Re: [gmx-users] About cutt-off scheme ..

-- 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] About cutt-off scheme ..

abnormal(I.e simulation is wrong ) or I have to select the option system on prompting ??? I am very new to these simulation field.. so all suggestion are appreciable ... On Thu, Mar 29, 2012 at 5:05 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: rama david

Re: [gmx-users] About cutt-off scheme ..

, 2012 at 5:05 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: rama david wrote: Hi Gromacs users , as per the link given on gromacs website... Introduction to Molecular Dynamics Simulations and Analysis http

Re: [gmx-users] How to fix Water during simulation ?

trying to work with. That becomes a huge pain and will likely make you question whether you need to go to all this trouble ;) Note that freezing and restraining are separate concepts (see the manual and webpage). -Justin -- Justin A. Lemkul Ph.D

Re: [gmx-users] Not able to continue with Equilibration

breaking the underlying physics. -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] Not able to continue with Equilibration

/Mailing_Lists -- 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] About Distance.pl script

at ./Distance.pl line 30. How to rectify this error ? Those errors will only show up if the g_dist output was not created. There will be other error messages indicating this fact. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES

Re: [gmx-users] About Distance.pl script

! Please don't post (un)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

Re: [gmx-users] About desired Spacing in Distance.pl script

the coordinate files that can be used later for umbrella sampling. You decide what spacing you need, and by simply reading through the summary_distances.dat file, you identify which coordinate files to use. -Justin -- Justin A. Lemkul Ph.D. Candidate

Re: [gmx-users] how to optimize hydrogen bonds before simulation?

not require large changes, simple energy minimization will generally take care of such things. -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] System exploding

Lara Bunte wrote: Hello If gromacs gives the warning that the system could explode, what could be the reason for that? http://www.gromacs.org/Documentation/Terminology/Blowing_Up -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar

Re: [gmx-users] protein melting experiment by GROMACS

the manual regarding simulated annealing. -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] on MD at constant pH

of your molecule. You should not, of course, equate this with a true constant pH, but the model is often used. You can assign your molecule the predominant protonation state at a given pH. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral

Re: [gmx-users] Re: How to add dihedral information from the GAFF topology

, then you can always start over building your system in a known order, checking the alignment of the coordinate file and topology at every step. -Justin On Wed, Mar 28, 2012 at 08:55, Justin A. Lemkul jalem...@vt.edu wrote: Biswajit Gorai wrote: Dear Bipin, Edit your topology file

Re: [gmx-users] Where would I find the 45A4 GROMOS force field?

the files from ATB: http://compbio.biosci.uq.edu.au/atb/ They are formatted for use with the GROMOS MD package, but that's the only source of these files of which I'm aware. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee

Re: [gmx-users] a question related to REMD

energy is calculated for each system from all the normal equations and then a probability of exchange is calculated at the exchange interval according to the equation given in manual section 3.13. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral

Re: [gmx-users] Where would I find the 45A4 GROMOS force field?

of force fields available on ATB including the other one I am interested in 53A6. Thanks again. On Wed, Mar 28, 2012 at 2:50 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Marc Gordon wrote: Hi all I have never posted to the mailing list before

Re: [gmx-users] Re: How to add dihedral information from the GAFF topology

to think about that but just for the reference for you I am attaching the coordinate and topology files. On Wed, Mar 28, 2012 at 16:19, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Thanks for your inputs. I have checked the coordinate file thoroughly and the order of atoms are same

Re: [gmx-users] 200 CPU, 3ns/day for 80,000 atoms !!!!

ref_p= 1.0 1.0 pbc = xyz gen_vel = no optimize_fft = no constraints = hbonds constraint_algorithm = Lincs / Thank you very much best -- Justin A. Lemkul Ph.D

Re: [gmx-users] construction of homopolymer from non-standard monomers in gromacs

size you like. See the instructions and linked example at: http://www.gromacs.org/Documentation/How-tos/Polymers -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA

Re: [gmx-users] Re: How to add dihedral information from the GAFF topology

# --- Please provide your comments. On Tue, Mar 27, 2012 at 03:20, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Thanks for your reply. Yes, you are right that these topologies are self supporting and there is no need to to call any other

