Re: [gmx-users] on Umbrella Sampling

-Justin Cheers, Acoot *From:* Justin A. Lemkul *To:* Acoot Brett ; Discussion list for GROMACS users *Sent:* Sunday, 1 April 2012 10:32 PM *Subject:* Re: [gmx-users] on Umbrella Sampling Acoot Brett wrote: > Dear All, > In the on-line tutorial "

Re: [gmx-users] on Umbrella Sampling

d Enter to quit the program. If you have not specified any other output name, the default is "index.ndx." -Justin Cheers, Acoot *From:* Justin A. Lemkul *To:* Acoot Brett ; Discussion list for GROMACS users *Sent:* Sunday, 1 April 2012 10:32 PM *Subject:* Re: [gmx-users] on Um

Re: [gmx-users] on Umbrella Sampling

ng pdb2gmx. -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] on Umbrella Sampling

with chain B). The rationale for restraining chain B is explained in the article. -Justin Cheers, Acoot *From:* Justin A. Lemkul *To:* Discussion list for GROMACS users *Sent:* Sunday, 1 April 2012 11:04 PM *Subject:* Re: [gmx-users] on Umbrella Sampling Acoot Brett wrote: > Tha

Re: [gmx-users] Editing of the existing system

he time step for the initial 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 htt

Re: [gmx-users] a question related to force field on terminal residues

on or to the actual bonded and nonbonded calculations themselves? -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

Re: [gmx-users] pdb2gmx error

naming mismatch or a missing atom. -Justin I am looking forward to getting an explaination from you. Cheers, Acoot -- ======== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Bla

Re: [gmx-users] pdb2gmx 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://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

Re: [gmx-users] Re: Carbohydrate simulation: problem with the terminal atoms

pology? http://compbio.biosci.uq.edu.au/atb/ I think the results should be vastly more reliable than trying to reverse-engineer a faulty PRODRG topology. They also have a reasonably large database of building block molecules with which you can check your work. -Justin -- =

Re: [gmx-users] ions error

tpr.mdp -c sistema_ions.gro -p sistema.top -o sistema_stpr.tpr The more relevant information would have been your genion command, force field name, and Gromacs version. -Justin -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Dep

Re: [gmx-users] ions error

ustin *De:* Justin A. Lemkul *Para:* Eduardo Oliveira ; Discussion list for GROMACS users *Enviadas:* Segunda-feira, 2 de Abril de 2012 16:55 *Assunto:* Re: [gmx-users] ions error Eduardo Oliveira wrote: > Hi all, > &g

Re: [gmx-users] on the Umbrella Sampling on-line tutorial

ustin -- ==== 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] on the Umbrella Sampling tutorial

It wasn't necessary. The system is quite robust and my experience has indicated that NPT equilibration was sufficient. -Justin -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech

Re: [gmx-users] grompp error

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://www.bevanlab.biochem.vt.edu/Pages/

Re: [gmx-users] grompp error

tems. -Justin ---- *De:* Justin A. Lemkul *Para:* Eduardo Oliveira ; Discussion list for GROMACS users *Enviadas:* Terça-feira, 3 de Abril de 2012 15:54 *Assunto:* Re: [gmx-users] grompp error Eduardo Oliveira w

Re: [gmx-users] grompp error

*De:* Justin A. Lemkul *Para:* Discussion list for GROMACS users *Enviadas:* Terça-feira, 3 de Abril de 2012 16:51 *Assunto:* Re: [gmx-users] grompp error Eduardo Oliveira wrote: > Thanks! > Please keep the discussion on the list. From your .mdp file: t

Re: [gmx-users] the -extend function of the tpbconv command

w to process for the extension MD so that the curve of the rmsd.xvg (and all the other xvg files) will have x-axis from the 0 to the 2 ns (2 ns is the total MD time, including the 1 ns extended part)? There are two steps here: http://www.gromacs.org/Documentation/How-tos/Extending_Simul

Re: [gmx-users] on the Umbrella Sampling tutorial

libration was sufficient. -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.b

Re: [gmx-users] Bad box in protein.gro

Can any body tell me where i am going wrong.. Did you remember to increment the number of atoms on the second line of the .gro file after adding the ligand? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee

Re: AW: [gmx-users] Shape of box

ion of a single protein in solvent (as in your tutorial?). Not to mention the inherent geometry of a globular protein. The manual contains a nice discussion of box types and their geometries in section 3.2. -Justin -- ============ Justin A. Lemkul Ph.D. Candidate

Re: [gmx-users] do_dssp

handle that syntax. A patch has been proposed in the development version but it has not yet been incorporated into the git repository. You could make the modifications to the source yourself by following: https://gerrit.gromacs.org/#/c/687/ -Justin --

