Re: [gmx-users] Conceptual question: Why are MD production simulations usually run in the NVT ensemble?

is you're modeling and what the most appropriate conditions are. Knowing the ins and outs of thermostat and barostat algorithms would be very important in debating these issues. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department

Re: [gmx-users] (no subject)

mailing list archive. -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

Re: [gmx-users] Re: Melting simulations - regd

't find is there any generalized way to set up compressibility values. Most simulations probably just use the compressibility of water. As for the accuracy of your simulation if you do this, I cannot say. -Justin -- ============ Justin A. Lemkul, Ph.D. Res

Re: [gmx-users] g_saltbr speed

rely. -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-users@g

Re: [gmx-users] g_saltbr speed

27;re simply exhausting available memory, so the only advice is in the link I posted before - use fewer frames or use a machine that has more memory to do the analysis. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Vir

Re: [gmx-users] Re: Error in Membrane simulations with POPC bilayer

://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/03_tricks.html -Justin -- 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] Melting simulations - regd

ion = no." -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] Re: Error in Membrane simulations with POPC bilayer

. During equilibration, position restraints with a normal magnitude are appropriate. -Justin -- 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] Re: Error in Membrane simulations with POPC bilayer

-- 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 http

Re: [gmx-users] Re: Final state not reached in pulling simulation

group is free to move and thus smoothly goes along with the spring. Other forces within the structure may act in opposition. -Justin -- ============ Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.

Re: [gmx-users] Re: Error in Membrane simulations with POPC bilayer

-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-users@gromac

Re: [gmx-users] Re: Error in Membrane simulations with POPC bilayer

you'd strive for better balance, but since an inflated lipid system in vacuo is rather weird, you can ignore this as well. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.

Re: [gmx-users] Final state not reached in pulling simulation

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 Vir

Re: [gmx-users] more than one protonation per residue with pdb2gmx

/File_Formats/Coordinate_File#Sources -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] g_saltbr speed

group, but you can also use a custom index group as needed. The warning message is intended to note that the .tpr file you produce will not likely work for running an actual simulation. It should be fine for analysis. -Justin -- Justin A. Lemkul, Ph.D

Re: [gmx-users] g_saltbr speed

x file, or when you want to make e.g. a pure Calpha .tpx file. Note that you may need to use -nsteps -1 (or similar) to get this to work. WARNING: this .tpx file is not fully functional." -Justin -- ============ Justin A. Lemkul, Ph.D. Research Scientist Department

Re: [gmx-users] water bridge

vance g_hbond with suitable index groups. If you're looking for water-mediated hydrogen bonds, there are numerous discussions about ways to accomplish that if you search the mailing list archive. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Dep

Re: [gmx-users] g_saltbr speed

finish. But this was too long. So any suggestions? http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at

Re: [gmx-users] more than one protonation per residue with pdb2gmx

) are treated as any other residue. Gromacs will not magically build them; they need to be present. But how can I add the capping groups to the structure? You'll have to use some external modeling software for that. -Justin -- ==== Justin A. Le

Re: [gmx-users] Re: Error in Membrane simulations with POPC bilayer

ys the atom names from the top file will be used, is it safe to ignore this warning too? No. The naming mismatches imply that grompp is trying to map parameters for lipids onto water molecules. The resulting simulation will be nonsense and will probably crash immediately. -Justin --

Re: [gmx-users] g_saltbr speed

are many, the calculation might take a long time. Four days sounds ridiculous, and perhaps the program has frozen by exhausting the available memory. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech

Re: [gmx-users] more than one protonation per residue with pdb2gmx

he termini when running pdb2gmx so that no additional protons are added or removed; the first and last amino acids are then treated as internal residues with normal peptide bonds. -Justin -- ============ Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistr

Re: [gmx-users] pH and protein

in the topology produced by pdb2gmx. -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] More accurate potential energy in output?

d ; nsteps = 0 ; nstfout = 1 ; define = -DFLEXIBLE ; flexible/ rigid water -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blac

Re: [gmx-users] Time for NPT or NVT equilibration

st to converge. -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] Forcefield parameters for AcetylCoA

values in ffbonded.itp - it is not clear to me why they are missing. Most, if not all, of the missing bonds are between OA and H atoms, which are simple alcohol groups (bond type gb_1). -Justin Best regards Quoting "Justin A. Lemkul" : On 7/11/12 8:18 AM, Padmanabhan Anbazha

