Re: [gmx-users] including non standard amino acid CSD in topology file

/Adding_a_Residue_to_a_Force_Field -Justin ashu -- 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] PMF for Carbohydrate-Protein

ger simulations. -Justin I have uploaded the plots of profile and histograms. PMF Plot link: http://img801.imageshack.us/i/pmf.png/ Histogram link: http://img217.imageshack.us/i/histoy.png/ Thanks for your time Sai Ramadugu -- ============ Justin A. Lemkul

Re: [gmx-users] lipopeptide problem

and/or "crossing the line," then I won't attempt to do either. -Justin Best regards, Deniz On Thu, Mar 17, 2011 at 12:00 AM, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote: Emine Deniz Tekin wrote: Hi GROMACS Users, I am using the GROMACS

Re: [gmx-users] 1/viscosity in g_energy

nce Universiti Putra Malaysia 43400 UPM Serdang, Selangor MALAYSIA -- ============ 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] Re: change in structure after simulation

-609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com <mailto:monu46...@yahoo.com> -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Departm

Re: [gmx-users] ATP+Mg

most QM/MM studies would indicate. -Justin Thank you very much -- 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] LINCS and number of nodes

;Velocity generation gen_vel = yes gen_temp= 300.0 gen_seed= 173529 ;Bonds constraints = all-bonds constraint-algorithm = lincs

Re: [gmx-users] Re: gmx-users Digest, Vol 83, Issue 130

d Mg binding? Either. Fixed point charge models for metal binding sites are one significant limitation of molecular mechanics force fields. There are significant inductive effects that are not accounted for. http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species -

[gmx-users] Re: Fwd: pdb2gmx problem recognising capping on Gromacs 4.5.2

kipped the pdb2gmx step by supplying the topol.top file generated with Gromacs 4.0.7 the simulation went smoothly. Best regards, 'Jide Olubiyi German Research School for Simulation Sciences/ Institute of Complex Systems-6 Forschungszentrum Julich, Germany -- ======

Re: [gmx-users] C-terminal amidation of peptide

ly with a bit of geometry :) -Justin Best regards, Anna -- ============ 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.

[gmx-users] Re: compressing a system

= 173529 ;Bonds constraints = all-bonds constraint-algorithm = lincs -- ======== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at

Re: [gmx-users] Re: compressing a system

Moeed wrote: On 20 March 2011 15:23, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote: Moeed wrote: Dear experts, I am trying to build up a polymer in hexane system by increasing the density and use this for FE calculation. After PR step, my

Re: [gmx-users] Fw: g_membed tool

t;Box size should be taken from the membrane structure 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

Re: [gmx-users] Git tutorial for gromacs

AMMAD ALIF MOHAMMAD LATIF Laboratory of Theoretical and Computational Chemistry Department of Chemistry Faculty of Science Universiti Putra Malaysia 43400 UPM Serdang, Selangor MALAYSIA -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doc

Re: [gmx-users] including non standard amino acid CSD in topology file

/Parameterization -Justin Ashutosh On Thu, Mar 17, 2011 at 8:37 PM, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote: ashutosh srivastava wrote: hello I am using OPLS AA FF and my protein contains a non standard amino acid CSD for which the topology parameter

Re: [gmx-users] compressing in presence of voids

= 173529 ;Bonds constraints = none;all-bonds constraint-algorithm = lincs -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg,

Re: [gmx-users] Gromacs on other Operating Systems

ems almost always play nicely. Windows can be a challenge. -Justin Thanks in advance, Nancy -- ==== 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] Gromacs on other Operating Systems

, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote: Nancy wrote: Hi All, I've used used Gromacs under Linux, and I'm wondering whether it can be used under Windows 7 and/or Snow Leopard (10.6.6). Theoretically, Gromacs is compatible with any e

Re: [gmx-users] Annealing of shell polarizable water model

; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = yes gen_temp = 0 gen_seed = 1993 ;CONSTRAINTS constraints = hbonds constraint_algorithm = LINCS -- ==== Justin A. Lemkul Ph.D. Candi

Re: [gmx-users] single RNA nucleotide in CHARMM with phosphate problem with pdb2gmx

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 -- Maria G. Technical University of Denmark Copenhagen -- Justin A. Lemkul Ph.D. Candidate ICTAS

