Re: [gmx-users] Force Constants and Unit Systems

in molecular dynamics simulations? Force is also expressed as kJ/(mol nm) - see Chapter 2 of the Gromacs manual. Thus, since x is in units of nm (distance), then k has units of kJ/(mol nm^2). -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department

Re: [gmx-users] Force Constants and Unit Systems

. -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

Re: [gmx-users] Force Constants and Unit Systems

constant that is not have a length term in the denominator. Presumably the true units are kcal/(mol A^2), which can be easily converted to kJ/(mol nm^2) for use in Gromacs. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry

Re: [gmx-users] Place water away from existing atoms

On 5/17/12 4:45 PM, Steven Neumann wrote: On Thu, May 17, 2012 at 5:48 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: On 5/17/12 11:50 AM, Steven Neumann wrote: My tube is finite. I increased my box so the water could interact with all water

Re: [gmx-users] TFE Proper Dihedral types...

On 5/16/12 12:36 AM, rama david wrote: On Tue, May 15, 2012 at 10:24 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: The parameters are missing from ffbonded.itp, making the implementation incomplete. You can obtain a TFE topology from ATB: http

Re: [gmx-users] Coupling groups in protein-ligand-lipid simulation

groups, Protein, Lipid and Lig_SOL_CL? Any suggestion is welcome. If the ligand is bound to the protein, I would couple the protein and ligand as a single group. -Justin -- Justin A. Lemkul, Ph.D. Department of Biochemistry Virginia Tech Blacksburg, VA

Re: [gmx-users] do_dssp segmentation fault error

-- Justin A. Lemkul, Ph.D. 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] Minimization with DPOSRE

force constant for the restraints or use freezegrps to fix the atomic positions. -Justin -- Justin A. Lemkul, Ph.D. Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages

Re: [gmx-users] charge and ionization state at pH 6.5

histidines. -Justin -- Justin A. Lemkul, Ph.D. 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] grompp Unkown bond_atomtype C2

-- Justin A. Lemkul, Ph.D. 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] grompp Unkown bond_atomtype C2

parameters assigned, it is useless. -Justin -- Justin A. Lemkul, Ph.D. 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] Wierd results from Umbrella sampling

are your box dimensions? -Justin -- Justin A. Lemkul, Ph.D. 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] (no subject)

are still the same. -Justin -- Justin A. Lemkul, Ph.D. 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] forcefields for lipids

-- Justin A. Lemkul, Ph.D. 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] PMF profile from Umbrella - Plateau

to analyze your own system to decide what's happening and what you should do. -Justin -- Justin A. Lemkul, Ph.D. 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] bonded interactions as table

, how can i do that. See manual section 4.2.13. Supplying a suitable table_d*.xvg file, with appropriate references to the tabulated function type (discussed in the manual) should be what you need. -Justin -- Justin A. Lemkul, Ph.D. Department

Re: [gmx-users] PMF profile from Umbrella - Plateau

On 5/16/12 11:16 AM, Steven Neumann wrote: On Wed, May 16, 2012 at 3:38 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: On 5/16/12 10:25 AM, Steven Neumann wrote: Dear Justin, I pulled my ligad away of 6nm from the protein and obtained beautiful

Re: [gmx-users] Index selection in g_potential

the different groups (individually) each time. -Justin -- Justin A. Lemkul, Ph.D. 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] itp file problem

, which was a variant of Gromos87. Using 43a1 should solve the problem. -Justin -- Justin A. Lemkul, Ph.D. 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] constranit distance for pulling code

can be carried out. In the absence of actually seeing what your settings are, that's the best I can offer. -Justin -- Justin A. Lemkul, Ph.D. Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http

Re: [gmx-users] Two [ dihedrals ] sections in topology

-- Justin A. Lemkul, Ph.D. 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] topology file in DPPC

different. -Justin -- Justin A. Lemkul, Ph.D. 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] topology file in DPPC

Gromacs version and follow the tutorial directly. -Justin -- Justin A. Lemkul, Ph.D. 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] about trifloroehanol

