Re: [gmx-users] trjconv pbc membrane

nv -pbc mol > > The last two give somewhat different results, depending on the context, for > reasons I don't yet understand, but usually one of them works :-) > > -Justin > > maite lopez cabezas wrote: >> Hi: >> I equilibrated a DPPC membrane that I built. I wan

[gmx-users] trjconv pbc membrane

Hi: I equilibrated a DPPC membrane that I built. I want to take a snapshot for doing some protein-membrane simulations, but first i have to do somethings for eliminating the lipids out of the box. I have tried with pbc and fit options like people say in the list and it doesn't work. Anybody can he

Re: [gmx-users] g_sas Vdwradii.dat

, David van der Spoel <[EMAIL PROTECTED]> wrote: > Xavier Periole wrote: > >> On Sat, 07 Jun 2008 22:32:29 +0200 >> "Xavier Periole" <[EMAIL PROTECTED]> wrote: >> >>> On Sat, 7 Jun 2008 15:04:34 -0400 >>> "maite lopez cabezas"

[gmx-users] g_sas Vdwradii.dat

Hi: I'm using g_sas *to analyse a DPPC simulation but it gave the next warning: WARNING: could not find a Van der Waals radius for 128 atoms 3840 out of 6400 atoms were classified as hydrophobic I saw that the **Van der Waals radius for phophorous atoms doesn't appear in vdwraddi.dat. When I modif

Re: [gmx-users] area by lipid

Well I know that the x/y directions are scaled isotropically and the z direction is scaled independiently, and i must give just 2 compresibility valors, but people don't give this valor in the most of the papers about membrane simulations. For example i use on DPPC membrane compressibility

Re: [gmx-users] area by lipid

On Nov 24, 2007 6:00 PM, Alan Dodd <[EMAIL PROTECTED]> wrote: > I didn't think g_energy was useful for that - I've always used g_traj -ob to > get box dimensions. If noone has a better answer, you should probably just > try that and see if you get the same effect.

[gmx-users] area by lipid

Hi: I am working on membrane simulation under lipid (DPPC, from Peter Tieleman group site). I equilibrated dppc membrane for 10 ns and when i got the area by lipid (x*y/ # lipids) using g_energy, i obtained that the area is constant (0.64), there isn't any fluctuaction during 10 ns..althougth the

Re: [gmx-users] protein membrane simulation

gt; wrote: Hi Maite, You can use ffG45a3, which is an upgrade of ffG43a2; I've never heard of 43a4, but that's probably me. 45a3 and 43a2 are largely similar and AFAIK you don't need to renumber bonded interactions and such. Best, Tsjerk On 4/5/07, maite lopez <[EMAIL PROTE

Re: [gmx-users] protein membrane simulation

Hi all: Thanks a lot for replyng. You 're right, i include the popc.itp file in my .top and grompp runs well. I've changed to ffG43a2 force field, as David and Tsjerk said me, the ffG53a* isn't a good force field for lipids. The best of the gromos96 ff is ffG43a4 for membrane simulations, but

[gmx-users] protein membrane simulation

Hi all: I´m working on membrane peptides simulation under lipid (POPC, from Peter Tieleman group site). I downloaded the popc.pdb and lipid.itp file from this site and i want to use the ffG53a5 force field. Some days ago suggest to me i should to do something like this : http://www.gromacs.org/p

Re: [gmx-users] POPC membrane simulations

Hi Chris: I´ve created my own dppc.itp using the ffG53a5 force field. I did that running only a dppc lipid of the membrane that is available on Tieleman's site and i included it on my topology file and of course put in it the number of dppc molecules . i haven´t had any problem with this simulat

[gmx-users] POPC membrane simulations

Hi all: I ´m working on membrane peptides simulation under lipid (POPC, from Peter Tieleman group site) and i want to do a popc.itp file using ffG53a5 force field. Some days ago i was working with dppc membranes and i took one lipid and run it through pdb2gmx, using my favourite force field and

