Re: [gmx-users] Early registration period ending for 2013 GROMACS USA Workshop and Conference

Hi Prof. Shirts, I am sure that I speak for a lot of GROMACS users when I say that I want to attend the workshop, but I cannot. I would be willing to pay the whole workshop fee (and more) if you could kindly video the whole workshop and make it available to us. Thank you. On Tue, Aug 20, 2013 at

[gmx-users] Early registration period ending for 2013 GROMACS USA Workshop and Conference

Dear GROMACS users- I'd like to remind you all about the 2013 GROMACS USA Workshop and Conference at the University of Virginia Sept 13th-15th. There are still registration slots available, but the early registration deadline of Aug 22nd is coming up in just a few days; after the 22nd, the regist

Re: [gmx-users] NPT, freezegroups and Position Restraints.

Interestingly, removing position restraints does not have much of an impact. On Mon, Aug 19, 2013 at 1:40 PM, Justin Lemkul wrote: > > > On 8/19/13 11:58 AM, HANNIBAL LECTER wrote: > >> I usually use 1.0 for my systems and I get the correct values for the >> temperatures. If I couple it as a sy

Re: [gmx-users] want to apply electric field in membrane system

On 8/19/13 4:56 PM, sudipta wrote: Basically, few litterateurs suggested that the electric field generates a stable water pore inside a membrane. I am motivated by that fact and try to create a water pore for my system. I found few litterateurs on this topic. However, I am based on a protocol

Re: [gmx-users] want to apply electric field in membrane system

Basically, few litterateurs suggested that the electric field generates a stable water pore inside a membrane. I am motivated by that fact and try to create a water pore for my system. I found few litterateurs on this topic. However, I am based on a protocol as suggested by Marrinik et al (plos co

Re: [gmx-users] regarding umbrella sampling

On 8/19/13 4:35 PM, Abed Askari wrote: thank you for your reply. because without the position restraint the cylindrical shape of my molecule (CNT) changes. is it reasonble to use umbrella sampling along with the position restraint in y and z directions? Possibly, but it sounds more lik

Re: [gmx-users] regarding umbrella sampling

thank you for your reply. because without the position restraint the cylindrical shape of my molecule (CNT) changes. is it reasonble to use umbrella sampling along with the position restraint in y and z directions? - Original Message - From: Justin Lemkul To: Abed Askari ; Discussi

Re: [gmx-users] want to apply electric field in membrane system

On 8/19/13 3:15 PM, sudipta wrote: Thanks for your reply. Is that means my electric field is too high? Should I reduce the strength of electric field? Which value is suitable for the electric field? Is my protocol for controlling area and application of The answers here all depend on what you

Re: [gmx-users] regarding umbrella sampling

On 8/19/13 4:03 PM, Abed Askari wrote: Dear gmx-users I want to use umbrella sampling to calculate the PMF between two molecules and x-axis is the reaction coordinate. would you please tell me I can use position restraint in y and z directions for the pulling group or not? Why would you

[gmx-users] regarding umbrella sampling

Dear gmx-users I want to use umbrella sampling to calculate the PMF between two molecules and x-axis is the reaction coordinate. would you please tell me I can use position restraint in y and z directions for the pulling group or not?  any help would be appreciated. -- gmx-users mailing list

[gmx-users] regarding US

ear gmx-users I want to use umbrella sampling to calculate the PMF between two molecules and x-axis is the reaction coordinate. would you please tell me I can use position restraint in y and z directions for the pulling group or not?  any help would be appreciated. -- gmx-users mailing list

Re: [gmx-users] want to apply electric field in membrane system

Thanks for your reply. Is that means my electric field is too high? Should I reduce the strength of electric field? Which value is suitable for the electric field? Is my protocol for controlling area and application of electric field across the membrane fine. By the way I had modeled my system usi

Re: [gmx-users] PMF calculation

On 8/19/13 12:27 PM, Za Pour wrote: Dear gmx-users Iwould like to calculate the PMF between two nanotubes covered with some molecules. To do that, one nanotube has to be held fixedly and another one is supposed to be moved as a rigid entity. To generate configurations, for fixed nanotube

Re: [gmx-users] want to apply electric field in membrane system

On 8/19/13 1:02 PM, sudipta wrote: I am coming across the similar problem. In my case I was using semiisotropic pressure and set the compressiblity in x/y as 0.0 to construct the NPAT ensemble. The area in xy plane is not changing but the dimension of z has changed. The system behaves well with

Re: [gmx-users] NPT, freezegroups and Position Restraints.

