Re: [gmx-users] Force field

Dialing Pretty wrote: Dear All, Is the following force field still practical or not? GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) Is there some reason to suggest otherwise? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral

Re: [gmx-users] genconf

-- 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] genconf

of Sand solvent configuration contains 60 atoms in 10 residues Killed Would you please help me? Thanks alot Regards Saly -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech

Re: [gmx-users] genconf, grompp

-- 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] g_energy Kinetic Energy

-okr Note that information derived from velocities does not correct for the presence of constraints. You'll have to do that yourself. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry

Re: [gmx-users] g_select vs trjorder

you which atoms satisfy the given criteria. With trjorder, the coordinates of those atoms are reordered such that they are listed in sequence in the new trajectory. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee

Re: [gmx-users] Umbrella Sampling - Ligand Protein

distances that mdrun will interpret. They are printed to the screen. -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] g_select vs trjorder

in each selection for each frame. From trjorder -h: With option -nshell the number of molecules within a shell of radius -r around the reference group are printed. Thus the two output files should not be equivalent. -Justin -- Justin A. Lemkul Ph.D

Re: [gmx-users] g_select vs trjorder

, or otherwise using g_select to find OW atoms within whatever your distance is, since the count of OW will be the number of molecules of water within that distance. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee

Re: [gmx-users] Radial distribution function by COM

think you can do it with: g_rdf -com -rdf mol_com -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] (no subject)

, say a few hundred, then use genbox -cs -maxsol to fill a new box with the desired number of solvent molecules. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA

Re: [gmx-users] g_helix not recognizing protein backbone

-compile a test .tpr file. Try g_helix again using this .tpr file. If it works (or doesn't), please report back. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA

Re: [gmx-users] 'not allocate memory'

, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Act like Prometheus would (Gogol Bordello) : Cannot allocate memory -- Justin A. Lemkul Ph.D. Candidate ICTAS

Re: [gmx-users] Recommended protocol for cooling down temperature in 50 K steps

. However, I am not sure what this means as far as what to set continuation to in a2.mdp and a3.mdp. The continuation keyword applies to bond constraints and should not affect frozen groups. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar

Re: [gmx-users] Umbrella_pull_simulation

for DeltaG. Moreover, in the absence of any error estimates, you can't make any conclusions about these data. g_wham can generate error bars for you; I'd suggest you do it. -Justin Shahid Nayeem On Tue, Feb 28, 2012 at 7:44 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu

Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology

for the parametrization are out of a supporting information of a paper that did MD with my molecule. The System is my molecule (isoalloxazine) in water. Do you want to see my .rtp file? Thanks you for helping me. Greetings Lara - Ursprüngliche Message - Von: Justin A. Lemkul jalem

Re: [gmx-users] g_select problem (Invalid command line argument:)

it is interpreted as a single string. As it stands, the words resname, SOL, and, etc are being interpreted as arguments, which they are not. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech

Re: [gmx-users] hydrophobic and hydrophilic in implicit solvent

-- 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] Periodic molecules and minimum bonded cut-off

this in the manual. All of these messages have to do with the configuration of the DD cells. The details are explained in the Gromacs 4 paper: http://pubs.acs.org/doi/abs/10.1021/ct700301q -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES

Re: [gmx-users] grompp - Invalid command line argument

above is syntactically correct, so it's not what you typed ;) Check carefully for typos and spacing, particularly if you have mis-spaced or omitted the -o flag, which would cause the file name to be incorrectly interpreted. -Justin -- Justin A. Lemkul

Re: [gmx-users] [ pairs ] section in topology

-- 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] Two [ dihedrals ] Sections in Topology

dihedral) while the second indicates improper dihedrals. -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] Missing Interactions in [ angles ] Section in Topology

to topology but what could be the reason for this problem? What exactly is missing? By default, pdb2gmx generates all possible angles. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry

Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology

interaction referenced in the topology that does not exist in ffbonded.itp, grompp will fail with a fatal error. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul

Re: [gmx-users] Inconsistent shifts - is it something wrong with pbc

correctly. Presumably you're dealing with an infinite sheet (thus bonds extend across periodic boundaries), and thus you need to set periodic_molecules = yes in the .mdp file. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT

Re: [gmx-users] g_sdf - and g_spatial

. -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] a warning in grompp

. Unless you understand the exact implications of overriding these warnings, you shouldn't be blindly pushing forward. As the warning states, your time step is too long to be stable in the absence of constraints. -Justin -- Justin A. Lemkul Ph.D. Candidate

Re: [gmx-users] Simple LJ system

-- 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] Re: how modify the forcefield amino acid definitions for non-naturally occuring amino acids?