Re: [gmx-users] more than one protonation per residue with pdb2gmx

electrostatic analysis. Please read pdb2gmx -h. There are tons of available options to control protonation of any and all titratable residues. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg

Re: [gmx-users] Forcefield parameters for AcetylCoA

-- 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] question about the output of minimization

ease tell me how I can prevent my box to shift? There is no box shift; it's just a visual representation of the dodecahedral box. You can "correct" it (for visualization purposes) by running trjconv -pbc mol -ur compact. -Justin --

Re: [gmx-users] question about the output of minimization

prevent my box to shift? There is no box shift; it's just a visual representation of the dodecahedral box. You can "correct" it (for visualization purposes) by running trjconv -pbc mol -ur compact. -Justin -- Justin A. Lemkul, Ph.D. Res

Re: [gmx-users] (no subject)

45 PM, Justin A. Lemkul wrote: On 7/11/12 6:00 AM, amir abbasi wrote: Hi All! I want to use Implicit solvent to simulate a nucleic acid sequence. How can I do it? I use this command: genion -s ions.tpr -o nucleic_ions.gro -p nucleic.top -pname K+ -nname CL -neutral -conc 0.1 ions.tpr file is

Re: [gmx-users] question about the output of minimization

representation of the dodecahedral box. You can "correct" it (for visualization purposes) by running trjconv -pbc mol -ur compact. -Justin -- ======== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg,

Re: [gmx-users] (no subject)

. -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] sovation with tip3p

e_file -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-users@g

Re: [gmx-users] refcoord_scaling

in pressure calculation. This is my understanding of the implementation; if it is incorrect or incomplete, hopefully someone will chime in. -Justin -- ============ Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalem

Re: [gmx-users] POPC in water

but a thoroughly equilibrated membrane will reduce the time needed in equilibrating the membrane protein system. -Justin -- ======== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[a

Re: [gmx-users] node decomposition' problem

On 7/9/12 4:25 PM, Justin A. Lemkul wrote: On 7/9/12 4:23 PM, Thales Kronenberger wrote: I'm trying to run a kinase (what means that I had ATP - large charged group) energy minimization and then MD. But when I put my protein together with its ligands I gotcha the follow error me

Re: [gmx-users] node decomposition' problem

.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm The large size you have obtained indicates there are likely problems with the .mdp file, topology, or both. -Justin -- ============ Justin A. Lemkul, Ph.D. Research Scientist Department of B

Re: [gmx-users] Re: DNA simulations

de in VMD), then the size associated with the system is much smaller. Using -d re-centers the system within the defined box, thus shifting the coordinates. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia

Re: [gmx-users] force field parametrs for Mn2+

a85eb75dbd174c8e11727dc8 -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] Reg dimers

simulation???kindly help me in this regard. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu

Re: [gmx-users] error in mdrun

0.1010 0.9949 0.1010 Is there something wrong with my temperature coupling? I doubt it. Decrease your timestep (as I've said twice now) and try again with something sensible for dt. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scie

Re: [gmx-users] error in mdrun

al adjustments in the .mdp file. See any basic tutorial for examples of how to simulate other ensembles, if this is your goal. -Justin -- ============ Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[

Re: [gmx-users] error in mdrun

ble, you need several adjustments in the .mdp file. See any basic tutorial for examples of how to simulate other ensembles, if this is your goal. -Justin -- ============ Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jale

Re: [gmx-users] large radius problem

bonds are so long that radius of gyration changes from 1.2 nm to 3.5 nm. That sounds like a PBC issue to me. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department

Re: [gmx-users] Peptide folding simulation

licit ?? ... Please reply . What evidence do you have that you should expect to see a folding event in such a short time? Most people will use more extensive sampling methods like REMD to observe peptide folding. -Justin -- ==== Justin A. Lemkul, Ph.D. Res

Re: [gmx-users] Re: Two questions about index files

be necessary (or exceptionally useful) here. Maybe someone with more experience with it can comment. I certainly doubt it will suppress Gromacs screen output. -Justin -- ======== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia T

Re: [gmx-users] define a new residue

-- 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] Two questions about index files

ons are dependent upon user choice, they can't be suppressed, at least in the quick trials I just did. I suppose you could modify the source to prevent this printing, but whether or not that's worth the effort is up to you. -Justin -- ============ Justi