-- Justin A. Lemkul, Ph.D. 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 http

Re: [gmx-users] Generating_tpr_file from.xtc

-- Justin A. Lemkul, Ph.D. 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] about trifloroehanol

OCH2C* The corrected line would read: 12HTOTCH2TCT This is a small bug that should probably be fixed, though in your case, with proper input, use of the .hdb file is unnecessary. -Justin -- Justin A. Lemkul, Ph.D

Re: [gmx-users] ATB SWISSPARAM Topologies

-- Justin A. Lemkul, Ph.D. 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 http://lists.gromacs.org

Re: [gmx-users] How to calculate the center of the mass in gromacs

On 5/15/12 11:35 AM, xu zhijun wrote: Is there the simple method to calculate the center of the mass for a group of atoms? I want to post-process the traj date file. This is a function of g_traj. -Justin -- Justin A. Lemkul, Ph.D. Department

Re: [gmx-users] itp file for flavins

-- Justin A. Lemkul, Ph.D. 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 http

Re: [gmx-users] TFE Proper Dihedral types...

-- Justin A. Lemkul, Ph.D. 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 http

Re: [gmx-users] Measure angle with g_sgangle

file? The second column is the cosine of the angle. The third column is the actual angle. -Justin -- Justin A. Lemkul, Ph.D. Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http

Re: [gmx-users] Two [ dihedrals ] sections in topology

if it's not something you thought of previously or defined explicitly in the .rtp entry. -Justin -- Justin A. Lemkul, Ph.D. Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu

Re: [gmx-users] itp file for flavins

-- Justin A. Lemkul, Ph.D. 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] Virtual Sites - remove from GRO

-- Justin A. Lemkul, Ph.D. 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] Test Particle Insertion

. Have you tried plotting the file to see what it contains? The legends will be far more obvious if you do. -Justin -- Justin A. Lemkul, Ph.D. Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http

Re: [gmx-users] validation of a .rtp file

-- Justin A. Lemkul, Ph.D. 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 http

Re: [gmx-users] fatal error: missing H atom in .pdb file

use -missing option, Can't I? There are very limited cases where the -missing option should be used. This is not one of them. -Justin -- Justin A. Lemkul, Ph.D. Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231

Re: [gmx-users] Atom Names or Atom Types in the force field paramerization

. -Justin -- Justin A. Lemkul, Ph.D. 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] Atom Names or Atom Types in the force field paramerization

On 5/14/12 2:34 PM, Lara Bunte wrote: Hi Justin In my flamol.rtp file that I create in my force field order CHARMM27 Atom names are correct in the .rtp file. -Justin -- Justin A. Lemkul, Ph.D. Department of Biochemistry Virginia Tech Blacksburg

Re: [gmx-users] Atom Types in ffbonded.itp

there. The atom types present in ffnonbonded.itp can then be used in bonded interactions defined in ffbonded.itp. -Justin -- Justin A. Lemkul, Ph.D. 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

systemically incorrect in what you've set up. Based on a few snippets of topology and force field files, unfortunately it's impossible to say at this point. -Justin -- Justin A. Lemkul, Ph.D. Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul

Re: [gmx-users] *.ITP file

of work to improve the PRODRG topology: http://pubs.acs.org/doi/abs/10.1021/ci100335w ATB is another option. It is newer and performs better. http://compbio.biosci.uq.edu.au/atb/ -Justin -- Justin A. Lemkul, Ph.D. Department of Biochemistry Virginia

Re: [gmx-users] dipole moment

version 2.P of the force field (which contains polarizable water), MARTINI uses a single, uncharged particle to represent water. If there are no charges, there is no dipole. -Justin -- Justin A. Lemkul, Ph.D. Department of Biochemistry Virginia Tech

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

*From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Saturday, May 12, 2012 10:12 PM *Subject:* Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

*From:* Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org *Sent:* Saturday, May 12, 2012 10:12 PM *Subject:* Re: [gmx-users] Fatal error: No atoms found in .rtp file

Re: [gmx-users] How to get md_0_2. prefix for all output files during entexding production run, like got during first run md_0_1.

