Re: [gmx-users] mdrun -v output

s mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interf

Re: [gmx-users] How to add DMSO as solvent?

g. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ====== Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street

Re: [gmx-users] Trajectories

ease 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 -- == Peter C. Lai

Re: [gmx-users] Writing and compiling new analyses for gromacs

/justin> > > > > ==**== > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > > Please sea

Re: [gmx-users] Writing and compiling new analyses for gromacs

On 2012-06-04 05:23:10PM -0400, Justin A. Lemkul wrote: > > > On 6/4/12 5:16 PM, Shay Teaching wrote: > > > > > > 2012/6/4 Justin A. Lemkul mailto:jalem...@vt.edu>> > > > > > > > > On 6/4/12 2:59 PM, Shay Teaching wrote: > > > > Dear Gromacs users, > > > > I want to write new

Re: [gmx-users] PME nodes

> www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAU

Re: [gmx-users] mutational analyses: Cystine and indels

lease 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 -- == Peter C. Lai

Re: [gmx-users] no pr.gro file for energy minimization

e 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 -- == Peter C. Lai| University of Alabama-Birmingham

Re: [gmx-users] Coordinate file for lipid bilayer

sers > Please search the archive at > http://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

Re: [gmx-users] Simulation protocol for Protein-DNA-complex

info/gmx-users > Please search the archive at > http://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? Re

Re: [gmx-users] constraints between protein ligand - metal chelation

sons for parametrizing the > > ligand and the protein as a separate system. I dont think that the ligand > > and protein can be parametrized as a single system, but will definitely try > > doing it as a single system and see if it works. > > Regards > > Vijayan.R > > &

Re: [gmx-users] constraints between protein ligand - metal chelation

t; www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst

Re: [gmx-users] Different Lipids into one Moleculetype (for position restrain)

). On 2012-05-18 11:00:55PM -0400, Justin A. Lemkul wrote: > > > On 5/18/12 10:28 PM, Peter C. Lai wrote: > > Synopsis: position restraints are coupled to the moleculetype. So you need > > to > > define position restraints individually for each molecule type contiguou

Re: [gmx-users] Different Lipids into one Moleculetype (for position restrain)

sers mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface

Re: [gmx-users] forcefields for lipids

sting! > 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 -- == Peter

Re: [gmx-users] system cooling down when runing NVE

you have position restraints on, which I expect would damp collisions between solvent and solute. temp drops towards some sort of equilibrium, which doesn't necessarily match your starting temp even though energy of the system is conserved ..sounds like expected behavior to me? -- Sent from my

Re: [gmx-users] Formyl parameters

Where does swissparam get its parameters for charmm? and does it use custom atomtypes for generic molecules? I have been using CGenFF-derived parameters for molecules that aren't in base c36 and I think it's working well for me... -- Sent from my Android phone with K-9 Mail. Please excuse my bre

Re: [gmx-users] CHARMM36 and Dispersion correction

r send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Ge

Re: [gmx-users] NBFIX to gromacs

with the given pair parameters that you want to specify. On 2012-05-02 12:35:17PM -0700, Ricardo O. S. Soares wrote: > Dear Mr. Peter C. Lai, > > I appreciate your kind response. > > I apologize for the delay on my part. > This NBFIX parameters that I'm working with ca

Re: [gmx-users] some hardware questions

On 2012-05-02 06:13:04PM +0200, Mirco Wahab wrote: > Hello Peter, > > Am 02.05.2012 17:44, schrieb Peter C. Lai: > > > You can wait for ivy bridge, then stick some Kepler GPUs (nvidia gtx > > 680) in it. That should max the performance. asm is pretty much stagnant >

Re: [gmx-users] CHARMM36 format POPC

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 -- =

Re: [gmx-users] some hardware questions

When considering compute hardware today, you're gonna have to shop like a gamer. A rig that can get high Battlefield 3 or Arma 2/3 framerates should also be able to get you some nice ns/day. I think most people consider Bulldozer mostly a flop. AMD masks lower cycle speeds with more cores per c