Re: [gmx-users] changing charged groups in CHARMM RNA

field, you should not use charge groups. Each atom should be its own "group." -Justin Thanking you in advance Maria -- Maria G. Technical University of Denmark Copenhagen -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGE

Re: [gmx-users] changing charged groups in CHARMM RNA

maria goranovic wrote: This must be specific to charmm's implementation in gromacs? Out of curiosity, why can one not use charge groups ? http://lists.gromacs.org/pipermail/gmx-users/2010-September/054106.html -Justin On Tue, Mar 22, 2011 at 2:45 PM, Justin A. Lemkul <mail

Re: [gmx-users] AFM pulling simulations

/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling -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] Hydroixde Ion

error, No such moleculetype OH. Your .top still does not have a functional [ moleculetype ] OH. You're probably not using the #include "ions.itp" mechanism correctly. Mark -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar

[gmx-users] Various web issues

no effect. -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] Various web issues

Thanks for the fix! -Justin Rossen Apostolov wrote: Hi again, On 3/22/11 6:57 PM, Justin A. Lemkul wrote: I posted this a few days ago, but the problem persists - the "search" feature on the Gromacs site either returns an error or completely nonsensical content. Can someone p

Re: [gmx-users] Hydroixde Ion

eculetype ] > > ; molname nrexcl > > OH1 > > > > [ atoms ] > ! > ; id at type res nr residu name at name cg nr charge > > 1 OH 1 OHOH 1 -1 > > Use two atoms, like you did for your .rtp entry. > > > The genion adds

Re: [gmx-users] Hydroixde Ion

gt; > > > Don't. The .atp defines *atom* types. > > > > > I ran into the error: No such moleculetype OH > > > > > > I further included information in the ions.itp as follows: > > > > > > [ moleculetype ]

Re: [gmx-users] Parameterization of a molecule containing a radical (oxygen)

de a suitable atom type for the O radical or its effects on the rest of the molecule. I still don't know if parameterization would be possible for a standard MM force field (though it very well might), but this might get you started. -Justin -- Simone Cirri -- ===========

Re: [gmx-users] unit of surface tension, KJ/mol?

? Can anyone help please. Is this from g_energy output? In past versions, everything was printed as "kJ/mol," even quantities that obviously weren't, like temperature, pressure, etc. -Justin Thanks -- ============ Justin A. Lemkul Ph.D. Candidate

Re: [gmx-users] unit of surface tension, KJ/mol?

Elisabeth wrote: On 22 March 2011 22:31, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote: Elisabeth wrote: Hello, I did two simulations on the same system using versions 4.0.7 and 4.5.3. It seems like the unit of surface tension is not the

Re: [gmx-users] unit of surface tension, KJ/mol?

39020288.3 -174.289 (bar nm) On 22 March 2011 23:56, Mark Abraham <mailto:mark.abra...@anu.edu.au>> wrote: On 23/03/11, *Elisabeth * mailto:katesed...@gmail.com>> wrote: On 22 March 2011 22:46, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote:

Re: [gmx-users] %hbond number problem

d is what you should use (without the newline, which is printed by the program to the screen as help information). -Justin -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg

Re: [gmx-users] no output dgdl file

= yes nstdhdl = 10 separate_dhdl_file = yes dh_hist_size = 0 dh_hist_spacing = 0.1 Best -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech

Re: [gmx-users] account for PBC

-- Ahmet YILDIRIM -- ============ 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/P

Re: [gmx-users] no output dgdl file

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] no output dgdl file

couple-lambda1 = none couple-intramol = yes nstdhdl = 10 separate_dhdl_file = yes dh_hist_size = 0 dh_hist_spacing = 0.1 Best -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT

Re: [gmx-users] no output dgdl file

://lists.gromacs.org/pipermail/gmx-users/2011-March/059631.html -Justin Cheers -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Thursday, 24 March 2011 12:35 PM To: Discussion list for GROMACS users Subject:

Re: [gmx-users] no output dgdl file

g_bar gives the total DeltaG over all lambda intervals according to the BAR algorithm. -Justin Cheers, -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Thursday, 24 March 2011 12:54 PM To: Gromacs U

