Re: [gmx-users] how to convert CGenFF into .itp file?

-26 12:29:29PM +0100, Albert wrote: > On 12/26/2012 12:18 PM, Peter C. Lai wrote: > > You don't. CGenFF is a forcefield, like CHARMM36. You install it, add rtp > > entries then use pdb2gmx to generate a ligand's topology .itp file > > THX > but the proble

Re: [gmx-users] how to convert CGenFF into .itp file?

You don't. CGenFF is a forcefield, like CHARMM36. You install it, add rtp entries then use pdb2gmx to generate a ligand's topology .itp file On 2012-12-26 11:35:46AM +0100, Albert wrote: > hello: > > I found the script charmm2gromacs-pvm.py >

Re: [gmx-users] Pre-equilibrated CHARMM lipid bilayers

gt; parametrising my protein by means of pdb2gmx? > > > James > > > 2012/12/20 Peter C. Lai : > > (As a side note, Gromacs shouldn't use charge groups when using > > all-atom charmm forcefields.) > -- > gmx-users mailing listgmx-users@gromacs.org &g

Re: [gmx-users] Pre-equilibrated CHARMM lipid bilayers

I don't know. Parachem outputs stuff like this (CHARMM toppar format): (propionic acid, C3H2O5) RESI PROA -1.00 GROUP ATOM C2 CG321 -0.28 ATOM C1 CG2O30.62 ATOM H21 HGA2 0.09 ATOM H22 HGA2 0.09 ATOM O1 OG2D2 -0.76 ATOM O2 OG2D2 -0.7

Re: [gmx-users] Pre-equilibrated CHARMM lipid bilayers

arametrized by > Swiss-param ( make topology for the ligands in charmm27 ff). So > because receptor and bilayer will be parametrized in charmm36 I'm not > sure about proper working of Swiss's topology with that complex. > > James > > 2012/12/19 Peter C. Lai : > > ht

Re: [gmx-users] Energy minimization

oblem? > > It might be clashes in the system but How can I find the overlapping atoms > and the reason of clashe among a vast number of atoms? > > > Sincerely, > Shima > > > - Original Message - > From: Peter C. Lai > To: Shima Arasteh > Cc: Discus

Re: [gmx-users] Pre-equilibrated CHARMM lipid bilayers

http://cesium.hyperfine.info/~peter/gromacs/popc36/ has a fully gromacs compatible charmm36 238 POPC bilayer with 21524 waters On 2012-12-18 09:07:22PM -0800, James Starlight wrote: > Justin, thanks again. > > As I understood gromacs already had had parameters for charmm lipid so > the main appro

Re: [gmx-users] SDS micelle simulation in TFE solvent

On 2012-12-19 10:16:09AM +0530, Archana Sonawani wrote: > Hi, > > I want to simulate a peptide using SDS micelle. The peptide is random > coil, > but I want it to be helical; therefore, I will use TFE for inducing > helix. You use TFE in a wet lab to physically induce helicity in real life.

Re: [gmx-users] Energy minimization

if I move them, I may get some > other clashes, may I not? > Any other suggestion? > > Thanks. > > >   > Sincerely, > Shima > > > ----- Original Message - > From: Peter C. Lai > To: Shima Arasteh ; Discussion list for GROMACS > users >

Re: [gmx-users] Energy minimization

It depends on what the atom is overlapping with and some conjecture as to what might be causing the overlap: You can always manually move it, either by editing the .gro file directly or using a tool like VMD to move it or the molecule/fragment it's attached to with the mouse and then display the

Re: [gmx-users] gold-S simulation

Where is the .itp file for the system? On 2012-12-15 01:40:27PM -0800, fatemeh ramezani wrote: > hi > > > I'm simulating gold atom interaction with  aminoacidcys. I have made > gold-cys.pdb by hyperchem software: > > HETATM    1  N   CYS 1   0.000   1.335   0.000 > HETATM    2  CA  CY

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

On 2012-12-08 03:20:54AM -0800, James Starlight wrote: > 1- on what assumptions that blocks were generated ? This appears to be a swissparm-specific question. I don't know what algorithms it uses to match what are essentially pharmacophores in the new molecule with the common individual blocks it

Re: [gmx-users] area per lipid

Not if you aren't going to run those. I assume nvt.mdp and npt.mdp are restrained runs to remove/dampen clashes and prevent crashes but if you are already running a full md simulation then you don't need to redo those steps. Also, I don't use DispCorr for C36 lipids (some debates about that can b