Re: [gmx-users] saltbridges newbie question

t? Read http://www.gromacs.org/Support/Mailing_Lists -- ============== Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu

Re: [gmx-users] NBFIX to gromacs

ist. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ========== Peter C. Lai| University of Alabama-Birmingham Programmer/A

Re: [gmx-users] sigma and epsilon.

you will have to find the parameters for a carbocation in this configuration from someone who has derived them before, if acpype doesn't know about the species in this configuration, or derive them yourself using ab initio/semiempiracle methods (i.e. gaussian). Also remember you'll need angle a

Re: [gmx-users] Make an index file

#2 Generally a good idea to keep the names consistent, however - why are you using POP in the coordinate file instead of POPC? -- Sent from my Android phone with K-9 Mail. Please excuse my brevity. Shima Arasteh wrote: Dear gmx users, I want to simulate POPC in water. In equilibration step,

Re: [gmx-users] Question about starting Gromacs 4.5.4 parallel runs using mpirun

s compared to the typical openmpi setup on identical hardware and infrastructure. -- Sent from my Android phone with K-9 Mail. Please excuse my brevity. "Peter C. Lai" wrote: possibly. Make sure PATH includes /usr/local/bin and LD_LIBRARY_PATH includes the path where libmd_mpi.so a

Re: [gmx-users] Question about starting Gromacs 4.5.4 parallel runs using mpirun

possibly. Make sure PATH includes /usr/local/bin and LD_LIBRARY_PATH includes the path where libmd_mpi.so and libgmx_mpi.so are located. try using mdrun -v and > somelogfile after the mpirun line (like mpirun blah -np 8 mdrun -v -deffnm etcetc > mpilog). the contents of mpilog will tell you wha

Re: [gmx-users] gen_pairs to calculate absent 1-4 interactions in CHARMM36c FF

btw you only need explicit 1-4 for charmm when the 1,4 from the original charmm prm is actually different/specified (i.e. non-conjugated carbons) -- Sent from my Android phone with K-9 Mail. Please excuse my brevity. "Ricardo O. S. Soares" wrote: Hi Mark, yeah, I'll try it. Thanks for yo

Re: [gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

ng_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 -- ==

Re: [gmx-users] Best Force Field for a Membrane Protein

ibe 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 -- == Peter C. Lai| University of Alabama-Bi

Re: [gmx-users] GROMOS87 and CHARMM27

On 2012-04-16 10:14:01AM -0700, Shima Arasteh wrote: > So, I can not use the coordinates of the output files of gromos runs. Right? You can but you may need to rename the atoms for each residue for pdb2gmx to work. > > > ____ > From: Peter C. Lai &

Re: [gmx-users] GROMOS87 and CHARMM27

system will be different from your old one anyway. In addition, you may need to rename the atoms in the coordinate files obtained from previous gromos runs to match those in the charmm27 residue files. -- ========== Peter C. Lai

Re: [gmx-users] Atom MNZ1 in residue LYS 107 was not found

gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 2

Re: [gmx-users] how pdb2gmx calculate the total charge of a protein

ad http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don'

Re: [gmx-users] on PDB2gmx

ld really determine what criteria to choose for histidine protonation state and assign them manually for best effect. Justin already answered this question in a different way. Perhaps there is a language barrier/problem involved? -- ==========

Re: [gmx-users] Charmm36_lipids with gromacs

l error: > There is no domain decomposition for 2 nodes that is compatible with the > given box and a minimum cell size of 13.9221 nm > Change the number of nodes or mdrun option -rdd > Look in the log file for details on the domain decomposition This looks related to the POPC255+WAT

Re: [gmx-users] MD after equilibration phase

ut gro file without -t, then it will take coordinates and velocities from the .gro but the problem there is the limited precision (3 decimal points for each). -- == Peter C. Lai| University of Alabama-Birmingham Prog