Re: [gmx-users] Re: Simulation in the high temperature conditions

-- 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] do_dssp

yet been incorporated into the git repository. You could make the modifications to the source yourself by following: https://gerrit.gromacs.org/#/c/687/ -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MIL

Re: [gmx-users] Re: Simulation in the high temperature conditions

300. After that, it is irrelevant. Do you mean ref_t? In this case, the annealing temperature values override ref_t, so it doesn't matter. -Justin -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of B

Re: [gmx-users] Re: Simulation in the high temperature conditions

uld be equal to the ref_t value you wish to use for the simulation. If your gen_temp and ref_t values are not the same, then it is quite possible that the simulation will crash or give very unexpected results due to potential instabilities in the thermostat algorithm. -Justin -- =======

Re: [gmx-users] Atom N not found....

atom in ACE, but ACE only contains CA, C, and O. The N atom should be the first atom in the next residue, not ACE. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech

Re: [gmx-users] the different protonation state of HIS

> 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 -- ===

Re: [gmx-users] Zn Coordination

nable choice. -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] g_hbond

if using -nitacc), so you can probably trick it into thinking that's what they are. -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] Different results from identical tpr after MD

ed at all. Please consult: http://www.gromacs.org/Documentation/Terminology/Reproducibility -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] Different results from identical tpr after MD

ieve the statement made by several research papers based > on unconverged simulations. > > On Thu, Apr 5, 2012 at 23:12, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote: >> >> >> >> bipin singh wrote: >>> >>> Hi all, >>

Re: [gmx-users] Different results from identical tpr after MD

ldn't trust any conclusions drawn from demonstrably unconverged simulations. Not everything that's published has been done correctly. Peer review is an imperfect system, so be careful what you read and apply good scientific judgment. -Justin On Thu, Apr 5, 2012 at 23:12, Justin A. Lemku

Re: [gmx-users] Re: job failed

system being simulated would be even better :) -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] Different results from identical tpr after MD

energetic properties may be of interest, but these are things you should define before you even sit down at your terminal to begin. -Justin Cheers, Acoot *From:* Justin A. Lemkul *To:* Discussion list for GROMACS users *Sent:* Friday, 6 April 2012 4:41 AM *Subject:* Re: [gmx-users] Different

Re: [gmx-users] Further question on protonation state of histiding

answered this yesterday: http://lists.gromacs.org/pipermail/gmx-users/2012-April/070129.html Please pay attention to advice you've already been given, or else people become less likely to give it. -Justin -- ==== Justin A. Lemkul Ph.D. Candidate

Re: [gmx-users] Atom N not found....

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 Scholar MILES-IGERT Trainee Departmen

Re: [gmx-users] MD after equilibration phase

.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 <mailto:gmx-users-requ...@gromacs.org>. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] MD after equilibration phase

ted or supplied), zero is used. Integration proceeds from there, and this may or may not be stable, and certainly will not have the desired temperature (yet)... Mark On Fri, Apr 6, 2012 at 19:10, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote: bipin singh wro

Re: [gmx-users] SS bond forcing

o the manual section and figures cited on that page for more information. -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

Re: [gmx-users] Charmm36_lipids with gromacs

ash anyway due to physical instability. -Justin Any comment will be appreciated. Thanks in Advance. Cheers, Fernando. -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech

Re: [gmx-users] MD after equilibration phase

algorithms you're using. -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/Per

Re: [gmx-users] on PDB2gmx

ustin -- ==== 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] Re: Protein charge

these states using pdb2gmx. -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] Error message in reading AMBER's mdcrd files?

myself, but it seems to me that you have to install VMD first, then when configuring Gromacs, you need to invoke the --with-dlopen option during configuration. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee

Re: [gmx-users] Error message in reading AMBER's mdcrd files?

st.mdcrd > > For more information and tips for troubleshooting, please check the GROMACS > > websit! e a t http://www.gromacs.org/Documentation/Errors > > == > > > > Please kindly instruct if I have done anything wr

Re: [gmx-users] mdrun -rerun

rexcl around 100 is taking a lot of time, while the default nrexcl=3 was grompp ed much faster. Why excluding bonds in this way is time consuming? It's going slower because it's doing exponentially more work. -Justin -- ============ Justin A. Lemkul Ph.D.