Re: [gmx-users] barium ion simulation

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 Gene

Re: [gmx-users] How to avoid adding ions close to ligand

There is nothing stopping you from replacing the ion in your binding pocket with the original water and then replacing another water elsewhere with the ion at the oxygen's coordintes, then running genconf to renumber the gro file. On 2012-11-26 06:25:47PM -0800, Yun Shi wrote: > I did hope the ion

Re: [gmx-users] a question on trajcat settime

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 Prog

Re: [gmx-users] Re: are wall atoms virtual ?

s.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 -- ===

[gmx-users] g_rms/rmsf: fit vs. nofit

trajectory on an atom near the starting COM would minimize distances traveled due to COM diffusion through the solvent. -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A

Re: [gmx-users] Type 9 dihedral in Gromacs topology

the force constant k_phi? Yes, although the CHARMM people call it KChi. -- ========== Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p.

Re: [gmx-users] Box size/type confusion for bilayer system

On 2012-10-18 03:58:22PM -0400, Justin Lemkul wrote: > > > On 10/18/12 3:55 PM, Peter C. Lai wrote: > > On 2012-10-18 02:53:38PM -0400, Justin Lemkul wrote: > >> > >> > >> On 10/18/12 2:43 PM, klexa wrote: > >>> Hi Gromacs users, > >

Re: [gmx-users] Box size/type confusion for bilayer system

On 2012-10-18 02:53:38PM -0400, Justin Lemkul wrote: > > > On 10/18/12 2:43 PM, klexa wrote: > > Hi Gromacs users, > > > > I think I am a bit confused about the proper way to handle boxes that are > > not > > standard cubes. I'm trying to run a membrane simulation where a cyclic > > undecapeptid

Re: [gmx-users] Re: The problem of converting CGenff parameters to those of Gromacs

ww 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] The problem of converting CGenff parameters to those of 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] Lennard-Jones Parameters

from 43a1 then they are obviously not using gromos96 43a1 :) > > > Best regards, > > > > Cuong > > > > On 15 October 2012 16:43, Peter C. Lai wrote: > > > >> Is there no [atomtypes] section in the top file? > >> > >> On 2012-10

Re: [gmx-users] losing data in trjconv?

> * 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 St

Re: [gmx-users] Lennard-Jones Parameters

and epsilon values). I can change the charge in the top file, yet I do not > know how to change sigma and epsilon values. > > Best regards, > > Cuong > > On 15 October 2012 13:57, Peter C. Lai wrote: > > > It's hard to understand your question. What do you m

Re: [gmx-users] Problem with equilibrated lipid bilayer structure

* 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] VMD problem?

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 Ala

Re: [gmx-users] Problem with equilibrated lipid bilayer structure

rs 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

Re: [gmx-users] Lennard-Jones Parameters

ng_Lists<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! &

Re: [gmx-users] Re: small tc-group

l tc_group.? > > Can this different elections of the tc_grps affect the final PMF profile? > If you have significant temperature fluctuations they will, by definition... -- ========== Peter C. Lai| Univer

Re: [gmx-users] small tc-group

t; * 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.g

Re: [gmx-users] Model of water

nfo/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? Read http://www.gromacs

Re: [gmx-users] Temperature in simulation

t, > is reporting the results in a paper. How would it be? > > Thanks for your suggestion Peter. > >   > Sincerely, > Shima > > > - Original Message - > From: Peter C. Lai > To: Discussion list for GROMACS users > Cc: > Sent: Wednesday,

Re: [gmx-users] Temperature in simulation

e > 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] Ion conduction through a protein-membrane system

ternal electrical field to study ion > conduction in a system? > The manual appears suggests such a thing might be possible to some extent. You'll probably want to look for yourself to see if your use-case is supported. --

Re: [gmx-users] pdb2gmx with more than 9999 residues

ng! > * 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.

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

field [ moleculetype ] ; name nrexcl Protein_chain_A 3 nonbonded interactions between atoms that are no further than nrexcl bonds away are excluded. See also http://lists.gromacs.org/pipermail/gmx-users/2011-May/061072.html -- ==

Re: [gmx-users] Assignment of new velocities for multi-runs

ists/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] Do not want to add hydrogens to intial pdb structure

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

Re: [gmx-users] Installation in a SGI Cluster

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-

Re: [gmx-users] Water molecule can not be settled - mdrun error

On 2012-09-24 12:34:53PM -0400, Justin Lemkul wrote: > > > On 9/24/12 12:31 PM, Peter C. Lai wrote: > > As I noted before, you can safely ignore the gromacs notices when setting > > them to the correct cutoffs I listed. > > > > Agreed. Please use the cutoffs t