Re: [gmx-users] the g_rms function after we trjcat the trajectory files before and after extension

p://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 -

Re: [gmx-users] further discussion on the mdrun -append function

On 2012-04-06 01:30:20AM -0400, Roland Schulz wrote: > On Fri, Apr 6, 2012 at 12:24 AM, Peter C. Lai wrote: > > > Sounds like there is a lanugage barrier? > > > > Anyway, some cluster filesystems don't support append (e.g. lustre). > > > > I often use

Re: [gmx-users] further discussion on the mdrun -append function

gt;   > Will you please explain the function of "-n index.ndx " in "grompp -f md.mdp > -n index.ndx -p topol.top -c minimized.gro -o md-1ns.tpr" with some specific > examples? >   > Cheers, >   > Acoot > > > > &g

Re: [gmx-users] further discussion on the mdrun -append function

send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div.

Re: [gmx-users] Help: Anyone worked with "Wall"?

d) > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the lis

[gmx-users] Re: job failed

using? (pcoupl) -- ========== Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461

Re: [gmx-users] jobs failed

RROR): The error message in the job > record is as follows: > BE_MPI (ERROR): "killed with signal 6" > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.grom

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

#x27;t post? Read > > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > > > > > > -- > --- > *Regards,* > Bipin Singh > -- > gmx-users mailing list gmx-users@gromacs.org > http://

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

on a simple geometric criterium, specified by the maximum hydrogen-donor-acceptor angle and donor-acceptor distance, which are set by -angle and -dist respectively." -- ========== Peter C. Lai| University of

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

On 2012-04-05 08:55:24PM +0800, lina wrote: > On Thu, Apr 5, 2012 at 7:14 PM, Acoot Brett wrote: > > Dear All, > > > > For the different protonation state of HIS, what are there 3-letter code for This is also somewhat forcefield dependent (and how you name the histidines in the PDB as well). > >

Re: [gmx-users] how to change the timestamp of a xtc file

On 2012-04-05 06:18:34PM +0800, lina wrote: > On Thu, Apr 5, 2012 at 6:07 PM, Mark Abraham wrote: > > > > > > On 05/04/12, lina wrote: > > > > On Thu, Apr 5, 2012 at 4:42 PM, Peter C. Lai wrote: > >> trjcat -settime or trjconv -t0 > > > >

Re: [gmx-users] how to change the timestamp of a xtc file

erface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ========== Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst |

Re: [gmx-users] Monitoring of Salt bridges during simulation Run

rch the archive at > http://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/Mail

Re: [gmx-users] grompp error

e at > http://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 -- =

Re: [gmx-users] index.ndx files

; gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the >

Re: [gmx-users] large scale simulation?

Yeah I usually average 21ns/day on a openmpi-over-qdr infiniband cluster using fewer than 300 nodes and with a 100K system with 60K TIPS3P (hydrogen LJ terms) waters (single precision gromacs, ffw3, and openmpi compiled with icc 10.0.3) It's going to depend on your forcefield and how you've opt

Re: [gmx-users] About the function of "-v' in mdrun

e 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 -- == Pet

Re: [gmx-users] Adjust time intervals

at > http://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 -

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

e .rtp file. If you have missing atoms, they must be modeled in using > external software. I wonder if there is a way to overload the hydrogen-adding mechanism to add heavy atoms too. -- == Peter C. Lai| University of Ala

Re: [gmx-users] CHARMM27 topology for DOPC

2C313 > C313H13X > C313H13Y > C313 C314 > C314H14X > C314H14Y > C314C315 > C315H15X > C315H15Y > C315C316 > C316H16X > C316H16Y > C316C317 >

Re: [gmx-users] a question related to energy minimization "mdrun -v -deffnm em"

t; http://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 -- =

Re: [gmx-users] Problems with simulation on multi-nodes cluster

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 -- == Pete

Re: [gmx-users] hydrogen hydrogen interaction

x-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ========== Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div

