system. -Justin On Mon, May 23, 2011 at 23:06, Justin A. Lemkul wrote: bipin singh wrote: Thanks for your reply, I have already done with the final simulation, and now if I have to change the method

Re: [gmx-users] Re: Gromacs Installation Error on Powerbook G4 Running OS 10.5.8

../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h: In function ???tMPI_Atomic_cas???: ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h:57: warning: implicit declaration of function ???__sync_bool_compare_and_swap??? If anyone has any suggestions, they would be greatly

Re: [gmx-users] Helix to coil

- no easy answer :) -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] what's the philosophy of -ci option in "genbox"?

========= 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 mail

Re: [gmx-users] Potential of mean force

vals should be used. The parameters given are for Gromos96. -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] Charmm36 in Gromacs: missing dihedrals

1000 1000 1000 #endif ; Include topology for ions #include "charmm36.ff/ions.itp" [ system ] ; Name Protein [ molecules ] ; Compound#mols Other 1 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar

Re: [gmx-users] How to make a membrane system with 512 DPPCs

! 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 -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar M

Re: [gmx-users] How to make a membrane system with 512 DPPCs

Peter C. Lai wrote: On 2011-05-25 08:00:32AM -0500, Justin A. Lemkul wrote: Du Jiangfeng (BIOCH) wrote: Dear Gromacs Users, There are easy to get membrane with 64 DPPC or 128 DPPC for all atoms simulation or coarse grained simulation, but is it possible to get a membrane with 512 lipids

Re: [gmx-users] sphere around a protein

. -Justin -- Thanks a lot in advance. Sorry about reviving few days old thread. Thanks, SN On Mon, May 9, 2011 at 6:21 AM, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote: shivangi nangia wrote: Hi Justin,

Re: [gmx-users] sphere around a protein

the open spaces of the box in which 6sys.gro is sitting. How can I place all the anions and then Li+ ions specifically inside the sphere? That's what genion is for. -Justin -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-

Re: [gmx-users] sphere around a protein

Justin A. Lemkul wrote: shivangi nangia wrote: Hi Justin, Thanks a lot! Things worked. Now I, however, have a different problem in extension to what I am doing. I was able to created a sphere of water and methanol around a polypeptide and 1 Li+ ion. editconf -f 1li.gro -c -box 12 12

Re: [gmx-users] sphere around a protein

before. -Justin Thanks, SN On Wed, May 25, 2011 at 3:43 PM, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote: Justin A. Lemkul wrote: shivangi nangia wrote: Hi Justin, Thanks a lot! Things worked. Now I, howeve

Re: [gmx-users] To get PMF using pull geometry of cylinder

ms written are z and dz, since, in principle, x, y, dx, and dy are all fixed, with the last two terms being zero. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg,

Re: [gmx-users] Charge group problem from pdb2gmx

fields, rlist=rcoulomb=0.9 and rvdw=1.4 are correct settings. I suspect you're trying to use some sort of switch or shift function, and hence rlist > rvdw. You shouldn't. vdwtype=cutoff and coulombtype=PME are the best settings. -Justin -- =====

Re: [gmx-users] query regarding replica exchange

-- 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] To get PMF using pull geometry of cylinder

nks again for your help! Dejun From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Wednesday, May 25, 2011 7:44 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] To get PMF using pull geometry of c

Re: [gmx-users] To get PMF using pull geometry of cylinder

Dejun From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Thursday, May 26, 2011 11:26 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] To get PMF using pull geometry of cylinder Lin, Dejun wrote: Than

Re: [gmx-users] electron density

quot;2" in the text is just a typo when I sent the email. So actually there is no partial charge in the electrons.dat file. Thanks, Justin. Jianhui Date: Sat, 01 Jan 2011 13:56:45 -0500 From: "Justin A. Lemkul" mailto:jalem...@vt.edu>> Subject: Re:

Re: [gmx-users] Re: Error of installing gromacs v4.5.4

#x27;ll be able to > compile the code, but it will run *much* slower than with the > accelerated kernels. > > -- > Szil嫫d -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia

Re: [gmx-users] solvent implicit error

tp://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_xxx See Chapter 5 of the manual. If you need further guidance, please post a relevant snippet of the .top before and after the #include statement shown to provide context. -Justin -- ============ J

Re: [gmx-users] Error while trying REMD on cluster

ng on one processor. You probably need "mpirun -np 40" rather than just "mpirun" in the command. -Justin -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blac

Re: [gmx-users] g_velacc

would seem not. -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] oplsaa vs. charmm

some unknown phenomenon. Keep in mind that a single trajectory for either is not necessarily conclusive of anything. Replicates and good sampling will be more informative. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT

Re: [gmx-users] protein-ligand interaction

Otherwise, the most common quantity measured is backbone RMSD. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Tr

Re: [gmx-users] about POPC in Gromacs

kind helps. The root of the problem and possible solutions are here: http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database -Justin -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar M

Re: [gmx-users] How to simulate spc216.pdb in different water potentials

er [ molecules ] SOL 216 -Justin Thank you in advance *With Regards,** * * * *Ravi Kumar Venkatraman,* *c/o Prof. Siva Umapathy,** * *IPC Dept., IISc.,* *Bangalore, INDIA.* *Phone No: +91-9686933963* -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doc

Re: [gmx-users] gmembed

lose, forward, print or use it without the permission of the sender. __ -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia

Re: [gmx-users] GridMatMD and CGMD

should work the same way as an atomistic membrane. Please let me know if you encounter any problems. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul

Re: [gmx-users] GridMatMD and CGMD

different are the results? -Justin Thanks a lot again. Regards, Anirban On Mon, May 30, 2011 at 4:40 PM, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote: Anirban Ghosh wrote: Hi ALL, I have simulated a CGMD system consisting of multiple copies of a

Re: [gmx-users] Problem with pdb2gmx in gromacs 4.5.3

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-

Re: [gmx-users] PMF curve

y be local minima and other metastable states along the way. -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] PMF curve

result and you will need substantially more simulation time in each window. -Justin -- ============ 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] PMF curve

at region. Your histograms should show you this, as well. You need more windows and more time in each. Based on what you've shown, your simulations are simply unconverged. -Justin -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILE

Re: [gmx-users] PMF curve

ltaG. Because there is a difference about 0.5 kcal/mol . So there are some energetic differences in these windows. Watch the trajectories to figure out why. -Justin -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Tra

Re: [gmx-users] Box size error during attempted NPT equilibration

nm npt-eq -cpo npt-eq.cpt Thank you very much for your time! I really appreciate it. Andrew DeYoung Carnegie Mellon University -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech

Re: [gmx-users] implicit solvent LINCS errors

ngular You'd have to run with mdrun -pd (particle decomposition), but the end result can be quite fast and you avoid potential periodicity effects. -Justin -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department

Re: [gmx-users] Fwd: Simulation of protein with phosphate ion...

ee energies after you've determined plausible binding sites. -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] Fwd: Simulation of protein with phosphate ion...

est. Otherwise, you can pull the phosphates from whatever binding sites you've determined to get free energy changes for any of these processes. -Justin -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of B

Re: [gmx-users] Fwd: Simulation of protein with phosphate ion...

s and small molecules through transporters and channels. -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] Fwd: Simulation of protein with phosphate ion...

find. -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] implicit solvent LINCS errors

0, Michael D. Daily wrote: Thanks Justin, this is very helpful. I'll attempt these fixes tomorrow. Mike On 5/30/2011 5:50 PM, Justin A. Lemkul wrote: Michael D. Daily wrote: Hi all, I'm trying to run implicit solvent calculations in gromacs 4.5 with the charmm forcefield. I am able to

Re: [gmx-users] Grompp error on index file

file and topology, if it is small enough to paste into an email. -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] Grompp error on index file

eate an index group to accommodate the system. In other cases, it means you're using a group that is simply not applicable. -Justin --- On *Tue, 5/31/11, Justin A. Lemkul //* wrote: From: Justin A. Lemkul Subject: Re: [gmx-users] Grompp error on index file To: "