Re: [gmx-users] no output dgdl file

[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Thursday, 24 March 2011 1:36 PM To: Gromacs Users' List Subject: Re: [gmx-users] no output dgdl file Emanuel Birru wrote: Hi Justin, It good that the issue is solved. As per my experience if you want to do a seri

Re: [gmx-users] no output dgdl file

foreign. Based on the .mdp file, I don't know how this could have happened, but all signs point to some sort of problem with the input. -Justin Cheers, Emanuel -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul

Re: [gmx-users] no output dgdl file

that it can be fixed. -Justin Here <http://hydra.pharm.monash.edu.au/md_project/penteg.top> it is my topology file. Cheers, -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Thursday, 24

Re: [gmx-users] GROMACS 4.5.1 mdrun re-compile for MPI

ot;mdrun" executable with my changes? Thanks in advance, Adam -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9

Re: [gmx-users] ethanol and dmso files

advance -- Ahmet YILDIRIM -- 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] Problems with a three domain protein in a membrane

ong_posre.itp for each chain? Yes. http://www.gromacs.org/Documentation/How-tos/Position_Restraints http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds -Justin Looking forward to hear your comments... Cheers, Ramon Garduno -- =

Re: [gmx-users] Problems with a three domain protein in a membrane

Justin A. Lemkul wrote: Dr. Ramón Garduño-Juárez wrote: Dear all, Dear Justin, We have been working on setting up an MD experiment in which our system is made of three separate domains of a protein embedded in a DMPC bilayer surrounded by water. We have generated a PDB file in which

Re: [gmx-users] The "correct" way to equilibrate a membrane / lipid bilayer w/water?

stin/gmx-tutorials/membrane_protein/index.html Even though your purposes may not involve a protein or the same force field, you may find some of the general information useful. -Justin Thanks for any ideas/hints/suggestions -- Justin A. Lemkul Ph.D. Ca

Re: [gmx-users] units for atomic coordinates in traj.xtc? nm?

o use gmxdump to convince yourself of this fact. -Justin Thanks -- ==== 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] Citation for NICS

acs.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

Re: [gmx-users] flexible spc water model

#include "spc.itp" in my .top file. Does it correct? Presumably. Check the post-processed topology that grompp gives you (-pp argument). -Justin I am using gromacs 4.0.7 version. Thanks Nilesh -- ==== Justin A. Lemkul Ph.D. Candi

Re: [gmx-users] Automated RMSD Calculations

/Documentation/How-tos/Making_Commands_Non-Interactive -Justin Thanks in advance, Nancy -- 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] Re: Alcohol Dehydrogenase MD simulation....Reg

; imp NBS CBQ H8M HBS 4 1 5 6 2 0.0 167.40.0 167.4 ; imp CBQ NBS OBT CAV 6 4 9 7 2 0.0 167.40.0 167.4 ; imp CAV CBQ CBE CAN -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Sc

Re: [gmx-users] mdrun cannot append to file larger than 2Gb

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

Re: [gmx-users] RMSD Calculation

/2011-March/059697.html If there's some reason you can't get that to work, then don't simply re-post the same original question. Iterative calls to g_rms are quite straightforward to script. -Justin Thank you very much, Nancy -- ============ Justin

Re: [gmx-users] mathematical expression to obtain the C6 and C12 LJ terms for the GROMOSXX ff family

. g_sigeps can do this for you. Otherwise, you can convert between the two common forms of the Lennard-Jones equation. -Justin Thank you for your help. SA -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of

Re: [gmx-users] dihedral angles

file, it's all based on what's found in the topology. -Justin KIndly let me know if there is an easy way out. Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGE

Re: [gmx-users] mathematical expression to obtain the C6 and C12 LJ terms for the GROMOSXX ff family

geps can do this for you. Otherwise, you can convert between the two common forms of the Lennard-Jones equation. -Justin > Thank you for your help. > > SA > -- ======== Justin A. Lemkul Ph.D. Candidate

Re: [gmx-users] Re: mathematical expression to obtain the C6 and C12 LJ terms for the GROMOSXX ff family

> g_sigeps can do this for you. Otherwise, you can convert between the two common forms of the Lennard-Jones equation. -Justin > Thank you for your help. > > SA > -- ==

