Re: [gmx-users] unable to access redmine

e was down earlier, and apparently still is. I'm CC'ing this to Rossen in case he's not reading gmx-users. -Justin -- ============ Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.

Re: [gmx-users] Re: Dihedral Constraints

-tos/Dihedral_Restraints -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation

On 6/14/12 4:06 AM, ms wrote: Ok, I tried some of your suggestions and the Coulomb-SR energies still fall down very quickly. I wonder if: On 13/06/12 16:59, Justin A. Lemkul wrote: 4. What happens when you use the Andersen thermostat? That's not implemented yet for CPU calculations (t

Re: [gmx-users] Regarding error.

=10 Kindly tell me how to overcome this error. The .trr file contains time frames only up to 10 ps, so you can't dump out a frame at 500 ps - it doesn't exist. -Justin -- ============ Justin A. Lemkul, Ph.D. Research Scientist Department of Bioche

Re: [gmx-users] help!!

ded in the tutorial. -Justin -- ============ Justin A. Lemkul, Ph.D. Research Scientist 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] Bootstrapping using g_wham

each. Do you need that many? What happens if you run with values of 200 of -bins and -nBootstrap? -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080

Re: [gmx-users] Re: Positive Potential Energy after equilibration

paper and in the Gromos96 references that have been published over the years. This topic has also been discussed at length in the mailing list archive, so I would encourage you to look for the threads. -Justin -- ============ Justin A. Lemkul, Ph.D. Research Scientist D

Re: [gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation [SOLVED]

thing. There should be some indication in the .log file that there might be a problem and/or problems with the temperature should be apparent. -Justin -- ============ Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, V

Re: [gmx-users] problem regarding installation of gromacs-4.5.5

nstallation -Justin -- ============ Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gm

Re: [gmx-users] simulation box shape and length

symmetry of the system. For membranes, a rectangular or cubic box is appropriate. For proteins, it's usually a waste. These topics are discussed in the manual, section 3.2. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochem

Re: [gmx-users] problem regarding installation of gromacs-4.5.5

sion, you can simply remove it. http://www.gromacs.org/Documentation/Removing_Installation -Justin -- ============ Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.

Re: [gmx-users] Tutorial KALP-15 in DPPC

statements in the tutorial to this effect; it is the only time it is used. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu

Re: [gmx-users] Tutorial KALP-15 in DPPC

eated with a text editor. It can easily be adapted to suit any lipid type for which you have an .itp file. Please check its contents, it is quite straightforward. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia

Re: [gmx-users] protein near the edges of simulation box

visualization through operations involving -center or -pbc. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] protein near the edges of simulation box

from trjconv into VMD, not the original. If you visualize trajectory A, then manipulate it to produce trajectory B, then trajectory B is no use to you unless you actually use it. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochem

Re: [gmx-users] Simple question (confout)

by using trjconv -dump to output the last frame of a trajectory and then use trjconv -pbc whole. That result and confout.gro should be the same. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg

Re: [gmx-users] protein near the edges of simulation box

ng "centered.xtc" as the data for your initial configuration. -Justin -- ============ Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.b

Re: [gmx-users] simulating dimer proteins

<mailto:gmx-users-requ...@gromacs.org>. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ======== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://

Re: [gmx-users] problem in making a trajectory

cify what time point to which each frame corresponds. If that's not the case, please provide the command you are using. -Justin -- ============ Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA

Re: [gmx-users] simulating dimer proteins

em? pdb2gmx with the option (chainsep) has given these two .itp files to me. It's a perfectly reasonable approach, and in fact the easiest since pdb2gmx takes care of everything for you. -Justin -- ============ Justin A. Lemkul, Ph.D. Research Scientist Department

Re: [gmx-users] problem in making a trajectory

-settime -cat I'm using the settime command to have each structure at a different time step. If I was using it wrongly please correct me. You should be prompted to then set a time value for each frame, is that not the case? -Justin -- ==== Justin A. L

