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

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

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

of pdb2gmx? James 2012/12/20 Peter C. Lai p...@uab.edu: (As a side note, Gromacs shouldn't use charge groups when using all-atom charmm forcefields.) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive

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

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 p...@uab.edu: http://cesium.hyperfine.info/~peter/gromacs/popc36/ has a fully

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. For

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 approach

Re: [gmx-users] Energy minimization

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 p...@uab.edu To: Shima Arasteh shima_arasteh2...@yahoo.com Cc: Discussion list for GROMACS users gmx-users

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  CYS 1 

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] Energy minimization

them, I may get some other clashes, may I not? Any other suggestion? Thanks.   Sincerely, Shima - Original Message - From: Peter C. Lai p...@uab.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Sunday

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

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] barium ion simulation

/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| Birmingham

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

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

-- == 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 (205) 690-0808

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

the 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] Re: are wall atoms virtual ?

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 | KAUL

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

of the manual seems to say that in type 9, phi_s, k_phi, and the multiplicity are specified. Does this mean that cp corresponds to the force constant k_phi? Yes, although the CHARMM people call it KChi. -- == Peter C. Lai

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 undecapeptide is inserted

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, I think I am a bit confused about the proper way to handle boxes

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

://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] Problem with equilibrated lipid bilayer structure

-- == 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 (205) 690-0808

Re: [gmx-users] VMD problem?

-- == 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 (205

Re: [gmx-users] Lennard-Jones Parameters

). 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 p...@uab.edu wrote: It's hard to understand your question. What do you mean by reference parameters? You said you already

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

-- == 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 (205) 690-0808

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

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

Re: [gmx-users] Lennard-Jones Parameters

-- == 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 (205) 690-0808

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

profile? If you have significant temperature fluctuations they will, by definition... -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div

Re: [gmx-users] small tc-group

(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] Model of water

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] Temperature in simulation

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Re: [gmx-users] Temperature in simulation

, is reporting the results in a paper. How would it be? Thanks for your suggestion Peter.   Sincerely, Shima - Original Message - From: Peter C. Lai p...@uab.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Wednesday, October 3, 2012 5:16 PM Subject: Re: [gmx

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

/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL

Re: [gmx-users] Ion conduction through a protein-membrane system

to some extent. You'll probably want to look for yourself to see if your use-case is supported. -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div

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

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] Do not want to add hydrogens to intial pdb structure

-- == 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 (205) 690-0808

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

-- == 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 (205) 690-0808

Re: [gmx-users] packing lipids

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

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

-- == 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 (205) 690

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

a problem? I am really thankful for the big amount of help. Thank you. Lara - Ursprüngliche Message - Von: Peter C. Lai p...@uab.edu An: Discussion list for GROMACS users gmx-users@gromacs.org CC: Lara Bunte lara.bu...@yahoo.de Gesendet: 22:13 Freitag, 21.September 2012

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

-rescale tc-grps = ISO SOL   tau_t   = 0.1   0.1 ref_t   = 300   300 pcoupl  = no Greetings Lara - Ursprüngliche Message - Von: Peter C. Lai p...@uab.edu An: Lara Bunte lara.bu...@yahoo.de CC: gmx-users@gromacs.org gmx

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

: Peter C. Lai p...@uab.edu An: Discussion list for GROMACS users gmx-users@gromacs.org 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 how many threads to spawn on the local host. We

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

- Von: Peter C. Lai p...@uab.edu An: Lara Bunte lara.bu...@yahoo.de; Discussion list for GROMACS users gmx-users@gromacs.org CC: Gesendet: 17:58 Montag, 24.September 2012 Betreff: Re: [gmx-users] About mdrun -nt number A thread is like a process. (Except not all threads have

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

  = no I am totaly frustrated and shortly for giving it up :-(:-( :-( Best greetings Lara - Ursprüngliche Message - Von: Peter C. Lai p...@uab.edu An: Lara Bunte lara.bu...@yahoo.de CC: gmx-users@gromacs.org gmx-users@gromacs.org Gesendet: 17:57 Montag, 24

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 that have been posted explicitly 3-4 times

Re: [gmx-users] InflateGro methodology

-- == 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 (205) 690-0808

Re: [gmx-users] Visualizing the system

-- == 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 (205

Re: [gmx-users] About Bond in Topology

-- == 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 (205) 690-0808

Re: [gmx-users] About Bond in Topology

://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] Strong position restrain

-- == 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 (205) 690-0808

Re: [gmx-users] Domain decomposition error, is mdrun_mpi now obsolete?