Re: [gmx-users] No DD grid found

ibes often leads to nasty artifacts. Using more sensible values for these parameters will probably fix everything DD-related, as well as lead to reliable trajectories. -Justin Really appreciate the help, André -- ==== Justin A. Lemkul Ph.D. Candidate ICTA

Re: [gmx-users] flexible spc water model

designed to be rigid, not flexible: http://lists.gromacs.org/pipermail/gmx-users/2008-October/037571.html -Justin Nilesh On Fri, March 25, 2011 12:02 pm, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Hello, I am want to use flexible spc water model for my simulation. Might I inquire as

Re: [gmx-users] Gromacs for carbohydrates

Issac*/ */ /* -- ==== 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] oligoglycines

FAQs regarding ADDHYD and DELHYD commands), but since you can do it all with Gromacs anyway, it shouldn't be necessary. -Justin Thanks! Nisha P -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Bi

Re: [gmx-users] Placing ions at a required distance

? Measure the distance you want and establish the coordinate at which you wish to place the ion, then use editconf -center to place it at the proper location in the simulation box. -Justin Please guide. Thanks, Shivangi -- Justin A. Lemkul Ph.D

Re: [gmx-users] re: Gromos96 43A1

nge at all. -Justin Thx. Frank Neuhaus -- ==== 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/Page

Re: [gmx-users] Placing ions at a required distance

, so just #include that topology like you would any other system. -Justin Thanks, Shivangi On Mon, Mar 28, 2011 at 3:26 PM, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote: shivangi nangia wrote: Hello, I am a new gromacs user. I want to place Li+

Re: [gmx-users] PSF files from .top to .psf

ng. Sorry, that's just not what it was designed to do. Perhaps you can follow the logic of the script and design something more flexible for your needs. The framework is there, but I have never had the need or desire to re-work it. -Justin -- ============ Ju

Re: [gmx-users] Atomtype CCL4 not found

capitalization somewhere, i.e. CCl4 rather than CCL4. See atomtypes.atp. -Justin -- Ahmet YILDIRIM -- 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] Atomtype CCL4 not found

L4 are not the same. -Justin 2011/3/29 Justin A. Lemkul mailto:jalem...@vt.edu>> ahmet yıldırım wrote: Dear users, Force field: 43a1 water model: spc After this command:grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr

Re: [gmx-users] Atomtype CCL4 not found

ahmet yıldırım wrote: Then, what should I do? You've somehow created a topology that does not conform to the requirements of the force field. Fix it so that it does. -Justin 29 Mart 2011 16:36 tarihinde Justin A. Lemkul <mailto:jalem...@vt.edu>> yazdı: ahmet

Re: [gmx-users] pullx.xvg format

-0.0469381 8643.6006 1.01357 3.91115 3.75715 0.0796926 0.128354 -0.0687171 8643.9004 1.01555 3.90522 3.75396 0.0917188 0.140592 -0.0575233 -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Depart

Re: [gmx-users] pullx.xvg format

esults weren't completely nonsensical or buggy, then there's no reason to panic. -Justin Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi all I have a very quick question. The output for umbrella pulling simulations (pullx.xvg) often appears to have an irregular format, i

Re: [gmx-users] Effect of pH on catalytic side

als. -Justin Regards -- ============ 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] Check for bad contacts and/or reduce the timestep.

om my system? Please help. Thanks, Shivangi -- ==== 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] Error in GROMACS installation

(test ! -f $i && ln -s /usr/local/gromacs/bin/$i . ; exit 0); \ done /bin/sh: line 0: cd: /usr/local/gromacs/bin: No such file or directory make: *** [links] Error 1 Can anyone de-code thsi error and help me how should I successfully proceed for the same. Thanks in a

Re: [gmx-users] SO4

stin FYI, I use 4.5.1 version. Did I do something wrong in the pdb file? Can I ignore the warning message in #3? Thanks for you help in advance, Simon Sham -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Bi

Re: [gmx-users] Error in GROMACS installation

aving directory `/cygdrive/d/softwares/bioinformatics/gromacs-4.5.4/s rc/gmxlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/cygdrive/d/softwares/bioinformatics/gromacs-4.5.4/s rc' make[1]: *** [all] Error 2 make[1]: Leaving directory `/cygdrive/d/softwares/bioinformatic

Re: [gmx-users] index file

k you for your hints.. -- ============ 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/P

