Re: [gmx-users] membrane protein simulation

Thanks for the reply Tsjerk. In fact I am just wonding if the situation exist, i.e., for the 10th trans-membrane helices in the protein, the 8th and or 9th for example is/are a little shorter than the other several helices. Will you please give a comment on how to process this kind of membrane

[gmx-users] K+ ions instead of NA+ for neutralization

Dear gromacs users, For neutralizing the simulation system, can I use K+ ions instead of NA+? Best, Andrew -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] K+ ions instead of NA+ for neutralization

Hi. I'm new to simulation and haven't tried that. Below is what I heard. Most of the time, the force field just treat K+ and Na+ as a sphere with charge and with no orbitals. So, K+ and Na+ ions in simulations are only different in radius (of the sphere). I guess it is ok to use K+ instead of

[gmx-users] membrane protein simulation

Dear All, Suppose a membrane protein contains 10 trans-membrane helix, and as the cell membrane is round, the upper and lower part of the 10 trans- membrane are not horizontal as they are part of the rounded cell, will you please introduce to me how to make the lipid bilayer in curve to

Re: [gmx-users] miscelle formation using ligands only

So it means that my topology file should not contain any heading such as bonds, atoms, dihedral, and should only contain #include drug.itp of various molecules with system name and number of various molecules. Can I just make a box of water.pdb using packmol and use pdb2gmx to generategenerate a

Re: [gmx-users] calculation of persistence length

Hi. I guess g_polystat can't do that. The online reference for gmx polystat (( http://manual.gromacs.org/programs/gmx-polystat.html) says: "...the persistence length is defined as number of bonds where the average cos reaches a value of 1/e." The number of bonds is one number. I don't think it

Re: [gmx-users] membrane protein simulation

Hi Brett, So apart from the curvature of the membrane, there maybe the situation that there's just more of the protein in one leaflet than in the other. You'll need to account for that when embedding. Membrane builders typically check for overlaps to take care of this. Cheers, Tsjerk On Sep 13,

Re: [gmx-users] membrane protein simulation

Dear Tsjerk, Thanks for the reply. Will you please introduce to me sevral membrane builders whith results compatible with gromacs, especially on-line available membrane builders? Best regards. Brett At 2015-09-13 17:45:52, "Tsjerk Wassenaar" wrote: >Hi Brett, >

Re: [gmx-users] membrane protein simulation

Hi Brett, Say I'm designing this new type of truck. Because the earth it's riding over is round, do you think I need to adjust the wheel positions on front and back to match the curvature of the earth? Cheers, Tsjerk On Sep 13, 2015 08:52, "Brett" wrote: > > Dear All, >

Re: [gmx-users] membrane protein simulation

Hi Brett, If you mean an online server, then probably the CHARMM-GUI was made for you. If you mean downloadable, then you can try inflategro or insane (coarse-grained). In addition, Gromacs comes with g_membed integrated. Cheers, Tsjerk On Sep 13, 2015 12:00, "Brett"

Re: [gmx-users] Binding energy calculation

Thank you for your kind reply Which frame or which .pdb file is useful for starting calculation? On 13 Sep 2015 17:40, "Justin Lemkul" wrote: > > > On 9/13/15 8:56 AM, Malihe Hasanzadeh wrote: > >> Hi >> >> I have simulated a protein-ligand with gromacs and submitted it. My >>

Re: [gmx-users] K+ ions instead of NA+ for neutralization

Perhaps, K+ is even better. On Sun, Sep 13, 2015 at 4:10 AM, Andrew Bostick wrote: > Dear gromacs users, > > For neutralizing the simulation system, can I use K+ ions instead of NA+? > > Best, > Andrew > -- > Gromacs Users mailing list > > * Please search the

Re: [gmx-users] calculating total percentage of time from gibbs free energy landscape

can the following work? http://unix.stackexchange.com/questions/12068/how-to-measure-time-of-program-execution-and-store-that-inside-a-variable On Fri, Sep 11, 2015 at 7:57 AM, Naba wrote: > Is it possible to calculate total percentage of time invested to attain a >

Re: [gmx-users] K+ ions instead of NA+ for neutralization

Depends on what you are simulating. Na+ concentration inside cell is very low, comparing to K+. Thus, if you are simulating cell biomolecules, you should go for K+, and for other cases, Na+. Still, there are some issues with KCl crystal formation on some forcefields when simulating

[gmx-users] Binding energy calculation

Hi I have simulated a protein-ligand with gromacs and submitted it. My reviewer asked me about calculation of binding energy. Which tutorial is acceptable and suitable for me to do it? Thank you for your help Malihe -- Gromacs Users mailing list * Please search the archive at

[gmx-users] interaction potential parameters Between H2O And CO2

Dera GMX user, I have simulated CO2 in water, using SPC/E for water, EPM2 model for CO2. I decide to use Lorentz-Berthelot mixing rule for H2O-H2O and CO2-CO2 LJ interaction parameters. But for CO2-H2O LJ interaction paramters, I do not want to use Lorentz-Berthelot mixing rule, instead,

Re: [gmx-users] interaction potential parameters Between H2O And CO2

On 9/13/15 11:26 AM, Zhongjin He wrote: Dera GMX user, I have simulated CO2 in water, using SPC/E for water, EPM2 model for CO2. I decide to use Lorentz-Berthelot mixing rule for H2O-H2O and CO2-CO2 LJ interaction parameters. But for CO2-H2O LJ interaction paramters, I do not want to use

Re: [gmx-users] Binding energy calculation

On 9/13/15 9:21 AM, Malihe Hasanzadeh wrote: Thank you for your kind reply Which frame or which .pdb file is useful for starting calculation? That's only something you can answer, because you know what you've done and you know what the reviewer is asking. -Justin On 13 Sep 2015 17:40,

Re: [gmx-users] Binding energy calculation

On 9/13/15 8:56 AM, Malihe Hasanzadeh wrote: Hi I have simulated a protein-ligand with gromacs and submitted it. My reviewer asked me about calculation of binding energy. Which tutorial is acceptable and suitable for me to do it? Either free energy calculations (alchemical transformation)

Re: [gmx-users] struggles with cyclic peptides

Thank you very much Justine, now it making bond between first and last residue of amino acids but there as an extra oxygen atom is coming when i select any option other than None.but when i select None for the second terminals it shows an error as There is a dangling bond at at least one of