of -deffnm in the tutorial to set default output names. If you want your files to be called md_0_2.(extension) then you need to run: mdrun -deffnm md_0_2 -cpi md_0_1.cpt -Justin -- Justin A. Lemkul, Ph.D. Department of Biochemistry Virginia Tech Blacksburg

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

yourself. -Justin Cheers, Shima *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Sunday, May 13, 2012 8:36 PM *Subject:* Re: [gmx-users] Fatal error: No atoms

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

*From:* Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org *Sent:* Sunday, May 13, 2012 8:36 PM *Subject:* Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue

Re: [gmx-users] Should I use continuation = yes in my production dynamics following equilibration?

there are no constraints means there is uncertainty, which means you have some checking to do ;) -Justin -- Justin A. Lemkul, Ph.D. Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu

Re: [gmx-users] Re: Should I use continuation = yes in my production dynamics following equilibration?

in the case of constraints. -Justin -- Justin A. Lemkul, Ph.D. 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] Fatal error: No atoms found in .rtp file in residue pairs

-- Justin A. Lemkul, Ph.D. 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] Fatal error: No atoms found in .rtp file in residue pairs

On 5/12/12 1:37 PM, Justin A. Lemkul wrote: On 5/12/12 1:32 PM, Shima Arasteh wrote: Dear gmx users, I want to simulate a peptide in water. The peptide has a formyl residue as the N-terminus. I got the parameters of it and then add it to the .rtp file of charmm36.ff as below

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

it is the next residue and must also be prefixed with a + sign, as in the case of N. Using - (minus) indicates the previous residue, + the next, and no sign is the present residue. The correct line is: O C +N +CA -Justin -- Justin A. Lemkul, Ph.D

Re: [gmx-users] First Energy Minimization in a MD

is the force field itself and what it requires, as is true for all simulation process, EM or otherwise. -Justin -- Justin A. Lemkul, Ph.D. Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http

Re: [gmx-users] General amber force field in GROMACS

units, per Table 5.5 of the manual. Likely a simple unit conversion is all that is necessary, depending on the source of your parameters. -Justin -- Justin A. Lemkul, Ph.D. Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu

Re: [gmx-users] editconf and g_editconf confusion

-- Justin A. Lemkul, Ph.D. 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 http

Re: [gmx-users] Free energy calculation about ions (hope Justin A. Lemkul can give some suggestions )

On 5/9/12 10:37 PM, DeChang Li wrote: Dear all, I want to calculate the ion solvation free energy (e.g. an ion Na+ solvated in a water box) using Bennett Acceptance Ratio (BAR) method, following the tutorial by Justin A. Lemkul. However, if I turn off the Coulombic interaction

Re: [gmx-users] Formyl parameters

to information in the manual) can be found at: http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech

Re: [gmx-users] Itp file problem -- Atom type not found

the coordinate file is changed, so too must the topology. Some tools (genbox, genion) do this for you. Anything else is up to you to verify and apply. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department

Re: [gmx-users] Go model -error in generating topology

. Atom N is used in an interaction of type atom in the topology database, but an atom of that name was not found in residue number 1. Please suggest me a way , pdb2gmx is not suited for building such a topology. -Justin -- Justin

Re: [gmx-users] Formyl parameters

of the .itp file will be used to set up the .rtp entry. -Justin Cheers, Shima *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Wednesday, May 9, 2012 3

Re: [gmx-users] Restraining atoms

-- 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 -trj?!?

to provide additional help. -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] justin-lipid tutorial........

merry out of nothing, like in refugee camp (Gogol Bordello) Somehow you've badly broken the topology. At this point, it's hard to say how. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry

Re: [gmx-users] Formyl parameters

can probably guess a few more potential scenarios, but I'd rather not waste a lot of time ;) -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] restarting simulation after segmentation fault

indicates the system is unstable and will likely crash again. The log file will not indicate any errors, but information printed to stderr/stdout will. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department

Re: [gmx-users] radius of gyration

is appropriate to measure its radius of gyration. -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] Wild-card atomt types - regd

