Re: [gmx-users] protein-membrane simulation- number of lipids

On 10/6/12 1:23 PM, Shima Arasteh wrote: I want to simulate a system of protein and POPC. I downloaded popc.pdb file from Dr.Klauda website. This pdb file contains 72 lipids. I want to know if this number of lipids would be enough for protein-membrane simukation? Only if it's a very sm

[gmx-users] protein-membrane simulation- number of lipids

 I want to simulate a system of protein and POPC. I downloaded popc.pdb file from Dr.Klauda website. This pdb file contains 72 lipids. I want to know if this number of lipids would be enough for protein-membrane simukation? Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org h

Re: [gmx-users] protein/membrane simulation parameters

N-J.M. Macaluso a écrit : Hi, I have two questions that may seem quite simple, but I haven't found clear answers to them. It has to do with the md simulation parameters of a solvated protein/membrane system. The first question is about temperature. Some papers simulate at 300 K, others at 2

Re: [gmx-users] protein/membrane simulation parameters

N-J.M. Macaluso wrote: Hi, I have two questions that may seem quite simple, but I haven't found clear answers to them. It has to do with the md simulation parameters of a solvated protein/membrane system. The first question is about temperature. Some papers simulate at 300 K, others at 298

[gmx-users] protein/membrane simulation parameters

Hi, I have two questions that may seem quite simple, but I haven't found clear answers to them. It has to do with the md simulation parameters of a solvated protein/membrane system. The first question is about temperature. Some papers simulate at 300 K, others at 298 K, and others at physiol

Re: [gmx-users] protein membrane simulation

Hi Maite, Actually, that 45a4 is just a minor upgrade from 45a3, mainly formalizing some additions which I think are already available in 45a3 as present in Gromacs (but who needs nucleotides anyway ;)). Best, Tsjerk On 4/6/07, maite lopez <[EMAIL PROTECTED]> wrote: Hi Tsjerk: Of course, i w

Re: [gmx-users] protein membrane simulation

Hi Tsjerk: Of course, i was wrong, the force field i said is ffG45a4, not 43a4. In the article: A Biomolecular Force Field Based on the Free Enthalpy of Hydration and Solvation: The GROMOS Force-Field Parameter Sets 53A5 and 53A6. (2004) Ostenbrink et al. refers that: " The recent parameteriz

Re: [gmx-users] protein membrane simulation

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 PROTECTED]> wrote: Hi all: Thanks

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

Re: [gmx-users] protein membrane simulation

Hi Maite, In addition, you should be careful with G53a*. Beware that atom bond/angle/dihedral type definitions have changed. If these are referenced by a number (gb_/ga_/gd_) then you have to check each one of them. Also, it appears that the G53a* force fields have problems with the backbone dihe

Re: [gmx-users] protein membrane simulation

As mentioned by another user, you need POPC in the [ molecules ] section. In addition, I see a lack of reference to popc.itp in yout .top file. If it is truely absent, this next bit is important. You have referenced this link: 1) http://www.gromacs.org/pipermail/gmx-users/2006-September/023639.

Re: [gmx-users] protein membrane simulation

maite lopez wrote: 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 : ar

Re: [gmx-users] protein membrane simulation

Check the naming in index file. It might be saying POPC, instead of POP. On 4/4/07, maite lopez <[EMAIL PROTECTED]> wrote: 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 wa

[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