Re: [gmx-users] problem in making a trajectory

t an .xtc file? What does gmxcheck tell you about it? -Justin 2012/6/16 Justin A. Lemkul mailto:jalem...@vt.edu>> On 6/16/12 7:41 AM, francesca vitalini wrote: Dear Justin, this is my trjcat command /home/cocktail/vitalini/__gromacs_spec

Re: [gmx-users] How to compare two pdb files

y. Hence, the atoms with the given indices have different velocities, with (x,y,z) components listed. -Justin -- ============ Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu |

Re: [gmx-users] How to compare two pdb files

x27;s only printing velocities, all other information in the .tpr files is the same, but the velocities are different. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540

Re: [gmx-users] How to compare two pdb files

ustin -- ==== Justin A. Lemkul, Ph.D. Research Scientist 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@gromacs.org

Re: [gmx-users] How to compare two pdb files

output into a file, i.e. gmxcheck -s1 file1.tpr -s2 file2.tpr > diff.txt Alternatively, pipe the output through the 'more' command gmxcheck -s1 file1.tpr -s2 file2.tpr | more -Justin -- ======== Justin A. Lemkul, Ph.D. Research Scientist Department of

Re: [gmx-users] pressure-lyzozyme tutorial

http://www.gromacs.org/Documentation/Terminology/Pressure. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist 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] About Mike Harms python script

#x27;t have anything in it. What does it contain? -Justin -- ======== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bev

Re: [gmx-users] Distance of pull group is larger than half the box size

ues. Otherwise, your box needs to be at least twice the COM distance at all times. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9

Re: [gmx-users] SDF-error

mmand, you output only solvent. Then, you try to use a solvent-only trajectory to do fitting to a protein backbone. You should output the whole system in the first step. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistr

Re: [gmx-users] spatial distribution function

should be choosing your analysis based on what you want to measure or observe. An SDF for a protein and an SDF for solvent will be wildly different quantities. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech

Re: [gmx-users] Strange behaviour of bonds

and solve this problem? Anybody may suggest me in this about? Please read this page in its entirety: http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of

Re: [gmx-users] jalem...@vt.edu

e COM distance in each of those frames. What's more, the manner in which frames are written out separately is far more efficient than running g_dist to get the distances over time, then selectively run trjconv -dump to extract out however many specific frames you want. -Justin --

Re: [gmx-users] Strange behaviour of bonds

r For a simple protein in water system, comm-grps should be set to "System." Hopefully you're not resetting COM motion of some parts of the system and not others. In any case, this setting is irrelevant to the problem at hand. -Justin -- ===========

Re: [gmx-users] problem regarding installation of gromacs-4.5.5

10021. -- ==== Justin A. Lemkul, Ph.D. Research Scientist 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] (no subject)

There are 0 lipids... Illegal division by zero at inflategro.pl line 300. This error usually comes up when there is something wrong with the format of the input .gro file. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry

Re: [gmx-users] hello

/Periodic_Boundary_Conditions -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Solvation Free Energy calculation (g_bar)

now how the join the two results in order to get the solvation Free energy of the whole process (considering that this is possible, I don't know this as well). Since free energy is a state function, you simply take the sums of the two processes. -Justin -- ============

Re: [gmx-users] Re: Solvation Free Energy calculation (g_bar)

w the parameters were derived. -Justin -- ============ Justin A. Lemkul, Ph.D. Research Scientist 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] (no subject)

tation/Errors#Cannot_allocate_memory -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Analysis of the torsion Chi angles dynamics during simulation

analyze dihedrals and produce either time-dependent angle information or histograms showing the distributions. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080

Re: Fw: [gmx-users] segmentation fault-g_spatial

. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist 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] to know about constraints

gromacs.org/Documentation/Terminology/Constraints_and_Restraints Position restraints are a common part of many workflows. These are likely what you need. http://www.gromacs.org/Documentation/How-tos/Position_Restraints -Justin -- ============ Justin A. Lemkul,

Re: [gmx-users] pair interaction energy decomposition analysis

cussed in the manual, section 5.3.4. -Justin -- ============ Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/P