publications or any that refer to modifications of the original parameter set. Details can be sketchy depending on the force field, so be prepared to invest significant time in this endeavor. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar

Re: [gmx-users] Umbrella Sampling - NPT

previously conducted using constraints, so in that case, the distinction between the two is probably irrelevant. You should do whatever makes the most physical sense in your case. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT

Re: [gmx-users] Re: Lennard-Jones Interactions in Gromacs

. How and where do I give this information to gromacs? Could you give me just one line example syntax? Look in ffnonbonded.itp, in the [atomtypes] directive. The format and contents of this directive are explained in the manual. -Justin -- Justin

Re: [gmx-users] Imitation of the protein part

-- 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] em.mdp file

rvdw = 1.0 nstenergy = 10 Thanks for help Greetings Lara -- 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] em.mdp file

Justin A. Lemkul wrote: Lara Bunte wrote: Hello Is this em.mdp file correct for a simple MD simulation? integrator = steep nsteps = 200 nstlist = 10 You should set nstlist=1 for energy minimization (which is not, by definition, MD). Hit send too soon... You have also specified

Re: [gmx-users] grompp error - bondedtypes

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.edu/Pages/Personal/justin

Re: [gmx-users] grompp error - bondedtypes

indicates there is a dihedral for which parameters do not exist. -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] a question related to MD by gromacs

command to reinstiate the gromacs after it has stopped for example at 0.1 ns, which means I will restart from 0.1 ns? http://www.gromacs.org/Documentation/How-tos/Doing_Restarts#Version_4.x -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral

Re: [gmx-users] Is TRO defined correctly in the ffG43a1p forcefield file?

. TPOH is the -1 form of the phosphate and thus there is a proton on the phosphate group. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu

Re: [gmx-users] how modify the forcefield amino acid definitions for non-naturally occuring amino acids?

tutorials? The atom names used are standard nomenclature for amino acids. Also I am interested in knowing on how the topology files are created from scratch? Sorry, I don't understand what you mean here. -Justin -- Justin A. Lemkul Ph.D. Candidate

Re: [gmx-users] impropers and residue number

-- 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-users

Re: [gmx-users] Re: Re: mdrun -multi flag (Mark Abraham)

for each simulation). More can be used, but it must be a multiple of the number of simulations, as the error message indicates. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia

Re: [gmx-users] Re: Lennard-Jones Interactions in Gromacs

, but that's not necessarily relevant here. -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] [ bondedtypes ]

. Check gmx.ff/aminoacids.rtp for a complete description of each of the 8 possible columns and the order that they must follow. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia

[gmx-users] Re: Umbrella Sampling - ligand

-- 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

Re: [gmx-users] Segmentation fault - Implicit solvent

-- 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] Random option - genion

options), the syntax is genion -norandom. -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] Segmentation fault - Implicit solvent

, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: Dear Gmx Users, I am trying to run nvt simulation (equilibration) of the protein in implicit solvent. My mdp

Re: [gmx-users] genconf -renumber merges atom number and ID columns

Gromacs tools) has done its job correctly. -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] Segmentation fault - Implicit solvent

Steven Neumann wrote: On Thu, Mar 1, 2012 at 5:43 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: On Thu, Mar 1, 2012 at 3:58 PM, Steven Neumann s.neuman...@gmail.com mailto:s.neuman...@gmail.com mailto:s.neuman

Re: [gmx-users] PBC - Protein and Ligands

-- 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-users

Re: [gmx-users] Implicit solvent - Gromacs 4.5.4

/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 -- Justin A. Lemkul Ph.D. Candidate

Re: [gmx-users] Umbrella_pull_simulation

of the system. Looking at the interactions between your proteins, the stability of those proteins, etc. is far more informative, like you would for any simulation (even those that do not make use of the pull code). -Justin -- Justin A. Lemkul Ph.D. Candidate

Re: [gmx-users] add ion SCN - in OPLS-aa ff

-- 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 - Gromacs 4.5.4

. It can be argued that rigid bonds are a more realistic representation of ground state bonds, in addition to making the simulations more efficient. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department

Re: [gmx-users] Dihedrals Parametrization in the .rtpf File

] for improper dihedrals - in ffbonded.itp you would specify parameters for the impropers within a [dihedraltypes] block and specifying the correct function type for the interaction. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT

Re: [gmx-users] quality of a topology and pdb2gmx

. It's not likely a consequence of bad parameterization, rather bad construction of the necessary input files. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA

Re: [gmx-users] HIS residue in Charmm27

fields. If you are unsatisfied with the chosen protonation, there are command line options to interactively change the protonation state of any titratable residues. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee

Re: [gmx-users] problem in mdrun

-- 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

Re: [gmx-users] Implicit solvent - Gromacs 4.5.4

an in vacuo minimization work (i.e., just turn off the GB parts)? -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] Topology files

to http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field. If the molecule is a standalone species like a ligand, solvent, etc then all you have to do is #include an .itp file in the system topology. -Justin -- Justin A. Lemkul

Re: [gmx-users] Topology files

://www.gromacs.org/Documentation/How-tos/Polymers -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] Implicit solvent - Gromacs 4.5.4

Steven Neumann wrote: On Tue, Feb 28, 2012 at 6:33 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: I run energy minimization of my protein with implicit solvent: constraints = none integrator = steep

Re: [gmx-users] Topology files

) repetitive topology for a relatively large particle. You may or may not need to invoke specbond.dat for cross-links, as pdb2gmx can deal only with linear species via .rtp entries; other bonds are introduced with specbond.dat. -Justin On Tue, Feb 28, 2012 at 5:46 PM, Justin A. Lemkul jalem

Re: [gmx-users] change simulation temperature

-- 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: gmx-users Digest, Vol 94, Issue 159

-noappend and just concatenate your output later. Something in the filesystem thinks your .log file is still in use. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech

Re: [gmx-users] rc or rlist in minimum image convention?

Juliette N. wrote: On 24 February 2012 16:52, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Juliette N. wrote: On 23 February 2012 21:18, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.__au

Re: [gmx-users] about periodicity removal

-- 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

Re: [gmx-users] about periodicity removal....

is commonplace, but only in certain situations is it necessary to undo their effects. It does not sound to me like this is the case in your situation. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department

Re: [gmx-users] Re: Internal water in the membrane receptor

...@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 Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA

Re: [gmx-users] gromacs installation with mpi

or with similarly with autoconf, use the MPICC environment variable to point to the mpicc of choice. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul

Re: [gmx-users] gromacs installation with mpi

. -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_pull_simulation

the fist 1ns run for equilibriation. OK, so how did you decide that 10 ns was sufficient in each window? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul

Re: [gmx-users] about protein in periodic boundary condition..

://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions -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] Umbrella_pull_simulation

reasonable conclusions. -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] Calculate Dihedrals

-- 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

[gmx-users] Re: gen_temp, gen_seed

-- 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] Umbrella_pull_simulation

simulations to do so, but you can start by examining the physical properties of each window. What you're looking for is up to you, based on your knowledge of the system at hand. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES

Re: [gmx-users] HBonds with VMD

. Where is my mistake? Probably the atom names are wrong. This is a VMD question, so you're better off posting to the VMD mailing list for help on such topics. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee

Re: [gmx-users] rc or rlist in minimum image convention?

-- 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

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]vt.edu

Re: [gmx-users] Umbrella Sampling - gen_temp

-- 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

Steven Neumann wrote: On Thu, Feb 23, 2012 at 12:00 PM, Justin A. Lemkul jalem...@vt.edu 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

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

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. Lemkul Ph.D

Re: [gmx-users] Error note

significantly different energies. -Justin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin I saw this and had a question. How important is it for a charge group to be neutral? It isn't. Conventional use dictates that the charge group bear an integral charge. With PME

Re: [gmx-users] Determining energies between a solute and solvent

requires that energygrps are specified when running the simulation. Otherwise, the applicable terms in the .edr file are not decomposed. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia

Re: [gmx-users] Re: Determining energies between a solute and solvent

. -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: Determining energies between a solute and solvent

you want to consider, you have to create complementary groups for all the rest, i.e.: enerygrps = fragment Protein_not_fragment sol_fragment SOL_not_sol_fragment -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee

Re: [gmx-users] Peptide protonation inside membrane

to do pKa estimates, for instance: http://biophysics.cs.vt.edu/ -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] Protonation state of the ionisable residues

. 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 MILES-IGERT

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

-- 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 - spacing

-- 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

Re: [gmx-users] Umbrella_pull_simulation

Nayeem On Tue, Feb 21, 2012 at 1:04 AM, Justin A. Lemkul jalem...@vt.edu 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. ; Pull code

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 Department

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

. g_mindist -d 0.5 -on -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] Pressure coupling and membrane-type simulations

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. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar

Re: [gmx-users] Umbrella_pull_simulation

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 A. Lemkul Ph.D

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

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 Trainee Department of Biochemistry Virginia Tech Blacksburg, VA

Re: [gmx-users] Umbrella Pulling

-- 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

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