Re: [gmx-users] regarding rmsd and gyrate

g_polystat is more appropriate in this case. -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] SS bond forcing

with whatever evidence suggests the restraints didn't work. There are several examples provided in the manual, so the only things I would post as examples are already available. -Justin Thank you Pierre THEVENET Le 06/04/2012 17:19, Justin A. Lemkul a écrit : pitheve...@free.fr wr

Re: [gmx-users] regarding g_sas and rdf

l, section 8.4. -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: Simulation in the high temperature conditions

t two parts of a system in thermal disequilibrium, then you've got a very odd system with thermostats exchanging different amounts of energy with different portions of the system. I don't know how to predict the effects of such a setup, but I don't recall having seen anyt

Re: [gmx-users] pdb2gmx error

smatch. If the error arises due to a hydrogen atom, either use -ignh to ignore H atoms in the input and rebuild them, or fix the naming mismatch. If you need further help, we need complete information. -Justin -- Justin A. Lemkul Ph.D. Candidate

[gmx-users] Re: on the trr file of the production MD

se if you do not supply the -deffnm flag to mdrun, since traj.trr is the default output file name. Do not assume that md_0_1.trr and traj.trr are the same. -Justin -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Departme

Re: [gmx-users] SS bond forcing

ive rise to the structural changes you need to bring these atoms close together. Running a short MD simulation may work, though if the atoms are very far apart and you force them together quickly, you may have stability issues. -Justin -- ============ Justin A. Lemkul

Re: [gmx-users] Re: Simulation in the high temperature conditions

ng though. -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 -- gmx-users

Re: [gmx-users] SS bond forcing

transitions to accommodate, then you're probably in trouble. -Justin Thank you -- Pierre THEVENET Ph.D. Candidate INSERM - MTi Ecole Doctorale B3MI Université Paris Diderot - Paris 7 2012/4/10 Justin A. Lemkul mailto:jalem...@vt.edu>> pitheve.

Re: [gmx-users] lipid.itp for AMBER-GAFF

t has been contributed (last item in the list): http://www.gromacs.org/Downloads/User_contributions/Force_fields I've never used it, but there is a reference that should indicate if it is worthwhile for you. -Justin -- ============ Justin A. Lemkul Ph.D.

Re: [gmx-users] SS bond forcing

-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/Perso

Re: [gmx-users] on 2 different mini.mdp file

ong ;) -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 -- gmx-users mailing l

Re: [gmx-users] Re: Simulation in the high temperature conditions

James Starlight wrote: Justin, 10 апреля 2012 г. 16:21 пользователь Justin A. Lemkul <mailto:jalem...@vt.edu>> написал: I have never used the bd integrator so I cannot offer any help here. I don't see any magical reason why you should expect it to enhance s

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

a sign), or otherwise create 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 Doctoral Scholar MILES-IGERT Trainee Department of Biochemistr

Re: [gmx-users] NPT simulation with parinello-rahman pressure coupling

.org/Documentation/Terminology/Blowing_Up -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.

Re: [gmx-users] tau_t and tau_p values

ou should decide on the parameters to use based on your knowledge of the algorithms you seek to you. -Justin -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[a

Re: [gmx-users] tau_t and tau_p values

Justin A. Lemkul wrote: Shyno Mathew wrote: Hello, I am little confused about the values to be used for tau_t and tau_p. For sd integrator, the manual suggest to use tau_t as 2 ps and the default value for tau_p is 1 ps. I am using PME for electrostatics But I read in the mailing list

Re: [gmx-users] Re: Re: NPT simulation with parinello-rahman pressure coupling

Always make sure to include full information. It will help us figure out potential problems faster, rather than guess, which then gets you a resolution faster ;) -Justin -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGE

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

providing examples. -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/Perso

Re: [gmx-users] on the "tc-grps = Protein Non-Protein ; two coupling groups" in the on-line tutorial

uot; group is one that Gromacs generates automatically: http://www.gromacs.org/Documentation/Terminology/Default_Index_Groups As the name implies, it includes everything that is not protein. -Justin -- ======== Justin A. Lemkul Ph.D. Candidate ICTAS Doctor

Re: [gmx-users] the value of nsteps in the mdp file in the on-line tutorial

-- 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] Converting a new-version .tpr file to an old-version .tpr file

on the keywords used). -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] %exist of hydrogen bonds + No -map specified!

t you omitted the -s flag originally, thus the search for proper arguments likely failed. -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] segmentation fault

ustin -- ==== 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] Gromos87

field that one can (and should) use. -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] simulations in vacuum in parallel

-- Best Regards, Qinghua -- ==== 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/Perso

Re: [gmx-users] Gromos87

Cheers, Shima ---- *From:* Justin A. Lemkul *To:* Discussion list for GROMACS users *Sent:* Thursday, April 12, 2012 9:07 PM *Subject:* Re: [gmx-users] Gromos87 Marz

Re: [gmx-users] on the NPT equilibration of the on-line tutorial of lysozyme

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 -- gmx-users mailin

Re: [gmx-users] -rcon parameter in mdrun - what values have sense?