Re: [gmx-users] define a new residue

full parameterization procedures, refer to the primary literature for CHARMM. It should detail how to derive parameters for new species. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemk

Re: [gmx-users] Re: Re: g_sham problem

-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] g_sham problem

comprehend it better. Use the -xmin and -xmax options to set suitable values. g_sham tries to guess, but in my experience, does a poor job of it and I usually have to set everything manually. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist

Re: [gmx-users] Crashes during protein-ligand simulation

elated to the ligand, either its topology or placement. -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] error in grompp

xfcyfcz 11 1000 1000 1000 -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

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

Re: [gmx-users] define a new residue

-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- ============ Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA

Re: [gmx-users] Crashes during protein-ligand simulation

, RMSD, SASA, etc) you may be able to make some meaningful observations about ligand stability in the protein binding site. -Justin -- ======== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[a

Re: [gmx-users] error in grompp

rror message states, position restraints are only applicable per [moleculetype]. http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemist

Re: [gmx-users] Re: specifying the direction of Pull in US

all dimensions. -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] Crashes during protein-ligand simulation

in the manual. -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 listg

Re: [gmx-users] Crashes during protein-ligand simulation

ldn't be appropriate (as layers can slide with respect to one another, like a membrane) but three groups does not sound appropriate. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Te

Re: [gmx-users] Boundary

Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow -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.

Re: [gmx-users] Re: bilayers move apart by nanometers upon implementing dihedral restraints on lipid tails

got basically all the consecutive dihedrals in a very specific orientation - is that compatible with your system? Can you run a simulation of a single lipid in vacuo using these restraints? -Justin -- ============ Justin A. Lemkul, Ph.D. Research Scientist Departm

Re: [gmx-users] Error in Membrane simulations with POPC bilayer

H2). The second warning may or may not be problematic. If your charge groups are split across periodic boundaries, they will be reconstructed properly. If your molecules are already whole, then you have a separate issue. -Justin -- ==== Justin A. Le

Re: [gmx-users] Re: specifying the direction of Pull in US

reference. Set those (x,y,z) values to pull_vec1. -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] Crashes during protein-ligand simulation

e it? -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-users@g

Re: [gmx-users] Re: Problem with minimizing the energy of the solvated system

lways. -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-

Re: [gmx-users] Re: Problem with minimizing the energy of the solvated system

e wrong. I recall some previous version of Gromacs had issues reading and writing correct box vectors in .pdb files; I don't know which one. It's always safe to use .gro files for everything, though in principle, .pdb files should work as well. -Justin -- ==========

Re: [gmx-users] Problem with minimizing the energy of the solvated system

ollow the link? It's where you can find an answer to almost every error you'll encounter. For instance: http://www.gromacs.org/Documentation/Errors#The_cut-off_length_is_longer_than_half_the_shortest_box_vector_or_longer_than_the_smallest_box_diagonal_element._Increase_the_box_size

Re: [gmx-users] question about energy minimization

energy minimization. Also, assuming you're using single-precision Gromacs, an emtol of 10 is very low and unlikely to be achievable, especially using a single run of steepest descent EM. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Depar

Re: [gmx-users] bilayers move apart by nanometers upon implementing dihedral restraints on lipid tails

1100012 20 21 22 23 11100012 21 22 23 24 11100012 ... etc. Himanshu -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231

Re: [gmx-users] COM RDF

effective g_rdf is for this purpose. From your initial description, if you're just trying to track COM distance over time, why not use g_dist? That's precisely what it does. -Justin -- ============ Justin A. Lemkul, Ph.D. Research Scientist Depart

Re: [gmx-users] COM RDF

You also need to use the -com flag to use the COM of the reference group. -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

Re: [gmx-users] Nucleic acid simulation

both proteins and nucleic acids. The remaining workflow is basically the same. -Justin -- 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] Regarding parameters for pull_groups in mdp file for the pull code

ach of them (one for ligand and other for group of atoms) ? All groups specified in the .mdp file must be either valid default groups or custom groups provided in an index file. -Justin -- ============ Justin A. Lemkul, Ph.D. Research Scientist Department of Bioche

Re: [gmx-users] PMF trails off to infinity.