Re: [gmx-users] gromacs 4.5.5 cygwin installation error message

e1): undefined > >> reference to `_fftwf_destroy_plan' > >> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bf7): more undefined > >> references to `_fftwf_destroy_plan' follow > >> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2c37): undefined >

Re: [gmx-users] gromacs 4.5.5 cygwin installation error message

> >> > >> > >>.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bcb): undefined reference > >>to `_fftwf_destroy_plan' > >>.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2be1): undefined reference > >>to `_fftwf_destroy_plan'

Re: [gmx-users] gromacs 4.5.5 cygwin installation error message

ard to getting a reply from you. >   > Cheers, > Wholley > > > > From: Peter C. Lai > To: Wholly Peach ; Discussion list for GROMACS users > > Sent: Sunday, 11 March 2012 11:20 AM > Subject: Re: [gmx-users] gromacs 4.5.5 cygw

Re: [gmx-users] gromacs 4.5.5 cygwin installation error message

--disable-threads? >   > Wholley > > > > From: Mark Abraham > To: Discussion list for GROMACS users > Sent: Sunday, 11 March 2012 11:43 AM > Subject: Re: [gmx-users] gromacs 4.5.5 cygwin installation error message > > On 11/03/2012 1

Re: [gmx-users] gromacs 4.5.5 cygwin installation error message

h 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 -- == Pete

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

On 2012-03-07 03:04:28PM -0500, Justin A. Lemkul wrote: > > > Peter C. Lai wrote: > > [ angles ] is defined in ffbonded.itp. If you have new angles you will > > need to specify them there. grompp will read ffbonded.itp and try to > > correlate > > To be clear

Re: [gmx-users] grompp - Group protein not found

Ahh, case sensitivity? Protein vs. protein? On 2012-03-08 07:41:15AM +1100, Mark Abraham wrote: > On 8/03/2012 4:31 AM, Peter C. Lai wrote: > > Check the molecules section at the bottom of your top file. Each molecule > > entry there should match the corresponding name giv

Re: [gmx-users] HOW TO USE SILVER ATOMS IN AMBER99 FORCE FIELD

www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst

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

/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 > > -- > gmx-users mailing listgmx-users@gromacs.o

Re: [gmx-users] grompp - Group protein not found

to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Resea

Re: [gmx-users] Gromacs 3.3.3 on Lion Xgrid

://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://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

Re: [gmx-users] Extending simulation with -pd

considered enabled by default. I don't think -pd is one of them so you will have to specify it every time (it's safer to specify it anyway). -- ========== Peter C. Lai| University of Alabama-Birmingham Progra

Re: [gmx-users] how to use charmm ff in gmx and carbohydrate forcefield

s://uab.hyperfine.info/trac/molsim/wiki/gromacs Charmm FF Conversion information. -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research |

Re: [gmx-users] HIS residue in Charmm27

ers mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface

Re: [gmx-users] trjconv -dump problem

g > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://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...@gr

Re: [gmx-users] Re: Placing ions in the specified positions

ing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://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

Re: [gmx-users] Pressure coupling and membrane-type simulations

upling > as they may buckle. Seems to me this should be the principal concern. > > -Justin > Another consideration is that the documentation states when using built-in implicit walls at z=0 and z=zbox to use anistropic pressure coupling with the x/y compressibility set to 0 "

Re: [gmx-users] Re: Using CHARMM force fields in Gromacs, pt. 2

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 -- =

Re: [gmx-users] Using CHARMM force fields in Gromacs, pt. 2

gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www in

Re: [gmx-users] Placing ions in the specified positions

ce or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics,

[gmx-users] how to interpret tilt from g_helixorient?

do I interpret the tilt angles from g_helixorient? If I specify 4 CA atoms in the center of my helix, it seems to give me a running average of some sort with 0 angle angle 0. What is this angle in relation to? -- == Peter C

Re: [gmx-users] charmm27 in gromacs

interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | K

Re: [gmx-users] a question about membrane simulation

t; 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 -- == Peter C. Lai

Re: [gmx-users] Force Field for Vacuum simulation

asurements are better suited for their narrative. Maybe start looking at what the protein folding people are doing too, since they also use the point mutation technique to probe stability and transition states through various stages of (un)folding... -- ===========

Re: [gmx-users] Force Field for Vacuum simulation

ith the protein... You will have to judge how much of that paper specifically applies to your individual case... -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div.