Re: [gmx-users] to know about constraints

a position restraint does not completely prevent motion, it just disfavors it. The magnitude of the energy penalty for displacement depends on the force constant set in posre.itp. You can also use freezegrps to completely immobilize any subset of atoms in the system. -Justin --

Re: [gmx-users] Regarding pdb file of a polymer

-Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist 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] Re: Regarding pdb file of a polymer

ve some unique names. You can have a million internal monomers with the same name (Eth or whatever) as long as the ends are different. -Justin -- ============ Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[a

Re: [gmx-users] only three options for genrestr

herwise overriding the default groups by using another index file (which we can't tell because you haven't provided your command line). Check the contents of your files. -Justin -- ============ Justin A. Lemkul, Ph.D. Research Scientist Department of B

Re: [gmx-users] plzz help

ssue to attract attention, and avoid text-speak to attract the right kind of attention ;) -Justin -- ============ Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab

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

12 O TER Best regards, Eva -- ============ Justin A. Lemkul, Ph.D. Research Scientist 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] Residue 'DUM' not found in residue topology database

HOH A 527 25.281 -35.299 13.147 1.00 37.03 O HETATM 36214 O HOH A 528 46.452 -27.955 -20.733 1.00 19.63 O HETATM 36215 O HOH A 530 32.439 -23.614 -26.720 1.00 27.12 O TER Best regards, Eva -- ============ Justin A. L

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

://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] center an atomic group

;re looking for. -Justin -- ============ Justin A. Lemkul, Ph.D. Research Scientist 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] Top file

w-tos/Adding_a_Residue_to_a_Force_Field It also sounds like you are not setting termini properly using pdb2gmx -ter. Please provide your complete pdb2gmx command any any relevant screen output. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Departme

Re: [gmx-users] Rotation aroud the z axis

e membrane is wrong. So my question is: how can I rotate the protein around the z axis? editconf -rotate -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231

Re: [gmx-users] H-atoms in .hdb file

aren't achieving the desired behavior, you will have to be a lot more specific about what you're doing and what you're observing. -Justin -- ============ Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg,

Re: [gmx-users] H-atoms in .hdb file

obably comes from an incorrect assignment of terminus state. -Justin -- ============ Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/P

Re: [gmx-users] H-atoms in .hdb file

on of FOR. -Justin -- ============ Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gm

Re: [gmx-users] H-atoms in .hdb file

idue_to_a_Force_Field -Justin -- ======== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-u

Re: [gmx-users] Lipid-protein simulation....

nergy minimisation??? The purpose of InflateGRO is to pack lipids around a protein. If you don't need to embed the protein in the membrane, there is no point to using InflateGRO, or programs like g_membed. -Justin -- ==== Justin A. Lemkul, Ph.D. Research

Re: [gmx-users] Fwd: About Justin Lipid-protein simulation tutorial

-- Justin A. Lemkul, Ph.D. Research Scientist 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] H-atoms in .hdb file

is identified itself but "not" identified as protein. How so? What line did you add to residuetypes.dat, and what was the exact problematic output of pdb2gmx? -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistr

Re: [gmx-users] error using grompp: number of coordinates in coordinate file does not match topology

cating the number of DPPC molecules, which appears to be 122 (9900-3800 = 6100 = 122 * 50). -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231

Re: [gmx-users] Fwd: About Justin Lipid-protein simulation tutorial

restraints. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Fwd: About Justin Lipid-protein simulation tutorial

ly?? Is it wrong simulation??? How to check these parameter affect my result sensitivity??? The pressure might be slightly off. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.