Re: [gmx-users] Re: How to add dihedral information from the GAFF topology

Protein_chain_A 1 Ion_chain_A21 SOL 565 1-octanol 1 SOL 8422 Please provide suggestions. On Tue, Mar 27, 2012 at 17:59, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Thanks for your inputs. I have

Re: [gmx-users] Re: How to add dihedral information from the GAFF topology

the SOL entries in this way. -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: How to add dihedral information from the GAFF topology

://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin

Re: [gmx-users] About center of mass removal

-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT

Re: [gmx-users] Equilibrate the water around my molecule

is a simple naming mismatch in an .mdp file. Perhaps I've missed something along the way. -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] Re: How to add dihedral information from the GAFF topology

(at this specific location) will add the new [atomtypes] at the appropriate level of precedence, before any [moleculetypes] are declared. -Justin On Mon, Mar 26, 2012 at 18:46, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Thanks for your reply. But as far as I understood, in order

Re: [gmx-users] Problem: pdb2gmx with a more complex system

, but then again CHARMM has a different modus operandi. Thanks in advance for any help, Jernej Zidar -- 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] Adjust time intervals

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

Re: [gmx-users] Adjust time intervals

correction DispCorr = EnerPres ; account for cut-off vdW scheme Thanks, Afsaneh On 3/25/12, Justin A. Lemkul jalem...@vt.edu wrote: Peter C. Lai wrote: In the .mdp file what is nstenergy set to? I'd further ask what the rest of the .mdp file says, as well. If this is the output

Re: [gmx-users] Adjust time intervals

is no longer ongoing, so fixing any potential bugs there is not likely to happen. If the problem is reproducible in the newest version, it will need to be investigated further. -Justin Thanks Afsaneh On 3/25/12, Justin A. Lemkul jalem...@vt.edu wrote: afsaneh maleki wrote: Thanks Dear Peter

Re: [gmx-users] Fatal error: Atom CG is used in the topology database...

a rotamer library and the naming conforms to the normal standard so there are no issues when using the fixed files as input into pdb2gmx. -Justin Thanks On Mar 23, 2012, at 5:39 PM, Justin A. Lemkul jalem...@vt.edu wrote: Andy Somogyi wrote: Hi All, I'm trying to generate topology for a PDB from

Re: [gmx-users] RMSD analysis during production MD

-- 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 automate genion completely?

, and passed via 'echo' like other commands. See http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts. Thus you can use something like echo SOL | genion -s topol.tpr -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar

Re: [gmx-users] REMD equilibration

temperatures, the box itself may vary more widely and when the system is exchanged, the algorithms can fail. This phenomenon has been reported by a number of other users. With NVT, this does not happen. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral

Re: [gmx-users] Re: Neigborsearching, Electrostatics and vdw options

/rvdw. isnt it?/ Yes. -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] genbox

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

Re: [gmx-users] BUG: Free energy calculation

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

Re: [gmx-users] refcoord_scaling

Acoot Brett wrote: Dear All, For the npt.mdp downloaded from the Justin Lemkul tutorial, it seems we need to add a line of refcoord_scaling*.* If so, its value should be all or com? I am looking forward to getting a reply from you. Either should work. I doubt that for this case

Re: [gmx-users] parameters of em.mdp

reported before: http://lists.gromacs.org/pipermail/gmx-users/2009-January/039113.html -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] parameters of em.mdp

, especially in single precision. The energy values and maximum forces achieved don't change appreciably in most cases. Regarding nstlist, for EM it should be set to 1. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee

Re: [gmx-users] Do checkpoint files contain energies?

in a manner similar to how they are present in an .edr 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) 231-9080 http

Re: [gmx-users] Fatal error: Atom CG is used in the topology database...

in using external software. -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] renumber charge group

-- 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] Box Size in MD

-- 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] Re: Creating an atomtype where all nonbonded interactions are enumerated

