[gmx-users] Re: Conserved energy ("Conserved En.") in NVT simulation

Thanks for your comments Mark, If I understood correctly, you are saying, that maybe linear drift in "Conserved En." could indicate conservation of that quantity, which we actually should be interested. However, I made meanwhile some additional calculations and noticed that drift in "Conserved

[gmx-users] Conserved energy ("Conserved En.") in NVT simulation

semble may introduce drift in "Conserved En.", when NVT ensemble is used? Or is it just purely (only reason for drift) indication that some temperature coupling methods"work better" than others in this sense? Regards, Janne Hirvi-- gmx-users mailing listgmx-users@gromac

[gmx-users] Test-set problem with Gromacs 3.3.3

differences? Thanks for your help, Janne -- Janne Hirvi, MSc(Physical Chemistry), Researcher University of Joensuu, Department of Chemistry, P.O.Box 111 80101 Joensuu, FI Tel: +358 13 2514544 & +358 50 3474223 E-mail: [E

[gmx-users] Re: Pbc and Com in simulation video

r your time and help in advance, Janne ------ Janne Hirvi, MSc(Physical Chemistry), Researcher University of Joensuu, Department of Chemistry, P.O.Box 111 80101 Joensuu, FI Tel: +358 13 2514544 & +358 50 3474223 E-mai

[gmx-users] Pbc and Com in simulation video

-- Janne Hirvi, MSc(Physical Chemistry), Researcher University of Joensuu, Department of Chemistry, P.O.Box 111 80101 Joensuu, FI Tel: +358 13 2514544 & +358 50 3474223 E-mail: [EMAIL PROTECTED] & [EMAIL P

[gmx-users] Re: Potential energy positive. Can be?

Hi! I am just wondering that why the potential energy couldnt be positive? It must have been negative after minimization at 0 K, but in the simulation at specific temperature the energy of the intramolecular interactions increases increasing the potential energy... Janne > Dear Mark, > Thank you

Re: [gmx-users] Problems about sigma & epsilon to C6 & C12

Hello! Could you please help me to understand solution as well? I just plotted these functions so that I combined sigma and epsilon values using rule 3 sigma(ij)=(sigma(i)*sigma(j))^(1/2) epsilon(ij)=(epsilon(i)*epsilon(j))^(1/2) and corresponding C6 (4*epsilon*sigma^6) and C12 (4*epsilon*sigma^

[gmx-users] Re: Energy conservation of crystal surface (specification)

>>Hello again! >> >>In earlier message I said that double precision (actually same with single >>precision) simulation with 4 processors terminates pretty soon and distinct >>momentary increases in energy at intervals of 0.05ps can be observed until >>that point. >> >>Now I have made more tests an

[gmx-users] Energy conservation of crystal surface (specification)

Hello again! In earlier message I said that double precision (actually same with single precision) simulation with 4 processors terminates pretty soon and distinct momentary increases in energy at intervals of 0.05ps can be observed until that point. Now I have made more tests and noticed that a

[gmx-users] Energy conservation of crystal surface

Hello gmx-users! Sorry that I am bothering you all the time with energy conservation issues but this time I have problems with a crystal surface consisting of infinite polymer chains. I think that simulation and interaction parameters employed should be conserving the total energy: time step o

[gmx-users] RE: Energy conservation in collision

Hello gmx-users! I am still struggling with the energy conservation in the system where a water droplet (consisting of rigid molecules) collides with a frozen structured surface. The total energy is well conserved at the beginning of NVE simulation when the droplet is appro

[gmx-users] RE: Energy conservation in collision

>>Hello gmx-users! >> >>I am still struggling with the energy conservation in the system where a >>water droplet (consisting of rigid molecules) collides with a frozen >>structured surface. The total energy is well conserved at the beginning of NVE >>simulation when the droplet is approaching the

[gmx-users] Energy conservation in collision

Hello gmx-users! I am still struggling with the energy conservation in the system where a water droplet (consisting of rigid molecules) collides with a frozen structured surface. The total energy is well conserved at the beginning of NVE simulation when the droplet is approaching the surface and o

[gmx-users] Re: Energetics in collision

First thanks for your reply! >>Hello gmx-users! >> >>I am studying the effect of impact velocity of a water droplet in collision >>with a frozen surface in NVE ensemble. A droplet has extra translational >>energy,which corresponds to a specific velocity, in addition to thermal energy >>at 300K. >>

[gmx-users] Energetics in collision

Hello gmx-users! I am studying the effect of impact velocity of a water droplet in collision with a frozen surface in NVE ensemble. A droplet has extra translational energy, which corresponds to a specific velocity, in addition to thermal energy at 300K. I supposed that at the collision extra tra

[gmx-users] Heat transfer in collision

Hello gmx-users! I am trying to simulate the effect of impact velocity of a water droplet in collision with a surface. Translational energy of the water droplet is expected to turn into the heat of the droplet and the surface in collision when NVE ensemble is used (as in real world). Earlier sim

[gmx-users] Re: Frozen atoms and energy group exclusion

> Hello, > Thanks for the fast response. I went through my dppc.itp file and > chose > atoms such that the group of frozen atoms has a net charge of 0 as does the > rest of the molecule. When running this through grompp, the error before > about the atoms being in different charge groups is

[gmx-users] 5xRe: Impact velocity

recalculate > the energies (including temperature). > Bob > > On 2/22/07, Janne Hirvi <[EMAIL PROTECTED]> wrote: > > Hi! > > > > Still one check because g_traj even with com -option actually gives total > > temperature not the center of mass temperature as y