Re: [gmx-users] Water molecule can not be settled - mdrun error

= 100   > > nstvout = 100   > > nstenergy   = 100   > > nstlog  = 100   > > > > tcoupl  = V-rescale > > tc-grps = ISO SOL   > > tau_t   = 0.1   0.1     > > ref_t

Re: [gmx-users] About mdrun -nt number

Greetings > Lara > > > > > > ----- Ursprüngliche Message - > Von: Peter C. Lai > An: Lara Bunte ; Discussion list for GROMACS users > > CC: > Gesendet: 17:58 Montag, 24.September 2012 > Betreff: Re: [gmx-users] About mdrun -nt number > > A thread is like a process. (Exce

Re: [gmx-users] About mdrun -nt number

> > - Ursprüngliche Message - > Von: Peter C. Lai > An: Discussion list for GROMACS users > CC: > Gesendet: 17:43 Montag, 24.September 2012 > Betreff: Re: [gmx-users] About mdrun -nt number > > # of mdrun threads > > -nt N is used to basically tell mdrun

Re: [gmx-users] Water molecule can not be settled - mdrun error

  > nstenergy   = 100   > nstlog  = 100   > > tcoupl  = V-rescale > tc-grps = ISO SOL   > tau_t   = 0.1   0.1 > ref_t   = 300   300 > > pcoupl  = no > > Greetings > Lara > &

Re: [gmx-users] Water molecule can not be settled - mdrun error

ith previous and current coordinates > > Are the .mdp Options still a problem? > > > I am really thankful for the big amount of help. Thank you. > Lara > > > > > > > - Ursprüngliche Message - > Von: Peter C. Lai > An: Discussion list fo

Re: [gmx-users] About mdrun -nt number

u...@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

Re: [gmx-users] packing lipids

gt; * 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.gromac

Re: [gmx-users] InflateGro methodology

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] Domain decomposition error, is mdrun_mpi now obsolete?

be 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-Birming

Re: [gmx-users] Strong position restrain

omacs.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-use

Re: [gmx-users] About Bond in Topology

> 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] About Bond in Topology

acs.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

Re: [gmx-users] Visualizing the system

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 Genetic

Re: [gmx-users] About Presence of Bond In Topology

> 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] TIP4P water model

a Naithani > -- > 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 t

Re: [gmx-users] Water molecule can not be settled - mdrun error

would still go bck to check the specific water that could not settle and see what the other particles near it are since that is probably the root of the problem. Also, we haven't been told what the results of the energy minimzation was... -- =

Re: [gmx-users] Re: v-rescale

es of 4.5.x tutorials written by Justin himself, with explanations of why certain steps are conducted. (also when certain features may be implemented differently, such as the introduction of the v-rescale thermostat). -- ========== Peter C

Re: [gmx-users] Re: v-rescale

st (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| University

Re: [gmx-users] Energy Minimization of Alanin

ase 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/Support/Mailing_L

Re: [gmx-users] Extracting bond information from topol.tpr file using template.c

se 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] Extracting bond information from topol.tpr file using template.c

..@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 So

Re: [gmx-users] LINCS warning in md run

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/Sup

Re: [gmx-users] make index groups with make_ndx

sts.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. > * C

Re: [gmx-users] Charmm for Proteins

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 p...@uab.edu

Re: [gmx-users] MD problem with nwall=2

On 2012-09-06 02:46:21PM +0200, Bogdan Costescu wrote: > On Wed, Sep 5, 2012 at 8:37 PM, Peter C. Lai wrote: > > Could be a result of not setting x/y compressibility = 0 as the manual > > suggests you should do... > > As one who has also tried to use walls recently,

Re: [gmx-users] MD problem with nwall=2

t. 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] Is there a way to redirect utility output to the screen, rather than to a file?

rg/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research

Re: [gmx-users] Adding phosphate to protein

t;> 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! > >> >> *

Re: [gmx-users] Adding phosphate to protein

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] Adding phosphate to protein

iling_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] Hydrogen bond breaking process

]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gr

Re: [gmx-users] what's the difference between gen_seed and ld_seed?

the processor number. > > when should we turn this option on? As stated, you use this option for use with the bd or sd integrators. -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst

Re: [gmx-users] very strange area/lipid value for POPC membrane system

.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] Protein-POPC bilayer

d before, if the box vectors and area per lipid are in equilibrium by the end of the equilibration, you should be fine. > > > Sincerely, > Shima > > > - Original Message - > From: Peter C. Lai > To: Shima Arasteh > Cc: Discussion list for GROMACS users &