On 8/19/13 11:58 AM, HANNIBAL LECTER wrote: I usually use 1.0 for my systems and I get the correct values for the temperatures. If I couple it as a system, the low T-CNT yields a different value than the target 300K. What about changing the integrator to md? What happens if you remove restr

Re: [gmx-users] want to apply electric field in membrane system

I am coming across the similar problem. In my case I was using semiisotropic pressure and set the compressiblity in x/y as 0.0 to construct the NPAT ensemble. The area in xy plane is not changing but the dimension of z has changed. The system behaves well without the application of electric field o

[gmx-users] Re: GPU version of Gromacs

Hi Grita, Yes it is. You need to re-compile a GPU version of Gromacs from source codes. You also need to use Verlet cutoff-scheme. That is, place a new line like cutoff-scheme = Verlet in your mdp file. Finally, run the GPU version of mdrun, adding a parameter -gpu_id 0if you have o

[gmx-users] PMF calculation

Dear gmx-users Iwould like to calculate the PMF between two nanotubes covered with some molecules. To do that, one nanotube has to be held fixedly and another one  is supposed to be moved as a rigid entity. To generate configurations,  for fixed nanotube  I used position restraints in all direc

Re: [gmx-users] NPT, freezegroups and Position Restraints.

I usually use 1.0 for my systems and I get the correct values for the temperatures. If I couple it as a system, the low T-CNT yields a different value than the target 300K. On Mon, Aug 19, 2013 at 11:48 AM, Justin Lemkul wrote: > > > On 8/19/13 11:42 AM, HANNIBAL LECTER wrote: > >> Thanks Justi

Re: [gmx-users] NPT, freezegroups and Position Restraints.

On 8/19/13 11:42 AM, HANNIBAL LECTER wrote: Thanks Justin. I am not sure how it is fundamentally incompatible. Especially with refcoord-scaling = com. Can you please provide with some more input on that? The refcoord-scaling option doesn't matter with frozen groups. Anything that is froze

Re: [gmx-users] NPT, freezegroups and Position Restraints.

I am performing NPT here but this artifact is independent of whether one is using NPT or NVT. On Mon, Aug 19, 2013 at 11:42 AM, HANNIBAL LECTER < hanniballecte...@gmail.com> wrote: > Thanks Justin. > > I am not sure how it is fundamentally incompatible. Especially with > refcoord-scaling = com.

Re: [gmx-users] gromacs installation in mac osx 10.8

This is a known issue (e.g. http://bugzilla.gromacs.org/issues/1021). I have literally no idea if CUDA is even available for this hardware. You do have the option of cmake -DGMX_CPU_ACCELERATION=SSE4.1, which might be imperceptibly slower than AVX given the use of a GPU. There are rumours of OpenM

Re: [gmx-users] NPT, freezegroups and Position Restraints.

Thanks Justin. I am not sure how it is fundamentally incompatible. Especially with refcoord-scaling = com. Can you please provide with some more input on that? The outputs are from g_energy. Here is the .mdp file. define = -DPOSRES_CNT constraints = all-bonds pbc

Re: [gmx-users] NPT, freezegroups and Position Restraints.

On 8/19/13 11:32 AM, HANNIBAL LECTER wrote: Hi, I have been performing NPT simulations with CNT, Protein and water. However, when I freeze the CNT, the system crashes with segmentation fault. That is to be expected. Frozen atoms and pressure coupling are fundamentally incompatible. If

[gmx-users] gromacs installation in mac osx 10.8

Dear All, I am trying to install Gromacs 4.6.3 in my Macbook pro retina with 10.8. It has a GPU (NVIDIA GeForce GT 650M 1024 MB). I got really hopeful to use the GPU and the i7 (threaded 8 cores) for calculations. But I am finding it difficult to install Gromacs . Mac osx 10.8 comes with cla

[gmx-users] NPT, freezegroups and Position Restraints.

Hi, I have been performing NPT simulations with CNT, Protein and water. However, when I freeze the CNT, the system crashes with segmentation fault. If I use position restraints, the temperature of the system is lower than what it is expected to be. I am using sd coupling. If I couple the protein

Re: [gmx-users] Convert CNS .top into a GROMACS .itp for a small ligand?