Re: [gmx-users] Force Field for Vacuum simulation

the most appropriate > might be in that case? E.g I've found in the Justin's tutorial cyclohexan > layer as the membrane-like solvent but I suppose that ussage of the smaller > apolar mollecule might be more similar to acyl-like interior. > > James > > 2012/2/2 Peter

Re: [gmx-users] Force Field for Vacuum simulation

aters in the solvent accessible space" and the fact that since there is vaccum surrounding the outside of the TM bundle and waters inside the TM bundle, your protein may explode from the lateral motion of the waters inside the solvent accessible spaces pushing against the TMs... >

Re: [gmx-users] problem with make_ndx

, Anushree Tripathi wrote: > Yes I want to simulate the protein inside DPPC bilayer but how could I make > the index file. Everytime it is showing error that no DPPC found in index > file. > > On Thu, Feb 2, 2012 at 12:18 PM, Peter C. Lai wrote: > > > Are you actually tryin

Re: [gmx-users] problem with make_ndx

@gromacs.org. > >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > > > > > > > > > > > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please searc

Re: [gmx-users] Force Field for Vacuum simulation

> >> > >> <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > >> > > >> > >> > >> > >> > >> > > > > -- > > David van der Spoel, Ph.D., Professor of Biology > >

Re: [gmx-users] simulation killed

THE PROGRAM STOP ( KİLLED) SORRY FOR BAD ENGLİSH.. > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't

Re: [gmx-users] g_mindist on 51-frame trajectory gives 51 minimum distances but <51 atom pairs

. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst

Re: [gmx-users] Chromophore residue patch in gromacs

> www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analy

Re: [gmx-users] regarding NVT

; -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the &

Re: [gmx-users] Cytochrom C

+N > CH3 HH31 > CH3 HH32 > CH3 HH33 > O C > [ impropers ] > C CH3 +N O > > > On 1/6/12 12:40 PM, Peter C. Lai wrote: > > Corrected bonds section (sorry been up all night) > >

Re: [gmx-users] Cytochrom C

HH32 CH3HH33 CH3C C O Surprisingly, an .hdb entry for ACE exists so you don't need to create one. (and the .hdb entry uses HH3 as the base hydrogen name in ACE) > > > On 2012-01-06 12:23:49PM -0600, Peter C. Lai wrote: > > Gromos96 53A6 has it. &g

Re: [gmx-users] Cytochrom C

0.514 OO -0.515 [ bonds ] CH3H1 CH3H2 CH3H3 CH3C C O Surprisingly, an .hdb entry for ACE exists so you don't need to create one. On 2012-01-06 12:23:49PM -0600, Peter C. Lai wrote: > Gromos96 53A6 has it. > > On 20

Re: [gmx-users] Cytochrom C

; -- > > Robert J. Hamers > > Wisconsin Distinguished Professor > > Univ. of Wisconsin-Madison > > 1101 University Avenue > > Madison, WI 53706 > > Ph: 608-262-6371 > > Web: http://hamers.chem.wisc.edu > > > > > > > -- > Kind Regards,

Re: [gmx-users] Membrane protein simulation: maintain protein in the box centre

of lipids in the xy-plane), > but I haven't managed to find anything that will maintain the protein > in the box centre throughout the simulation. > > Does anyone have any ideas? Please let me know if, as is usually the > case, I've left out an important bi

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