Re: [gmx-users] Fatal error in popc simulation: Atomtype LC3 not found

directives in ffnonbonded.itp and ffbonded.itp. See the approach in: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee

Re: [gmx-users] Fatal error

'XXX'_not_found_in_residue_topology_database -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http

Re: [gmx-users] a question about energygrps

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

Re: [gmx-users] a question about energygrps

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

Re: [gmx-users] a question about energygrps

) hardware. My rule of thumb is 1000 atoms/CPU, and then tweak from there if necessary. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231

Re: [gmx-users] Error in MD simulation

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

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

is easier, and using a plain text editor will be easiest, i.e.: [ my_group ] 1 2 -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231

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

you very much in advance! Antoine -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal

Re: [gmx-users] MD simulations of covalent bound protein-ligand complex by 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

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

+02 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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

residue or molecule. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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

which have calculated for other molecules? There is a large database at http://virtualchemistry.org/index.php but I don't know if there will necessarily be anything similar to what you're looking for. -Justin Best regards, Antoine On 26/04/12 16:55, Justin A. Lemkul wrote: On 4/26/12

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

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

Re: [gmx-users] Position Restraints

. -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] Position Restraints

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

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

255 srun: error: cu11n184: tasks 81,84,87: Exited with exit code 255 srun: error: cu09n164: tasks 57,60,63: Exited with exit code 255 10946,1 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral

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

-- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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

-- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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

tell, you shouldn't be doing this. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages

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

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

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

and will close when doing equilibration as the solvent fills in around the lipid headgroups. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu

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

, so you're likely getting very frequent output of velocities into the .trr file. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540

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

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

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

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

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

-- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx

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

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

Re: [gmx-users] Making Disulfide Bonds

mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul

Re: [gmx-users] Making Disulfide Bonds

adjusts. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

Re: [gmx-users] Make an index file

': help 'r': residue 'res' nr 'chain' char name: group 'case': case sensitive 'q': save and quit 'ri': residue index Now, what is the correct answer? Anybody can suggest me? Thanks in advance, Shima ge -- Justin A. Lemkul Ph.D

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

and membrane, as measured by g_dist? What is the length of your unit cell along the z-axis? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA

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

is reproducible in the latest Gromacs version (4.5.5), please file a bug report on redmine.gromacs.org so that it can be investigated. Please provide .tpr file of the system so that the developers can run what you are trying to do and see. -Justin -- Justin

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

. Order of arguments is irrelevant to all Gromacs commands. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http

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

output.pdb The -f flag specifies the file that is being operated on. The -s flag specifies a file from which (in this case) atom and residue names are being read. It is necessary because your output format (.pdb) requires this information. -Justin -- Justin

Re: [gmx-users] Umbrella Sampling Hypericin Dimer

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

Re: [gmx-users] New Gromacs Release

thus far I see no major changes to existing content. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http

Re: [gmx-users] Box of water

the -maxsol option when invoking genbox. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages

Re: [gmx-users] disre and posres together?

. Thank you for your time B.Mehrazma -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages

Re: [gmx-users] POPC: ff53a6 and CHARMM36 formats

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

Re: [gmx-users] segmentation fault during equilibration

. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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

)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral

Re: [gmx-users] segmentation fault during equilibration

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

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

and Close to ISO is group 5, you would type: 1 | 5 at the make_ndx prompt, which will create a group called Close_to_ISO_ISO, thus a merged group of all atoms in Close to ISO and ISO. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar

Re: [gmx-users] segmentation fault during equilibration

-- 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] File editing - only one layer of water around a molecule

-- 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] GROMOS87 and CHARMM27

the new parameters. -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:* Tuesday, May 1

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

new .tpr files using position geometry, though I don't know if g_wham will accept them or not. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS

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

molecule that can form the intermolecular disulfide because the two molecules will be considered as one [moleculetype], as Gromacs requires. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry

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

off by 15 atoms, which is exactly how many are in the ligand described in the tutorial. Go back and read the instructions closely, as appending the ligand to the protein coordinate file is discussed in detail. -Justin -- Justin A. Lemkul Ph.D

Re: [gmx-users] GROMOS87 and CHARMM27

, because the parameters are different for sure. Having little idea what you're doing, I'll tend to agree. -Justin Cheers, Shima *From:* Justin A. Lemkul jalem...@vt.edu *To:* Shima Arasteh shima_arasteh2

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

you correctly incremented the second line of conf.gro to indicate that more atoms have been added? Without it, editconf will read the wrong number of lines and exclude the ligand. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES

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

it all in one shot for simple systems of a couple peptides with trjconv -center -pbc mol -ur compact. Note that these corrections for PBC are only necessary for visualization, not the analysis itself. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS

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

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] 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] 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] 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] 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] 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] 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] 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] 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

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