[gmx-users] how to obtain binding energy?

Dear Justin thanks for your time and attention in address http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html in Tutorial 3: Umbrella Sampling, in Step One, you said '' For p

[gmx-users] Simulated annealing with implicit water model

Hi There, I am going to run a simulated annealing simulation on a system with implicit water model. I have tried running simulated annealing with explicit water model. Please suggest and comment if anybody have tried such simulation in gromacs. with thanks, Vivek -- gmx-users mailing listgmx-

Re: [gmx-users] how to obtain binding energy?

shahab shariati wrote: Dear Justin thanks for your time and attention in address http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html in Tutorial 3: Umbrella Sampling ,

Re: [gmx-users] surface tension of monolayer

Sriprajak Krongsuk wrote: Dear Users, I have perform the simulation of nonionic surfactant monolayer at the water-air interface. I started to run the system at the NPT-ensemble for 10 ns until it reached to an equilibrium. After that I continued to run it at the NVT-ensemble for 8 ns (

Re: [gmx-users] g_order output is mirrored

dear all, after justin contribution, the SN2 chain plot now looks a little different: [image: sn2_new.png] http://imm.io/5JAZ the real matter of this e-mail, although i really appreciate the help justin has provided regarding the proper use of this tool, is the fact that my plot looks mirrored f

Re: [gmx-users] g_order output is mirrored

Igor Marques wrote: dear all, after justin contribution, the SN2 chain plot now looks a little different: sn2_new.png http://imm.io/5JAZ the real matter of this e-mail, although i really appreciate the help justin has provided regarding the proper use of this tool, is the fact that my plot

[gmx-users] P-LINCS and nstlist

Dear Users, I am not sure if I understood properly how P-LINCS should parametrized for simulation. In manual it's written that "one coordinate communication step is required for the initial LINCS step and one for each iteration"; so as coordinate communication is tightly binded to neighbor sea

Re: [gmx-users] P-LINCS and nstlist

Sławomir Stachura wrote: Dear Users, I am not sure if I understood properly how P-LINCS should parametrized for simulation. In manual it's written that "one coordinate communication step is required for the initial LINCS step and one for each iteration"; so as coordinate communication is ti

Re: [gmx-users] P-LINCS and nstlist

Thank you very much for such quick reply. I misunderstood the meaning of "iteration" . I've confused the iteration of LINCS algorithm with molecular simulation step. Best wishes, Slawek Wiadomość napisana przez Justin A. Lemkul w dniu 2011-05-18, o godz. 17:39: > > > Sławomir Stachu

Re: [gmx-users] P-LINCS and nstlist

> nstlist is more directly related to dt, and is often connected to the force > field, as well.  Values of 5-10 are standard.  Setting nstlist = 1 is > usually only necessary for EM, not MD.  Excessive updating of the neighbor > list can result in performance loss, I believe. Not only can, but it

Re: [gmx-users] recovering topology

Hey Rama,    I've lost my topology before, so I've used pdb2gmx to make new ones if I had the .gro file. Also I think that command can use an input .tpr file as well. Maybe that would help, Taylor --- On Tue, 5/17/11, Ramachandran G wrote: From: Ramachandran G Subject: [gmx-users] recoverin

[gmx-users] RHEL OS, g_mdrun

Dear Gromacs Users, I am trying to run a gromacs mdrun job (pbs script) on the cluster (RHEL operating system) using the recently installed gromacs version 4.5.3, but i think i could not run it paralleled on the nodes, as it is taking a long time to finish the job. The information regarding the

Re: [gmx-users] RHEL OS, g_mdrun

ram bio wrote: Dear Gromacs Users, I am trying to run a gromacs mdrun job (pbs script) on the cluster (RHEL operating system) using the recently installed gromacs version 4.5.3, but i think i could not run it paralleled on the nodes, as it is taking a long time to finish the job. The inform

Re: [gmx-users] RHEL OS, g_mdrun

Dear Justin, Thanks for the suggestion. Do we need to install FFTW libraries also while installing gromacs as I think FFT pack got installed as default when the gromacs is installed by the system admin using yum i.e. yum install gromacs. yum install gromacs_openmpi / yum install gromacs_mpich2,

Re: [gmx-users] RHEL OS, g_mdrun

Hi, You should really use fftw, it's *much* faster! (Btw: fftpack comes with Gromacs.) I'm not sure what versions of Gromacs are available through the RHEL packages, but as installing from source is not very difficult (especially for a sysadmin) you might be better of with getting a fresh install

Re: [gmx-users] RHEL OS, g_mdrun

On 2011-05-18 03:51:00PM -0500, Szilárd Páll wrote: > Hi, > > You should really use fftw, it's *much* faster! (Btw: fftpack comes > with Gromacs.) > > I'm not sure what versions of Gromacs are available through the RHEL > packages, but as installing from source is not very difficult > (especially

[gmx-users] (no subject)

http://www.dentalaparecida.com.br//images/mywork.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! P

[gmx-users] lipids per area charmm36 popc

Hello I am trying to equilibrate from scratch a 196 POPC bilayer using Tom's charmm36.ff. My box has a lot of TIPS3P (charmm) waters above and below the membrane with a box size around 8.5x8.5x12.7. My desired end state is to only use the setup for g_membed but I'd also like to get a pristine t

Re: [gmx-users] lipids per area charmm36 popc

Peter C. Lai wrote: Hello I am trying to equilibrate from scratch a 196 POPC bilayer using Tom's charmm36.ff. My box has a lot of TIPS3P (charmm) waters above and below the membrane with a box size around 8.5x8.5x12.7. My desired end state is to only use the setup for g_membed but I'd also l

Re: [gmx-users] P-LINCS and nstlist

On 19/05/2011 1:39 AM, Justin A. Lemkul wrote: Sławomir Stachura wrote: Dear Users, I am not sure if I understood properly how P-LINCS should parametrized for simulation. In manual it's written that "one coordinate communication step is required for the initial LINCS step and one for each

Re: [gmx-users] lipids per area charmm36 popc

I agree with Justin, 1 ns is just nowhere near long enough. Something in the tens of ns should do it. I have used pretty much the same settings as you (using the CHARMM water, as you have) and get APL's matching those published in the Klauda paper. You are correct that you should not use the d

[gmx-users] reg centre of mass in SMD

Thank you Dr Justinj,     To do SMD should i create centre of mass of my reference (protein) and pull group (ligand)? if i  need to create , which tool of gromacs generate to be used .? How to include this center of mass in SMD  .mdp files Thanks in Advance -- gmx-us

Re: [gmx-users] lipids per area charmm36 popc

On 2011-05-19 00.31, Thomas Piggot wrote: I agree with Justin, 1 ns is just nowhere near long enough. Something in the tens of ns should do it. I have used pretty much the same settings as you (using the CHARMM water, as you have) and get APL's matching those published in the Klauda paper. You a