Re: [gmx-users] g_energy -ravg option

advance. Simon Sham -- 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] Splitted DMPC bilayer

-tutorials/membrane_protein/advanced_troubleshooting.html -Justin Cheers, Ramon Garduno -- ==== 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] Heat of vap

imple: DHvap = - + RT I have seen this equation used in a number of other studies, as well. -Justin Thanking you all, Regards, -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia

Re: [gmx-users] Help on umbrella sampling

XX Please help me Thanks N Regards Raghuvir -- ======== 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] Help with Umbrella Sampling

artificial force. -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] Umbrella sampling

/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 A. Lemkul Ph.D. Candidate ICTA

Re: [gmx-users] CUT-OFFs for GROMOS96 43a1...Reg

-- KRISHNA KISHORE@IIT-MADRAS -- ======== 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] Heat of vap

Elisabeth wrote: in your mail: On 30 March 2011 15:30, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote: Elisabeth wrote: Dear all, I intend to obtain vaporization heat per volume for a /pure alkane system/. Here is the steps I am taking. Please c

Re: [gmx-users] adding a new residue in the ff

an with a pen, the man with the gun is a dead man" (Roberto Benigni, about Roberto Saviano) -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at

Re: [gmx-users] Heat of vap

Elisabeth wrote: On 31 March 2011 12:58, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote: Elisabeth wrote: in your mail: On 30 March 2011 15:30, Justin A. Lemkul mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu <mailto:jalem.

Re: [gmx-users] adding a new residue in the ff

rhaps someone has already done this work and it is published. If you're unlucky, you've got to do it all yourself. That's a good idea :) Cheers, Tsjerk -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee

Re: [gmx-users] Taking difference of forces in two trajectories

ences in two existing trajectories, but you can extract forces using g_traj and take the difference between the two output files. The file sizes may get extremely large for either long trajectories or many atoms. -Justin thanks sikandar -- ==== Jus

Re: [gmx-users] Taking difference of forces in two trajectories

option? I don't think there is currently any tool that can do this. With the xdrfile library, though, you might be able to write your own program that can do it. -Justin On Thu, Mar 31, 2011 at 4:44 PM, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote: Sikandar

Re: [gmx-users] FW: protein split over boundary

romacs.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] FW: protein split over boundary

egards, *From:* Justin A. Lemkul *To:* Discussion list for GROMACS users *Sent:* Fri, April 1, 2011 2:52:53 PM *Subject:* Re: [gmx-users] FW: protein split over boundary ana johari wrote: > Dear user, > > Tanks for your at

Re: [gmx-users] The solvent group Water is not continuous

tin Thanks -- Ahmet YILDIRIM -- ============ 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] The solvent group Water is not continuous

re 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 -- Ahmet YILDIRIM --

Re: [gmx-users] The solvent group Water is not continuous

the .top and not the .gro), you would have gotten a fatal error from grompp when creating em.tpr. -Justin 01 Nisan 2011 15:17 tarihinde Justin A. Lemkul <mailto:jalem...@vt.edu>> yazdı: ahmet yıldırım wrote: I tried SOL 44453 but I still the same error Are you

Re: [gmx-users] The solvent group Water is not continuous

have created a new .tpr file and you're still getting an error from genion? -Justin Thanks 01 Nisan 2011 15:33 tarihinde Justin A. Lemkul <mailto:jalem...@vt.edu>> yazdı: ahmet yıldırım wrote: Dear users, I created nonaminoacid TRS.itp and EDO.itp file

Re: [gmx-users] R: Re: adding a new residue in the ff

eone has already done this work and it is published. If you're unlucky, you've got to do it all yourself. That's a good idea :) Cheers, Tsjerk -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Depart

Re: [gmx-users] tpr file for trjconv command

pts yet, do what is most intuitive and fit to your starting state. Doing so will produce a smooth trajectory that you can visualize very easily. -Justin Tanks -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Depart

Re: [gmx-users] Re: distance restraints for atoms on 2 chains

shall discover. -- ======== 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/P

Re: [gmx-users] OPLS parametrizaton

years. You should consult those to see what their specific recommendations are with respect to proper settings, although many of them focus on proteins. -Justin Best regards, Marcelo -- ============ Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-

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