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

Re: [gmx-users] Re: Creating an atomtype where all nonbonded interactions are enumerated

in the configuration file, for my system there is not any obvious order to use (such as N terminus, H attached to N terminus, C-alpha, etc). Yes, from everything I can tell the order that is used is the one found in the coordinate file. -Justin -- Justin A. Lemkul

Re: [gmx-users] problem in oplsaa ffbonded.itp

notation for a dihedral. -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] regarding em potential energy positive

for 7sol.. The average value of PE during EM lacks meaning. What is important is the potential energy reached at the end of the process and the maximum force. Those metrics will tell you how well EM succeeded. -Justin -- Justin A. Lemkul Ph.D

Re: [gmx-users] regarding em potential energy positive

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

Re: [gmx-users] Creating an atomtype where all nonbonded interactions are enumerated

, since they operate this way. LJ nonbonded interactions are generated using sigma and epsilon unless a special set of parameters is specified in [nonbond_params]. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee

Re: [gmx-users] Re: Creating an atomtype where all nonbonded interactions are enumerated

-- 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] Incorrect number of parameters - found 2, expected 5 or 5 for LJC-14 q

, qj, V, and W), unlike pair type 1, which only requires 2 (V and W). See Table 5.5 in the manual for the required format. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech

Re: [gmx-users] Incorrect number of parameters - found 2, expected 5 or 5 for LJC-14 q

they provided. -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] (no subject)

editconf -box (to define a particular box size) or genbox -maxsol (to set a maximum value of solvent). Whether or not you can accomplish what you want in a sound manner (or whether it is even necessary) is debatable. -Justin -- Justin A. Lemkul Ph.D

Re: [gmx-users] Group protein not found in index file

a group and name it such that grompp finds a match between the .mdp file and the .ndx 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

Re: [gmx-users] Group protein not found in index 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] FW: Problem installing Gromacs: What next?

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

Re: [gmx-users] HBonds between molecules

-hbn and -hbm. -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] Problem Installing 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 -- gmx-users

Re: [gmx-users] Problem installing Gromacs: What next?

feedback for improving the instructions, you're welcome to provide it. The instructions are assembled by users and improved by users. We've worked very hard to make sequential instructions available. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS

Re: [gmx-users] FW: Problem installing Gromacs: What next?

. -- 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] FW: Problem installing Gromacs: What next?

, Suhaila. -- 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] number of coordinates in coordinate file does not match topology

the contents of the [molecules] directive always matches that of the coordinate file, in terms of the number of molecules and the order in which they are present. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department

Re: [gmx-users] Simulated Annealing Protocol...

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

Re: [gmx-users] g_sas; could not find a Van der Waals radius

-- 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] How to do Normal Modes Analysis with Gromacs4.5.5?

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

Re: [gmx-users] Simulated Annealing Protocol...

, not a generalization that any particular ensemble was more suited for SA. The application of this technique and the use of restraints (or not) depends entirely upon what you hope to model and observe during the SA process. -Justin On Sat, Mar 17, 2012 at 19:56, Justin A. Lemkul jalem...@vt.edu wrote

Re: [gmx-users] opls topology for butanol, hexanol, heptanol

for the exact methods for charge derivation and atom type implementation. The methods are quite well explained in these papers. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia

Re: [gmx-users] g_sas

- what property or quantity do I can get from The SAS_calculations of residue protein in two ways? Likely a meaningful one and a useless one. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department

Re: [gmx-users] Simulated Annealing Protocol...

done similar things. -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] Gromacs installation question: Where is my Gromacs?

you. Kind regards Gudrun -- 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] Gromacs installation question: Where is my 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] Gromacs installation question: Where is my Gromacs?

you. Kind regards Gudrun Am 16.03.2012 um 20:28 schrieb Justin A. Lemkul: bestenborstel wrote: Did run sudo make install again, but before I executed configure with prefix=/usr/local/gromacs and I did mkdir gromacs in /usr/local before manually. Content in the gromacs folder: bin include

Re: [gmx-users] Umbrella_pull_simulation

to do your thinking for you, nor should they. The principal function of this list is to troubleshoot problems with Gromacs, of which there are none here. Good luck. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee

Re: [gmx-users] Information on .mdp files

? The entirety of Chapter 7 in the manual is devoted to this information. There is an online manual (linked from the PDF manual), but it contains the same information and is present mostly for convenience. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral

Re: [gmx-users] g_sas

independently; residue area arises from atom area. -Justin How to correlate area per residue for a selected residue with area per atoms for a selected residue? Thanks in advance, Afsaneh -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES

Re: [gmx-users] bug in g_msd

. Someone else mentioned something similar a few days ago, so I was just wondering if this was the case. Sounds like this is a known issue: http://redmine.gromacs.org/issues/774 -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT

Re: [gmx-users] clashes

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

Re: [gmx-users] Re: How the pressure is computed

the part of the box which is not vacuum. Is there any way to compute the density locally, i.e. in the part of the box actually occupied by molecules? I doubt it. The entire box volume is considered, as far as I know. -Justin -- Justin A. Lemkul Ph.D

Re: [gmx-users] clashes

commonly) the simulation was not initialized from a suitably low-energy state, implying either insufficient minimization (i.e. Fmax was too high) or inadequate equilibration. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT

Re: Fwd: [gmx-users] Generation of the Distance Restraints

not work (yet) with domain decomposition, use particle decomposition (mdrun option -pd) Thus the error message tells you how to proceed. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry

Re: Fwd: [gmx-users] Generation of the Distance Restraints

to be using mdrun -pd for your simulation to work. You can't use DD with all those restraints. -Justin James 14 марта 2012 г. 19:43 пользователь Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu написал: James Starlight wrote: Mark, My restrains on topology

Re: [gmx-users] hydrogen hydrogen interaction

-- 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] Generation of the Distance Restraints

? Should I obtain value for the initial Ca-Ca distance between my residues from the initial structure? How I could do it? See Figure 4.13 and equations 4.79 in the manual. r0 = low, r1 = up1, and r2 = up2. -Justin -- Justin A. Lemkul Ph.D

Re: [gmx-users] Reg final error

to cluster???please let me know and i am struggling with this from past 1month.Please tell me how to solve this The error says you are out of quota, i.e. out of disk space. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES

Re: [gmx-users] addition of two solvents

/Mixed_Solvents -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] How the pressure is computed

for an infinite z-dimension. There are limitations to this approach, as stated in the manual, but it may be more sound. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech

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

Steven Neumann wrote: On Sun, Mar 11, 2012 at 10:13 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: Hi Justin, As you advised I reduced number of my windows and I obtined histogram: http://speedy.sh/2b9dT

Re: [gmx-users] Generation of the Distance Restraints

question related to what you can't find or don't understand. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http

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

Steven Neumann wrote: On Mon, Mar 12, 2012 at 11:06 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: On Sun, Mar 11, 2012 at 10:13 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu

Re: [gmx-users] pdb file

for producing coordinate files. See, for instance: http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech

Re: [gmx-users] Calculating the center of mass of 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

Re: [gmx-users] Installing g_mdmat from Gromacs analysis package

-by-step instructions provided online. -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] genbox,genconf

tasks. If you want a specific answer to solve a specific task, ask a specific question. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu

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

is likely fine, you just may need a bit more sampling in each window to smooth things out. Also make use of the error estimates that g_wham can provide; they can be quite informative (and necessary). -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS

Re: [gmx-users] protein-ligand tutorial problem

likely possibilities. -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] Segmentation fault

fault Your simulation crashed. The fact that it did so immediately suggests inadequate energy minimization and/or equilibration. http://www.gromacs.org/Documentation/Terminology/Blowing_Up -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral

Re: [gmx-users] genconf,grompp

3DRGCAA 13 0.495 -0.175 -0.072 0. 0. 0. 3DRGCAB 14 0.483 -0.311 -0.143 0. 0. 0. Thanks Nahid -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department

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

constant. They will be looked up in ffbonded.itp. -Justin Greetings Lara - Ursprüngliche Message - Von: Justin A. Lemkul jalem...@vt.edu An: Discussion list for GROMACS users gmx-users@gromacs.org CC: Gesendet: 21:04 Mittwoch, 7.März 2012 Betreff: Re: [gmx-users] Missing

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