-- Any ideas what to do? Thank you in advance. Alex -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.

Re: [gmx-users] Simulation of the pure lipid bilayer

is no universal answer to this question. It depends on your criteria for convergence and contents of the system, among other considerations. -Justin -- ======== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemist

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

ur depends on a lot of factors and cannot be easily generalized. There is no special technique to force a simulation to converge, you just have to wait. -Justin -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department

Re: [gmx-users] Simulation of the pure lipid bilayer

ct of very short (2 ns or so) simulations produced many years ago. More equilibration is expected for more modern simulations. -Justin On Fri, Apr 13, 2012 at 5:28 PM, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote: James Starlight wrote: Dear Gromacs Users!

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

Anni Kauko wrote: Date: Wed, 11 Apr 2012 08:38:05 -0400 From: "Justin A. Lemkul" mailto:jalem...@vt.edu>> Subject: Re: [gmx-users] g_wham problem with negative COM differences To: Discussion list for GROMACS users mailto:gmx-users@gromacs.org>> Mess

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

do something. Also note the space in your "my mol_in_water.pdb" will cause problems as well. -Justin -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA

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

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

nly Justins mail adress, not the gromacs user list. I do it in cc Configure your mail client to reply-all by default or replace the address. -Justin -------- *Von:* Justin A. Lemkul *An:* Lara Bunte ; Discussion list for GRO

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

eded to assemble the .tpr file using grompp. -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.v

Re: [gmx-users] Justin protein-ligand complex...

, hence: pcoupl = Parrinello-Rahman -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] Justin protein-ligand complex...

rama david wrote: On Sat, Apr 14, 2012 at 6:12 PM, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote: > > > >> Hi Justin, Thank you for reply.. >> >> >> >> My query is ..Why Pressure Coupling is off in production MD

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

me SOL and within 0.5 of resname ISO' Does that work? -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] File editing - only one layer of water around a molecule

thing like that. Again after pressing answer the mail should go only to Justin. I put the mailing list in cc. Is here someone using yahoo also and know how to fix this? *Von:* Justin A. Lemkul *An:* Lara Bunte ; Discussion list for GROMACS users *Gesendet:* 16:56 Sams

Re: [gmx-users] Classical Ewald summation

upport parallel runs. Not starting any threads.\n"); nthreads = 1; } Thus the L-BFGS minimization algorithm and the Ewald electrostatics algorithms can only be run in serial, as the error message states. -Justin -- Justin A. Lemkul Ph.D

Re: [gmx-users] Define a new residue in oplsaa

bond as well. [ impropers ] CH3+NC O improper_O_C_X_Y There is no CH3 in a formyl group. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA

Re: [gmx-users] Define a new residue in oplsaa

:* Justin A. Lemkul *To:* Shima Arasteh ; Discussion list for GROMACS users *Sent:* Saturday, April 14, 2012 9:19 PM *Subject:* Re: [gmx-users] Define a new residue in oplsaa Shima Arasteh wrote: > Dear GROMACS users, > I wanna add add a FOR residue containing atom C and O. In oplsaa force

Re: [gmx-users] protein and DMPC in Charmm36 ff

ustin -- ==== 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/j

Re: [gmx-users] Re: Simulation in the high temperature conditions

I also don't know what R_fract is. -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 to install DSSP in linux with Gromacs 4.0.7

"Miscellaneous," click "Distribution" and you will find the "DSSPold" executables, which are the old version of DSSP that are compatible with Gromacs. -Justin -- ======== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MIL

Re: [gmx-users] Re: Simulation in the high temperature conditions

wide latitude. If that's what you want, then use the -disre_dist option without -disre_frac. -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 h

Re: [gmx-users] Re: Simulation in the high temperature conditions

d fix it? There are energy terms associated with distance restraints. They cause the .edr file to get large very fast if you have a lot of them. You'll have to decrease nstenergy to make the files smaller, or not use the restraints. -Justin -- ==========

Re: [gmx-users] Protein ligand molecular dynamics simulation

t you originally had. You don't want to do that. -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.bioc

Re: [gmx-users] Re: Re: NPT simulation for mutation study

nstability. The real lesson is you shouldn't make haphazard changes or take anything for granted as far as settings that "should work." Spending a few hours reading the literature will save you weeks of troubleshooting an elusive problem. -Justin -- =====

Re: [gmx-users] GROMOS87 and CHARMM27

...@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 Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Black

Re: [gmx-users] Re: NPT simulation for mutation study (Justin A. Lemkul)

to what went wrong. -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.bioche

Re: [gmx-users] ewald_rtol

cs.org/pipermail/gmx-users/2009-February/039806.html There are a number of other discussions about it in the list archive; I'd suggest you have a look. -Justin -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department

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