Re: [gmx-users] Indexing problem when using genconf

le. This should now match the number of atoms in the trajectory and the order in which they appear. The latter option seems to be much more efficient and will not require you to re-run any simulations, but I thought it would be worth mentioning the first method, since I use it all the time i

Re: [gmx-users] Indexing problem when using genconf

Justin A. Lemkul wrote: Ryan S Davis (rsdavis1) wrote: I wanted to copy a bilayer into a grid of 2x2x1 replicas. I used genconf and everything seemed to work fine exept that annoying feature that the command does not reorder the molecule types, so I end up with a .top file looking like

Re: [gmx-users] flexiblity

? Is it not just a matter of comparing the RMSF between the two proteins? -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

[gmx-users] Re: need help

ou, i need this type of graph (ligand interaction with specfic residues), for this which command i had to use. Untitled-3 copy.jpg Thaking you B. Babajan -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Departme

Re: [gmx-users] how to cite gromacs?

-- 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] Thermal_Unfolding

each temperature interval. If I can do this in gromacs then what should be the .mdp file for such increment in temperature at regular intervals. Start with the manual. http://manual.gromacs.org/online/mdp_opt.html#sa -Justin -- ==== Justin A. Lemkul Ph.D. Candidate

Re: [gmx-users] Pulling a ligand out of protein cavity

enlighten me as to what I am doing wrong? Thanks, -Shay P.S. Using gromacs 4.0.7. -- ======== 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] forgetten password

Hyunjin Kim wrote: Hi, I forgot my password to access the mailing list site. What should I do to fix this? You can get a password reminder at: http://lists.gromacs.org/mailman/listinfo/gmx-users -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS

Re: [gmx-users] number of molecules generated during pdb2gmx

d.itp" #include "molecule.itp" [ system ] my system [ molecules ] MOL 256 -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] Recommended way to run production using the same conditions as equilibration

r one makes sense to you. I tend to go with the grompp/mdrun combo. That offers you the ability to change .mdp options for I/O purposes, remove restraints, etc. -Justin -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT T

Re: [gmx-users] flexibility

shiva birgani wrote: Message: 1 Date: Tue, 31 May 2011 06:56:16 -0400 From: "Justin A. Lemkul" mailto:jalem...@vt.edu>> Subject: Re: [gmx-users] flexiblity To: Discussion list for GROMACS users mailto:gmx-users@gromacs.org>> Message-ID: <4de4

Re: [gmx-users] Steered Molecular dynamics

als, that's the place to look :) -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] .gro to .pqr

.ca> -- 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] .gro to .pqr

Justin A. Lemkul wrote: Mona Habibi wrote: Hi, I have a single file in .gro format and I want to change it to pqr format. I was wondering if there is anyway to make it? I tried to write the file with exactly the same format of pqr , but VMD can not read my file. editconf -mead outputs

Re: [gmx-users] .gro to .pqr

ivial; follow any tutorial. -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] compression to study pressure effect

bly aren't very well-converged and your system may still be equilibrating. Only for very small molecules (i.e., water and other small things) will you gather reasonable data in such short times. -Justin -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS D

Re: [gmx-users] scaling non-bonded interactions

small systems. There is an open issue on the redmine server about this, but no resolution yet. -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] Re: scaling non-bonded interactions

d. I don't know if that's the intent here, but it certainly does have an application. -Justin -- ============ 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: scaling non-bonded interactions

Vitaly Chaban wrote: Doesn't increased temperature work for this purpose? REMD can be useful, yes, but generalized Hamiltonian exchange, using lambda to scale the interactions between molecules can be very effective, as well. -Justin On Wed, Jun 1, 2011 at 3:27 PM, Justin A. L

Re: [gmx-users] scaling non-bonded interactions

Da-Wei Li wrote: I remember that 1-4 won't be scaled in the free energy code, right? True, but the desired 10% scaling in this case can be applied by changing the FudgeLJ and FudgeQQ values of the force field, I believe. -Justin dawei On Wed, Jun 1, 2011 at 3:24 PM, Justin A. L

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