. -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] radius of gyration

different states and thus your data are poorly converged with respect to that measurement. -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] radius of gyration

of how things are calculated, you'd have to go through the code for a real mathematical proof. -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] Positive potential energies for Dimethyl Aniline and Aniline

, and other observables may be important as well. -Justin Best, Debayan On Mon, May 7, 2012 at 12:31 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: On 5/6/12 11:42 AM, Debayan Chakraborty wrote: Dear Colleagues, I am trying to build

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

-- 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] itp file problem

for Biotechnology, Anna University, Chennai.* -- 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] ngmx

rendering programs capable of rendering publication-quality images (VMD, Chimera, PyMOL, etc) in a variety of formats. If there is something specific about ngmx you need help with, ask a specific question. -Justin -- Justin A. Lemkul Ph.D. Candidate

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

in the topology. If there is a bonded 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

Re: [gmx-users] ngmx

this problem, Please? If VMD is not working, then you'd be best served posting to the VMD mailing list. Likely you have some library dependency that is not met; in my experience, that has been the issue for an immediate exit by VMD. -Justin -- Justin

Re: [gmx-users] Positive potential energies for Dimethyl Aniline and Aniline

. -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] Topology parameters

Thanks in advance, Shima *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Saturday, May 5, 2012 9:16 PM *Subject:* Re: [gmx-users] Topology parameters

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

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[at]vt.edu | (540) 231-9080 http

Re: [gmx-users] choose a force field

section of gromacs.org. -Justin Thanks, Shima *From:* Justin A. Lemkul jalem...@vt.edu *To:* Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Friday, May

Re: [gmx-users] Justin-lipid tutorial...

the main tutorial does not have you invoke -DPOSRES_LIPID in any of the .mdp 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

Re: [gmx-users] Justin-lipid tutorial..

) If you changed any of the .rtp settings, then you need to use pdb2gmx. If you made changes to dppc.itp, then pdb2gmx will do nothing to help you and you should use the approach mentioned above to obtain your topology. -Justin -- Justin A. Lemkul

Re: [gmx-users] Topology parameters

field has different parameterization procedures and makes use of different atom types. A new force field requires a new topology. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia

Re: [gmx-users] How to build 1-4 pairs tables for -tablep 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

Re: [gmx-users] Topology parameters

On 5/5/12 11:39 AM, Shima Arasteh wrote: Can I use CHARMM-GUI to get the formyl parameters for CHARMM36 and CHARMM27? Maybe, try it and see. Swiss-Param might also be an option. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar

Re: [gmx-users] how to use the triplets index file generated by g_hbond

(to determine which groups are participating in those hydrogen bonds). -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] keep the nanotube cylindrical.

. Are you using impropers in the topology? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu

Re: [gmx-users] Determining which parallelization algorithm I used

calling mdrun? Another way to check would be the absence of DD-related information printed to the log. For instance, if you don't see Initializing domain decomposition on X nodes then it would be apparent that DD wasn't used. -Justin -- Justin A. Lemkul

Re: [gmx-users] how to keep nanotube cylindrical

not appear to use any defined impropers, but perhaps its workflow and information will yield better results. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA

Re: [gmx-users] missing gbsa parameters

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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES

Re: [gmx-users] missing gbsa parameters

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

Re: [gmx-users] choose a force field

that a different choice should have been made. -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] Help with free energy

-- 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] Help with free energy

to derive a high-quality topology. For general advice, consult: http://www.gromacs.org/Documentation/How-tos/Parameterization -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech

Re: [gmx-users] missing gbsa parameters

-- 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] membrane simulation

-- 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] 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. Candidate ICTAS

Re: [gmx-users] Lamb-Protein

-- 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 extract trajectories into individual pdb file?

...@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 Virginia Tech

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

that contains the MG2+ ion within the solvent 2. Add MG2+ to residuetypes.dat so that it is recognized as an ion 3. Couple the MG2+ and protein/ligand together, as might make the most physical sense -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral

<    1   2   3   4   5   6   7   8   9   10   >