-- == 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 (205) 690-0808

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

was... -- == 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 (205) 690-0808

Re: [gmx-users] TIP4P water model

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-Birmingham Programmer

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

! * 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] Re: v-rescale

steps are conducted. (also when certain features may be implemented differently, such as the introduction of the v-rescale thermostat). -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst

Re: [gmx-users] Energy Minimization of Alanin

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] Re: v-rescale

? 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

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

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 | KAUL

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

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

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 (205) 690-0808

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

://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] Charmm for Proteins

-- == 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 (205) 690-0808

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 p...@uab.edu 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, I've also found

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

/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 -- == Peter C. Lai

Re: [gmx-users] Adding phosphate to protein

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| University

Re: [gmx-users] Adding phosphate to protein

-- == 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] Adding phosphate to protein

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 -- == Peter C. Lai

Re: [gmx-users] Is there a way to redirect utility output to the screen, rather than to a file?

! * 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] Hydrogen bond breaking process

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 | KAUL 752A

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

or sd integrators. -- == 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] very strange area/lipid value for POPC membrane system

-- == 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 (205) 690-0808

Re: [gmx-users] Protein-POPC bilayer

-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 POPC was simulated in anisotropic pressure

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 work

Re: [gmx-users] Protein-POPC bilayer

. This is where I asked the question about. Thanks.     Sincerely, Shima - Original Message - From: Peter C. Lai p...@uab.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Friday, August 17, 2012 7:17 AM

Re: [gmx-users] Protein-POPC bilayer

, you should be fine. Sincerely, Shima - Original Message - From: Peter C. Lai p...@uab.edu To: Shima Arasteh shima_arasteh2...@yahoo.com Cc: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, August 17, 2012 8:19 AM Subject: Re: [gmx-users] Protein-POPC

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

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

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

/Mailing_Lists -- == 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

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

(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] desired no of water molecules

://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] desired no of water molecules

2.194 so certainly it does contain 668 water molecules. Thanks, On Tue, Aug 14, 2012 at 10:13 AM, Peter C. Lai p...@uab.edu wrote: Did you have waters in the system before adding another 612? I don't know how VMD counts waters, but another way is to grep -c for SOL in the resulting

Re: [gmx-users] NVT equilibration

/Mailing_Lists -- == 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] NVT equilibration

of a correct changes? You are supposed to use the cutoffs appropriate for your forcefield. Sincerely, Shima - Original Message - From: Peter C. Lai p...@uab.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Thursday, August 9, 2012 5:08 PM Subject

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

? 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 | Birmingham

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

-- == 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 (205) 690-0808 | == -- gmx-users mailing

Re: [gmx-users] GROMACS OR NAMD

/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 -- == Peter C. Lai

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

://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 | Birmingham AL 35294-4461 (205) 690

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

of the incorrect value of a new-defined residue in .rtp file? Sincerely, Shima - Original Message - From: Peter C. Lai p...@uab.edu To: gmx-users@gromacs.org Cc: Sent: Wednesday, July 18, 2012 9:00 AM Subject: Re: [gmx-users] Some interactions seem to be assigned multiple

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

. * 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] Some interactions seem to be assigned multiple times

-- == 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 (205) 690-0808

Re: [gmx-users] sovation with tip3p

! * 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] water model

/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 -- == Peter C. Lai

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

-- == 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 (205) 690-0808

Re: [gmx-users] Berger lipid

in Justin's tutorial , 323 K is proper, however it was a different system simulated and also many parameters are not the same as your system . Would you telling me about the reason of 310 K? Thanks in advance   Sincerely, Shima - Original Message - From: Peter C. Lai p

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

. * 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] Berger lipid

://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] Insertion protein in the membrane via G_membed

-- == 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] mdrun -v output

/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 -- == Peter C

Re: [gmx-users] Trajectories

-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 Research

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 jalem...@vt.edu mailto:jalem...@vt.edu On 6/4/12 2:59 PM, Shay Teaching wrote: Dear Gromacs users, I want to write new analyses

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

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-Birmingham Programmer

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