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

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. Research Scientist

Re: [gmx-users] (no subject)

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

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

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 of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http

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

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.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: 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

://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] g_saltbr speed

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 Virginia

Re: [gmx-users] g_saltbr speed

-- 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] 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 than one protonation per residue with pdb2gmx

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 Biochemistry Virginia Tech

Re: [gmx-users] g_saltbr speed

if there 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] Re: Error in Membrane simulations with POPC bilayer

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

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. Lemkul, Ph.D

Re: [gmx-users] g_saltbr speed

) and 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

Re: [gmx-users] water bridge

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 Department

Re: [gmx-users] g_saltbr speed

, 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 of Biochemistry

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] 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] Final state not reached in pulling simulation

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

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

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.edu | (540

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] sovation with tip3p

-- 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] (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] question about the output of minimization

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

Re: [gmx-users] (no subject)

, Justin A. Lemkul jalem...@vt.edu 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

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, VA jalemkul

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

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. Research Scientist Department of Biochemistry Virginia Tech

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] 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

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 jalem...@vt.edu: On 7/11/12 8:18 AM, Padmanabhan Anbazhagan wrote

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

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/justin

Re: [gmx-users] More accurate potential energy in output?

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

Re: [gmx-users] POPC in water

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

Re: [gmx-users] refcoord_scaling

. 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 jalemkul[at]vt.edu | (540) 231

Re: [gmx-users] Peptide folding simulation

?? ... 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. Research

Re: [gmx-users] large radius problem

it. These 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] error in mdrun

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[at]vt.edu | (540) 231

Re: [gmx-users] error in mdrun

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

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 Scientist

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] force field parametrs for Mn2+

-- 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: DNA simulations

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 Tech

Re: [gmx-users] node decomposition' problem

#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 Biochemistry Virginia Tech

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 message

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

Re: [gmx-users] top file

-- 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] error in grompp

numbers in the coordinate file. If you have a one-atom dummy [moleculetype], then the only valid content of posre_memb.itp is: [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 -Justin -- Justin

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

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

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

-- 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] define a new residue

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 jalemkul

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

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

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

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 Tech Blacksburg, VA jalemkul

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

-- 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] error in grompp

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 Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540

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

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

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

-- 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: 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] Error in Membrane simulations with POPC bilayer

). 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. Lemkul, Ph.D

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

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 Department of Biochemistry Virginia Tech Blacksburg

Re: [gmx-users] Boundary

/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.edu/Pages/Personal/justin

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

does not sound appropriate. -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

-- 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] bilayers move apart by nanometers upon implementing dihedral restraints on lipid tails

100012 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) 231-9080

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 Department

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

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_or_decrease_rlist -Justin -- Justin A. Lemkul

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

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 -- Justin A. Lemkul

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

. -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] Regarding parameters for pull_groups in mdp file for the pull code

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 Biochemistry Virginia Tech

Re: [gmx-users] Nucleic acid simulation

for 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] COM RDF

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.edu/Pages/Personal

Re: [gmx-users] COM RDF

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 Department of Biochemistry

Re: [gmx-users] problems with editconf

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.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages

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

) 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 Virginia Tech Blacksburg

Re: [gmx-users] mdrun no structural output

) 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 Virginia Tech Blacksburg, VA

Re: [gmx-users] question to mdp file

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

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

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/Personal/justin

Re: [gmx-users] Umbrella - Force constant

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. Research Scientist Department

Re: [gmx-users] question to mdp file

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

Re: [gmx-users] inquiry about SAS

. 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 jalemkul

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

= 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 = 1000 pull_kB1 = On 07/02/2012 04:38 PM, Justin A. Lemkul wrote

Re: [gmx-users] number of contact

-- 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] charmm36 parameters

+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 -- gmx-users

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

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 Blacksburg, VA jalemkul[at]vt.edu

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

#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/Personal/justin

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

profile and the force profile: http://s1064.photobucket.com/albums/u370/laurakingsley/?action=viewcurrent=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

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

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 Tech Blacksburg, VA

Re: [gmx-users] Re: 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) 231-9080 http

Re: [gmx-users] Berger lipid

his own POPC, which I am fairly certain will result 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

Re: [gmx-users] Berger lipid

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 A. Lemkul, Ph.D. Research

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

will be represented by a triclinic unit cell unless re-wrapped with trjconv -pbc mol -ur compact (which requires a .tpr file). -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540

Re: [gmx-users] Structure optimization failure

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

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

? Not sure. There used to be a public repository with tarballs available for each commit, but I don't know if that still exists. You should have what you're looking for though. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department

Re: [gmx-users] Structure optimization failure

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

Re: [gmx-users] error with grompp

What is wrong here? Best Eva -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

Re: [gmx-users] error with grompp

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

Re: [gmx-users] COM Pulling

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

Re: [gmx-users] Structure optimization failure

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

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