100 pull_nstfout = 100 ; Number of pull groups pull_ngroups = 1 ; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2) pull_group0 =JJJ pull_weights0 = pull_pbcatom0 = 0 pull_group1 = CPZ pull_weights1 = pull_pbcatom1 = 0 pull_vec1 = pull_init1 = 0 pull_rate1 = 0 pull_k1 = 10

Re: [gmx-users] inquiry about SAS

total SASA. Atoms are either polar (hydrophilic) or nonpolar (hydrophobic) and thus contribute to the total SASA based on their characteristics. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA j

Re: [gmx-users] question to mdp file

quot;nstep" is not a correct keyword, but "nsteps" is. -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] Umbrella - Force constant

hodology is written with hand-waving explanations as to what the authors did and why it worked, and I have a suspicion that most reviewers don't have a better idea so they can't refute such claims. -Justin -- ======== Justin A. Lemkul, Ph.D. Re

Re: [gmx-users] Implicit solvent setup for large protein

ll kernels are the only ones I use for implicit calculations. -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/Perso

Re: [gmx-users] question to mdp file

ot a correct keyword, but "nsteps" is. -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] mdrun no structural output

hereof) with information about maximum force and potential energy. If you're not seeing this information, mdrun isn't done or somehow got killed or hung up. -Justin -- ======== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Vi

Re: [gmx-users] bindng energy & H bond energy calculation

is information. 5) to calculate the distance between the residues(let say Tyr and Arg) in my protein. (Actually I want to check a key interaction between them) g_dist -Justin -- ============ Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virg

Re: [gmx-users] problems with editconf

requires a .tpr file) to see the dodecahedral unit cell with everything placed as you would expect. -Justin -- ============ Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.e

Re: [gmx-users] PMF trails off to infinity.

very close possibly crashing into the dummy atom. So from what you're saying, I'm thinking this might be the source of the problem. Sounds like it to me. -Justin -- ============ Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia

Re: [gmx-users] PMF trails off to infinity.

th the PMF profile and the force profile: http://s1064.photobucket.com/albums/u370/laurakingsley/?action=view¤t=pull_fig.jpg -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Monday, July 02, 2012 3:56 PM To:

Re: [gmx-users] PMF trails off to infinity.

t/Mailing_Lists#Mailing_List_Etiquette -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/

Re: [gmx-users] PMF trails off to infinity.

cable figures. It sounds to me like your ligand is crashing into something in your system, but that's just a guess based on incomplete information. -Justin -- ======== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Bla

Re: [gmx-users] charmm36 parameters

.38550e-01 2.44704e+00 -- ==== 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] number of contact

e, Turgay -- ==== 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] Re: COM Pulling

m/COM-Pulling-tp4998944p4998989.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- ======== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540)

Re: [gmx-users] Berger lipid

they chose "310" K? In his article, he explains that their study was done in mammalian cells. 310 K is physiological temperature for the human body. Peter, please correct me if this was not the intent of your study. -Justin -- ============ Justin

Re: [gmx-users] Berger lipid

in an identical file... Lipidbook seems to only have C36 POPE. I guess maybe I will upload ours. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Thursday, June 28, 2012 7:56 PM To: D

Re: [gmx-users] Re: .top file incoherent with the values in the ffbonded.itp file

nippets of files shown. You can, based on having a very careful look through all of your files. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231

Re: [gmx-users] error with grompp

opology. Perhaps there is some error as a result. -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] Re: .top file incoherent with the values in the ffbonded.itp file

ting force fields and the manual for examples. -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/Perso

Re: [gmx-users] .top file incoherent with the values in the ffbonded.itp file

ing blanks for the RB coefficients. What is the issue and why is my topl.top file inconsistent with the inputs given in the ffbonded.itp file? The blanks are normal; see above comments. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Dep

Re: [gmx-users] pdb file of polymer

file. There are lots of ways to generate a coordinate file. Here are some suggestions: http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia

Re: [gmx-users] Structure optimization failure

On 6/29/12 11:10 AM, massimo sandal wrote: On 29 Jun 2012 15:09, "Justin A. Lemkul" mailto:jalem...@vt.edu>> wrote: > > > > On 6/29/12 9:04 AM, massimo sandal wrote: >> >> >> On 29 Jun 2012 14:08, "Justin A. Lemkul" mailt

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

rge is considered done and ready for production. If this is not the case, a bug report needs to be filed ASAP. Please submit a report at redmine.gromacs.org with a minimal test case. -Justin -- ============ Justin A. Lemkul, Ph.D. Research Scientist Departm

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