Re: [gmx-users] Protein-POPC bilayer

to the consensus value of around 63–65Å per headgroup. > > This is where I asked the question about. > > Thanks. > >   > >   > Sincerely, > Shima > > > - Original Message - > From: Peter C. Lai > To: Shima Arasteh ; Discussion list for GROMACS &

Re: [gmx-users] Protein-POPC bilayer

;gen_temp= 300 ; temperature for Maxwell distribution ;gen_seed= -1; generate a random seed nstcomm = 1 comm_mode = Linear comm_grps = POPC SOL On 2012-08-16 09:32:17PM -0500, Peter C. Lai wrote: > You always use semi-isotropic for bilayer w

Re: [gmx-users] Protein-POPC bilayer

uestion about the Protein-POPC system: > To insert a protein in lipid bilayer, I am suggested to simulate POPC in > water separately before insertion, it might decrease the time of final > simulation. It's OK! > > In the article suggested me by dear Peter C. Lai, I read that

Re: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why?

> 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] CHARMM36 - Smaller Area per lipid for POPE - Why?

gt;>>> > > > > > >>>>>> On 2012-07-20 09:46:13AM -0300, Sebastien Cote wrote: > > > > > >>>>>>> Dear Gromacs users, > > > > > >>>>>>> > > > > > >>>>>>> My si

Re: [gmx-users] desired no of water molecules

.873 1.946 > 670SOLHW2 2023 0.054 1.876 2.050 > 671SOL OW 2024 1.901 2.939 2.162 > 671SOLHW1 2025 2.000 2.928 2.153 > 671SOLHW2 2026 1.861 2.853 2.194 > > so certainly it does contain 668 water molecules. > Thanks, >

Re: [gmx-users] desired no of water molecules

Only plain text messages are allowed! > * 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. > * Ca

Re: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why?

s. It is taken from the article Klauda, J. B. > > > >>>>>>> et al. 2010 J. Phys. Chem. B, 114, 7830-7843. > > > >>>>>>> > > > >>>>>>> At first, I tested normal TIP3P vs. CHARMM TIP3P and saw that > > > >>>>>>> normal TIP3P g

Re: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why?

t;> It is a POPE membrane of 80 lipids equilibrated in NPT at T=310K > > > >>>>>>> and P=1atm for 40 ns. It is taken from the article Klauda, J. B. > > > >>>>>>> et al. 2010 J. Phys. Chem. B, 114, 7830-7843. > > > >>

Re: [gmx-users] NVT equilibration

dw cutoffs? How would I be sure of > a correct changes? > You are supposed to use the cutoffs appropriate for your forcefield. > > Sincerely, > Shima > > > - Original Message - > From: Peter C. Lai > To: Discussion list for GROMACS users > Cc: > Se

Re: [gmx-users] NVT equilibration

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 Progr

Re: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why?

or a switch from 0.8 to 1.2 (as in Klauda's paper), I got Area > >>>>>>> per lipid of about 56.5 Angstroms2; whereas they got 59.2 in their > >>>>>>> paper, matching the experimental value of 59.75-60.75. > >>>>>>> 2- For a switch from 1.0

Re: [gmx-users] GROMACS OR NAMD

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] CHARMM36 - Smaller Area per lipid for POPE - Why?

al ensemble > > > for my peptide in solution. > > > > > > I am willing to send more information if you need. > > > > > > Thanks a lot, > > > Sincerely, > > > > > > Sébastien -- > > > gmx-users mailing list

Re: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why?

g/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * 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

Re: [gmx-users] Some interactions seem to be assigned multiple times

rror happen because of the incorrect value of a new-defined > residue in .rtp file? > > > > Sincerely, > Shima > > > ----- Original Message - > From: Peter C. Lai > To: gmx-users@gromacs.org > Cc: > Sent: Wednesday, July 18, 2012 9:00 AM > S

Re: [gmx-users] Some interactions seem to be assigned multiple times

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] sovation with tip3p

st (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| University of Alabama

Re: [gmx-users] water model

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 20th St

Re: [gmx-users] How to assign charge group for ester?

end 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 Genet

Re: [gmx-users] Berger lipid

rs > > * Only plain text messages are allowed! > > * 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] Berger lipid

-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * 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. U

Re: [gmx-users] no SOL in topology file after genbox command

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] Insertion protein in the membrane via G_membed

pport/Mailing_Lists/Search<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 >

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