Re: [gmx-users] H-atoms in .hdb file

minal ends. Select a proper terminal entry. Would you helping me with it with your useful suggestions? I honestly have no idea why that's not working. It's the exact same workflow used with all other capping groups and I use it routinely. -Justin -- ======

Re: [gmx-users] About Exclusion of bonded and non bonded parameters while running grompp

cg nsteps = 2000 ns_type = grid rlist = 1.2 coulombtype = pme vdw-type = cut-off rvdw = 1.2 rcoulomb = 1.2 ; ; Energy Minimization Stuff ; ; emtol = 0.001 emstep = 0.01 Thanking you in advance . Regards, Pavan Payghan -- ==== Justin A. Lemkul, Ph.D. Rese

Re: [gmx-users] Pulling ligand - Different Profiles (Force vs time)

nvergence is probably harder, but again you have to ask whether the differences are meaningful. http://www.gromacs.org/Documentation/Terminology/Reproducibility -Justin -- ============ Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tec

Re: [gmx-users] Pulling ligand - Different Profiles (Force vs time)

On 6/27/12 9:36 AM, Steven Neumann wrote: On Wed, Jun 27, 2012 at 1:51 PM, Justin A. Lemkul wrote: On 6/27/12 7:48 AM, Steven Neumann wrote: Dear Gmx Users, I obtained a protein-ligand complex from 100ns simulation. Now I am pulling my ligand away from the protein after the energy

Re: [gmx-users] make index

n the .mdp file (easiest), use a text editor to modify the name of the group in the .ndx file (same principle, probably a little more scrolling and/or find and replace), or use make_ndx to rename the groups (not very efficient in this case). -Justin -- ====

Re: [gmx-users] Re: pdb2gmx error

e 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. Research Scientist Department of Biochemistry Virginia Tech Blacksburg

Re: [gmx-users] Re: pdb2gmx error

the first three residues in your .pdb file so we can see what you're working with. -Justin Sincerely, Shima - Original Message ----- From: Justin A. Lemkul To: Shima Arasteh ; Discussion list for GROMACS users Cc: Sent: Wednesday, June 27, 2012 8:58 PM Subject: Re: [gmx-users] Re

Re: [gmx-users] Re: pdb2gmx error

does not give rise to this error, as all impropers are defined using only -C or +N. Just another reason to use a non-deprecated force field :) -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg

Re: [gmx-users] Re: pdb2gmx error

T THE SIMULATION WHIT A MODERN FF AS SOON AS POSSIBLE :) The sooner, the better. This is an ancient force field, and vastly better parameter sets exist. -Justin -- ======== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia T

Re: [gmx-users] Re: pdb2gmx error

ustin -- ==== Justin A. Lemkul, Ph.D. Research Scientist 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@gromac

Re: [gmx-users] Re: pdb2gmx error

rchive at Nabble.com. -- ============ Justin A. Lemkul, Ph.D. Research Scientist 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-us

Re: [gmx-users] Re: pdb2gmx error

ely, Shima - Original Message ----- From: Justin A. Lemkul To: Discussion list for GROMACS users Cc: Sent: Wednesday, June 27, 2012 10:25 PM Subject: Re: [gmx-users] Re: pdb2gmx error On 6/27/12 1:52 PM, shounakb wrote: Shima, I use gromacs-4.5.4. Without the FOR residue, my gmx.ff/aminoacid

Re: [gmx-users] Re: pdb2gmx error

s. You will then need to re-derive parameters for the formyl group based on the parameterization methodology required by the force field. -Justin Sincerely, Shima - Original Message ----- From: Justin A. Lemkul To: Discussion list for GROMACS users Cc: Sent: Wednesday, June 27,

Re: [gmx-users] Re: pdb2gmx error

es in N-teminals) . Then I got regretful to remove it. Don't you agree? Sincerely, Shima - Original Message - From: Justin A. Lemkul <jalemkul@> To: Discussion list for GROMACS users <gmx-users@> Cc: Sent: Wednesday, June 27, 2012 10:25 PM Subject: Re: [gmx-users] Re: pdb

Re: [gmx-users] Re: pdb2gmx error

uot;works" (i.e. produces a topology) but I do not necessarily endorse the use of the parameters shown. -Justin -- ============ Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu |

Re: [gmx-users] NVT, NPT and then pulling?

universally true. Your protocol should be based on how stable your systems are and how well your desired observables converge, but that much is true of every simulation. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia

Re: [gmx-users] Free energy between residues

and then can get the effective potential Ueff=-kTln If you are using PME, there is no trivial way to decompose the reciprocal space term. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalem

Re: [gmx-users] Justin's Paper

DeltaG. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Free energy between residues

On 6/28/12 6:51 AM, Steven Neumann wrote: On Thu, Jun 28, 2012 at 11:42 AM, Justin A. Lemkul wrote: On 6/28/12 6:33 AM, Steven Neumann wrote: On Thu, Jun 28, 2012 at 11:20 AM, lloyd riggs wrote: Dear Steven, Where are you working? I work in UK, London. Why are you asking? >F

Re: [gmx-users] editbox removes dummy atoms

atoms? The only reason I know of that editconf will truncate the file is if this line is incorrect. -Justin -- ======== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 2

Re: [gmx-users] g_bar ... the right answer for the wrong reason?

e do so. -Justin -- ======== Justin A. Lemkul, Ph.D. Research Scientist 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] editbox removes dummy atoms

e got dummy atoms that pdb2gmx won't recognize, unless you've done the leg work to incorporate them into your force field properly. -Justin -- ============ Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, V

Re: [gmx-users] g_bar ... the right answer for the wrong reason?

ata is the same, the two results differ by more than the error-bars question is, which one correct, and the warning, which i see in both cases, do i want to take it serious? I'd try to base a conclusion using the release-4-6 branch. -Justin -- ============ Ju

Re: [gmx-users] Berger lipid

for lipids than CHARMM27. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Berger lipid

ers were derived? The reproduction of experimental observables is quite good. Ultimately, the choice is yours, but be ready to justify that choice to a skeptical audience (reviewers). -Justin -- ============ Justin A. Lemkul, Ph.D. Research Scientist Depar

Re: [gmx-users] Berger lipid

n 1997 from a hybrid of OPLS and Gromos parameters. They are typically combined with Gromos force fields. -Justin -- ============ Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080

Re: [gmx-users] Berger lipid

-- Justin A. Lemkul, Ph.D. Research Scientist 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@gromacs.org

Re: [gmx-users] editconf do not center protein

hat you expect. The box will be represented by a triclinic unit cell unless re-wrapped with trjconv -pbc mol -ur compact (which requires a .tpr file). -Justin -- ============ Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksbur

Re: [gmx-users] Structure optimization failure

n_vel = yes; assign velocities from Maxwell distribution gen_temp= 300 ; temperature for Maxwell distribution gen_seed= -1; generate a random seed Thank you for helping me Greetings Lara -- ============ Justin A. Lemkul, Ph.D. Research Scientis

Re: [gmx-users] problem with git/4.6

check that. is there a way to simply get a tar-ball ? Not sure. There used to be a public repository with tarballs available for each commit, but I don't know if that still exists. You should have what you're looking for though. -Justin -- =

Re: [gmx-users] Structure optimization failure

said your goal was energy minimization. The script provided above is for equilibration after EM. The tutorial also contains an EM script that is more suitable but will still likely require some small adjustments. -Justin -- Justin A. Lemkul, Ph.D

Re: [gmx-users] error with grompp

s #include "amber03.ff/ions.itp" What is wrong here? Best Eva -- ============ Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.bioc

Re: [gmx-users] error with grompp

I always get the error: No such moleculetype NA+ although I already included the ion topology file: ; Include topology for ions #include "amber03.ff/ions.itp" What is wrong here? Best Eva -- ======== Justin A. Lemkul, Ph.D. Research Scientist Department of

Re: [gmx-users] COM Pulling

hould do to achieve the objection. You can use any valid group as a reference, provided that you specify it in an index group when running grompp. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksbur

Re: [gmx-users] Structure optimization failure

On 6/29/12 9:04 AM, massimo sandal wrote: On 29 Jun 2012 14:08, "Justin A. Lemkul" mailto:jalem...@vt.edu>> > > The settings in my tutorial are for use with OPLS-AA and are thus not suitable for a simulation with CHARMM. Cutoffs and other aspects will be different

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