[gmx-users] POPC membrane simulation (popc.itp)

Hi all: I ´m working on membrane peptides simulation under lipid (POPC, from Peter Tieleman group site) and i want to do a popc.itp file using ffG53a5 force field. Some days ago i was working with dppc membranes and i took one lipid and run it through pdb2gmx, using my favourite force field and

Re: [gmx-users] peptide-membrane simulations

Hi Justin : how Tsjerk said me yesterday i forgot to change the number of the atoms in the .gro file. Now i don't have this error when i run editconfig command. Thanks, Maite On 3/14/07, Justin Lemkul <[EMAIL PROTECTED]> wrote: > Fatal error: > Invalid line in peptide_dppc64_water.gro for a

Re: [gmx-users] peptide-membrane simulations

en help to solve problems. Best, Tsjerk On 3/14/07, maite lopez <[EMAIL PROTECTED]> wrote: > Hi: > I am working on peptide-membrane simulation under lipid (DPPC, from > Peter Tieleman group site). I've solvated the system using the x and y > vectors of the initial box (membran

[gmx-users] peptide-membrane simulations

Hi: I am working on peptide-membrane simulation under lipid (DPPC, from Peter Tieleman group site). I've solvated the system using the x and y vectors of the initial box (membrane box), but i increased the vector in the z axes . I've eliminated the water molecules that are interacting with the apo

Re: [gmx-users] grompp error in peptide-membrane simulations

in.top file. Hope it helps, Tsjerk On 3/3/07, Mark Abraham <[EMAIL PROTECTED]> wrote: > maite lopez wrote: > > > i've changed the atoms of the dppc.itp file by the atoms of the DPPC > > molecule that appear in the ffG53a5.rtp file (for example LC3 by CH3) > >

Re: [gmx-users] grompp error in peptide-membrane simulations

s to ffG53a5. Don't try to do it the other way around and convert everything to ffgmx. That force field is deprecated. Best, Tsjerk On 3/2/07, maite lopez <[EMAIL PROTECTED]> wrote: > Hi: > > This is the other part of my last email. > > I've done many things as

[gmx-users] grompp error in peptide-membrane simulations

Hi: This is the other part of my last email. I've done many things as suggested in mailing list for example: 1)If i don't include the lipid.itp file atomtype LC3 not found or if i put ";" in the line 9 of lipid.itp atomtype LC3 not found or if i put ";" in the line 9 of lipid.itp

[gmx-users] (no subject)

Hi gromacs users: I am working on membrane peptides simulation under lipid (DPPC, from Peter Tieleman group site). I have downloaded the lipid and dppc .itp from the same site. The steps that I am following are as follows and all my files are in the work directory: 1)pdb2gmx_331 -f peptide_moved

[gmx-users] genbox peptide-membrane simulation

Hi gromacs users: I'm simulating a peptide-dppc64 system. When i create my box with editconf program (editconf -f input.gro -o output.gro -bt triclinic -c -d 1.5) and i solvate, the molecule go out of the box. I used many kind of box and some box sizes. My system size is 4.936 4.408 and 10.503

Re: [gmx-users] pdbgmx warning long bond

Hi Stéphane Can you give me a better explanation and provide files on your website ? Cheers Maite ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the lis

Re: [gmx-users] pdbgmx warning long bond

Hi Tsjerk: But, i think the problems is that pdb2gmx program see the membrane how a protein and it tries to tie the peptide with the membrane. The topology of dppc membrane appear in the ffG53a5.rtp file of gromacs. What can i do? Should i create a peptide.top file and include it a lipid.itp an

[gmx-users] pdbgmx warning long bond

Dear Gromacs Users, I am trying to simulate a peptide in explicit lipid bilayer membrane environment (say, DPCC). I took well equilibrated dppc.pdb file from Dr. Peter tieleman site and i modified it put in the names of the atoms of the ffG53a5.rtp file . I changed DPPC x DPP in ffG53a5.rtp file