Re: [gmx-users] Question for bdc = xy

On 3/21/14, 4:43 PM, ookami a wrote: Hi, I just checked previous posts, they said increasing the size of z-direction to create a vaccum layer would be working. So I extend my z-direction with 3 times of the original box, when I run the pvt process, the vacuum layer disappeared. As you should

Re: [gmx-users] Question for bdc = xy

Hi, I just checked previous posts, they said increasing the size of z-direction to create a vaccum layer would be working. So I extend my z-direction with 3 times of the original box, when I run the pvt process, the vacuum layer disappeared. How could I modified my nvt.mdp file? From the pre posts,

Re: [gmx-users] Double parameters

Thank you, my system is not water, protein and ions. I have just mention them for example. My system is palmitic acid on NaCl surface, with water around. Problem is that I want use different set of palmitic acid charges actually for interaction between palmitic acid-NaCl and palmitic acid-water. I

Re: [gmx-users] Double parameters

No. Your protein parameters will be common to both, and your water-ion interactions are defined implicitly by whatever you'd choose for their interactions with protein. Moreover, you'd have no reason to suppose the combination would work. See http://www.gromacs.org/Documentation/Terminology/Force_F

[gmx-users] Double parameters

Hello dear gromacs users, lets say that we have 3 kinds of molecules in our system, for example water, protein and some ions. Is it possible to have one set Force field parameters of protein for protein-water and other for protein-ions interaction. Best Regards, Josip Lovrić -- Gromacs Users ma

Re: [gmx-users] Question for bdc = xy

On 3/20/14, 11:51 PM, ookami a wrote: Dear all: I'm trying to set up a bdc only with xy, so I edited my mdp file with changing the bdc =xyz to bdc = xy. However, I got a error message which is "Can not have Ewald with pbc=xy" Anyone know how to solve it? Per the manual, you can't use an Ewa

[gmx-users] Question for bdc = xy

Dear all: I'm trying to set up a bdc only with xy, so I edited my mdp file with changing the bdc =xyz to bdc = xy. However, I got a error message which is "Can not have Ewald with pbc=xy" Anyone know how to solve it? Thank you! -- Gromacs Users mailing list * Please search the archive at http:

Re: [gmx-users] User-defined potentials and meaning of table extension

With the group scheme, rlist constructs a neighbour list that is updated every nstlist steps. The relative size of rlist and (say) rcoulomb determines what that means, e.g. for having a buffer. If there is no potential modifier, then rcoulomb is not used in the kernel, so particles can diffuse past

Re: [gmx-users] User-defined potentials and meaning of table extension

On 3/21/14, 5:22 AM, Davide Mercadante wrote: Hello GMX users, I am testing the use of User-defined on a box of water and I came across the issue of table-extension option. I don't understand the use of it. If I specify a cutoff of 1 nm and then give a table extension of 0 nm then the cutoff

[gmx-users] User-defined potentials and meaning of table extension

Hello GMX users, I am testing the use of User-defined on a box of water and I came across the issue of table-extension option. I don't understand the use of it. If I specify a cutoff of 1 nm and then give a table extension of 0 nm then the cutoff will be 1 nm otherwise it will be cutoff+table-ext

Re: [gmx-users] Error: illegal instruction (core dumped)

On Mar 21, 2014 8:52 AM, "Ly Minh Nhat" wrote: > > http://gromacs.5086.x6.nabble.com/Guidance-on-how-to-install-Gromacs-5-0-beta2-td5014681.html > Hi all, > > When I was following the protein - ligand complex tutorial > (link< http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/

Re: [gmx-users] Question about topology construction.

No, but you can represent the molecule as truly linear using a virtual site to construct the position of the carbon from the oxygens. See past discussions on this list. Mark On Mar 21, 2014 8:40 AM, "sujith ks" wrote: > Hello Justin, > > Thanks for the response. In the EMP2 model the bond angl

Re: [gmx-users] Parameterisation of transition metal ions in gromacs

Please see http://www.gromacs.org/Documentation/How-tos/Parameterization On Mar 21, 2014 8:04 AM, "sukriti002" wrote: > > Hi, > > I have to do simulations in GROMACS with Vanadium ions (V+3,V+2,VO2+) but > non bonded parameters for vanadium are not present in gromos forcefield. > Can > anyone ple

Re: [gmx-users] Guidance on how to install Gromacs-5.0-beta2

Hi Pavan Kumar,Can you help me show the specific path to fftw? Thank you -- View this message in context: http://gromacs.5086.x6.nabble.com/Guidance-on-how-to-install-Gromacs-5-0-beta2-tp5014681p5015294.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users m

Re: [gmx-users] Multi-GPU calculation

On Mar 21, 2014 6:46 AM, "arrow50311" wrote: > > Hi, > > If I put in -gpu_id 0011, will it be the case that the gpu #0 from node 1 be > assigned to both rank 0 and rank 2? -gpu_id applies *per-node*, so 0011 is useful only with four ranks *per node*. Your original question wanted four ranks for

[gmx-users] Error: illegal instruction (core dumped)

http://gromacs.5086.x6.nabble.com/Guidance-on-how-to-install-Gromacs-5-0-beta2-td5014681.html Hi all, When I was following the protein - ligand complex tutorial (link), I met an error while running pdb2

Re: [gmx-users] Question about topology construction.

Hello Justin, Thanks for the response. In the EMP2 model the bond angle potential is of the harmonic form with the equilibrium angle 180. The only way I could include this in the .itp was though [angles]. The other two options [angle_restraints] and [angle_restraints_z] has a different form for

[gmx-users] Parameterisation of transition metal ions in gromacs

Hi, I have to do simulations in GROMACS with Vanadium ions (V+3,V+2,VO2+) but non bonded parameters for vanadium are not present in gromos forcefield. Can anyone please let me know how can I find parameters for vanadium or if anyone has found these parameters in literature? Also I tried to find