[gmx-users] 4xRe: Impact velocity

temperature coupling while temperature given by g_energy is smaller than the one given by g_traj? Thanks for your time and help, Janne > Janne Hirvi wrote: > > Hello David and other gmx-experts! > > > > I havent yet been able to extract thermal motion contribution for >

[gmx-users] 3xRe: Impact velocity

g_energy and g_traj temperatures but is it the exact method? Thanks for your time, Janne > Janne Hirvi wrote: > > Thanks for your quick replies David and Bob! > > > > I was icefishing all the weekend and wasnt able to comment on your > suggestions > > earlier but y

[gmx-users] Re: Impact velocity

ty to the droplet, and then study the collision > at constant energy. The real collision probably doesn't take place at > constant temperature anyway. The surface probably heats up a little > upon colliding with the water droplet. Anyway, Just my thoughts... > Bob > > On 2/16/0

[gmx-users] Impact velocity

Hello! I am trying to generate center of mass velocity to a water droplet so that I could study the effect of impact velocity in the collision with a solid surface. First, I simply tried to generate extra velocity and compensate the increase in temperature by decreasing other velocity components.

[gmx-users] Re: fudgeQQ (again ...)

-4 Coulombic (or 1-4 Lennard-Jones) interactions included in your case. Janne > Thanks, Janne! > > No, I tried not having [pairs] or having empty [pairs] because the manual > says it's not necessary if "generate pairs" = "yes". > > Lianqing > >

[gmx-users] Re: fudgeQQ (again ...)

Hello! Just a simple question - Do you have [pairs]-section in your topology file? Janne > Dear GMX-users, > > Here are a followup and more details for my problem. I really hope to get > through this, so I can move on ... > > I report the electrostatic energy (Uq, kJ/mol) for a molecule using

[gmx-users] Re: relative weight between the direct space sum and reciprocal space sum

Hello! Yes, I think you cant set the beta parameter directly but you can calculate it from the equation erfc(beta*r)/r = ewald_rtol at the cut-off (=rcoulomb) and so set the ewald_rtol parameter to match to the wanted beta parameter. Janne > HI, > > according to the 3.2 gromacs manual , t

[gmx-users] Gravity in MD-simulations

visualize real gravity effects within the time-scale of MD-simulations? Thanks for any help, Janne -- Janne Hirvi, MSc(Physical Chemistry), Researcher University of Joensuu, Department of Chemistry, P.O.Box 111 80101 Joensuu, FI

Re: Re: [gmx-users] [Fwd: Energy conservation]

culations more > accuracy may be needed. > I have made bulk simulations and wetting simulations (water droplet spreading on a surface) and I have to admit that I dont know what makes free energy calculations so special? I meant that even with perfect PME parameters we can't achieve energ

[gmx-users] Re: confused about rcoulomb<=rlist

Hello! I was delighted to see this conversation about the use of rcoulomb and rlist. I made my own three test simulations with bulk water (1372 SPC/E molecules & 2fs & 200ps) using double precision compilation with parameters nstlist = 5 vdwtype = Switch rvdw_switch = 1.0 rvdw

[gmx-users] 4xRE: COM motion removal (further clarification)

ion with comm_mode=none but without lateral motion on surface). However when removing COM motion of water droplet I have to use much larger nstcomm (>2000) to see as quick spreading as in case of comm_mode=none or comm_mode=linear with nstcomm=100. > Berk. Thanks again for helping me!!

[gmx-users] Re: Re: COM motion removal

clear spreading) so that I actually see that droplet spreads but I wont see large lateral motion of COM? Do you have a comment on that? > > Anyhow, set it to 1 you will not notice the difference in performance. > > Berk. Thanks, Janne ---

[gmx-users] COM motion removal

teps but I reset the development of net momentum for a while? Thanks for any comments in advance! Janne ------ Janne Hirvi, MSc(Physical Chemistry), Researcher University of Joensuu, Department of Chemistry, P.O.Box 111 80101 J

[gmx-users] NS in PME

gy conservation, and recommended for all PME runs. Thanks for any comments in advance! Janne ------ Janne Hirvi, MSc(Physical Chemistry), Researcher University of Joensuu, Department of Chemistry, P.O.Box 111 80101 Joensu

[gmx-users] Re: NS in PME

uld use parameters so that rlist=rcoulomb. Can you comment on this because Berk may have noted your request or then he have had no time to do that? Or is it so trivial that I should find explanation from some trivial text book? Thanks, Janne > Janne Hirvi wrote: > > Hello David! >

[gmx-users] NS in PME

someone could get the picture that rlist should be equal to rcoulomb and there are also different kind of opinions on mailing list? Thanks for any comments in advance! Janne ------ Janne Hirvi, MSc(Physical Chemistry

[gmx-users] rlist in PME

ecific reason for that? Thanks for any comments! Janne ------ Janne Hirvi, MSc(Physical Chemistry), Researcher University of Joensuu, Department of Chemistry, P.O.Box 111 80101 Joensuu, FI Tel: +358 13 2514544 & +358

[gmx-users] Energy conservation

at I have complete energy conservation? Thanks for any comments! Janne ------ Janne Hirvi, MSc(Physical Chemistry), Researcher University of Joensuu, Department of Chemistry, P.O.Box 111 80101 Joensuu, FI Tel: +358 13 2514544