Okay, clearer now. Will see what I can do. Thanks a lot for your help. Massimo 2013/8/19 Justin Lemkul > > > On 8/19/13 10:22 AM, massimo sandal wrote: > >> 2013/8/19 Justin Lemkul >> >> >>> >>> An .itp is just a topology, so it's identical to a .top except that it >>> does not have syst

Re: [gmx-users] Convert CNS .top into a GROMACS .itp for a small ligand?

On 8/19/13 10:22 AM, massimo sandal wrote: 2013/8/19 Justin Lemkul An .itp is just a topology, so it's identical to a .top except that it does not have system-level directives and does not #include a parent force field. Manual sections 5.7.1 and 5.7.2 describe the relevant contents.

Re: [gmx-users] Convert CNS .top into a GROMACS .itp for a small ligand?

2013/8/19 Justin Lemkul > > >> > An .itp is just a topology, so it's identical to a .top except that it > does not have system-level directives and does not #include a parent force > field. Manual sections 5.7.1 and 5.7.2 describe the relevant contents. > > > I know - just to be sure we're under

Re: [gmx-users] Convert CNS .top into a GROMACS .itp for a small ligand?

On 8/19/13 6:45 AM, massimo sandal wrote: Hi Justin, I have a small ligand that apparently PRODRG gets wrong -it completely alters the structure, borks angles etc. making it not what we want. So I used xplo2d to obtain a suitable set of files that I used for docking (with HADDOCK). Intere

Re: [gmx-users] Query regarding membrane-peptide simulation

On 8/19/13 6:27 AM, Aditya Padhi wrote: Dear Gromacs Users, I am new to Gromacs. Recently, I started working with Gromacs. I want to study the mechanism of interaction of certain peptides that are known to interact with membranes such as DOPC, POPC and so on. I have two sets of peptide

Re: [gmx-users] GPU version of Gromacs

On 8/19/13 5:38 AM, grita wrote: Hey guys, Is it possible to make a SD simulation with using the pull code in the GPU version of Gromacs? Have you tried it? -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceut

Re: [gmx-users] want to apply electric field in membrane system

On 8/18/13 11:21 PM, udels can wrote: Hi All, I am facing a strange problem when I was trying to apply electric field across a membrane, DMPC, water and ion system. To apply electric field across the membrane (in +ve z direction), I had used NPzAT ensemble, where the Pz is the constant pressu

Re: [gmx-users] question

So open your terminal app, type sudo apt-get install gromacs type your password at promt volia, gromacs is installed 2013/8/19 > I am a new user. > I have aquestion about install gromacs. > I want to install gromacs. > May guide me for install gromacs? > -- > gmx-users mailing listgmx-users

Re: [gmx-users] question

Hi! GROMACS is in the standart Ubuntu repo, so you can simply type sudo apt-get install gromacs in your terminal and after successfull installation call all gromacs utilities from the command line If you need some special versions of GROMACS or if you want to install it from source, you can take a

[gmx-users] question

I am a new user. I have aquestion about install gromacs. I want to install gromacs. May guide me for install gromacs? -- 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/

Re: [gmx-users] Convert CNS .top into a GROMACS .itp for a small ligand?

Hi Justin, >> I have a small ligand that apparently PRODRG gets wrong -it completely >> alters the structure, borks angles etc. making it not what we want. So I >> used xplo2d to obtain a suitable set of files that I used for docking >> (with >> HADDOCK). >> >> > Interesting. The hallmark of the

[gmx-users] question

Hi I am a new user. I have a questin for install gromacs on ubuntu. May guide me for install gromacs? -- 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 po

[gmx-users] Query regarding membrane-peptide simulation

Dear Gromacs Users, I am new to Gromacs. Recently, I started working with Gromacs. I want to study the mechanism of interaction of certain peptides that are known to interact with membranes such as DOPC, POPC and so on. I have two sets of peptides; out of which, one set of peptides are know

[gmx-users] Coordination number

Dear Gromacs Users, I have a query about the g_rdf utility. I have two different systems of water with Ionic Liquid 1 and Ionic Liquid 2. When I plot the rdf using g_rdf -f x_gro.pdb -s x.pdb -n rdf.ndx -o rdf1.xvg/rdf2.xvg -cn rdf1_cn.xvg/rdf2_cn.xvg -rdf res_com where rdf1/rdf2 is for water di

[gmx-users] GPU version of Gromacs

Hey guys, Is it possible to make a SD simulation with using the pull code in the GPU version of Gromacs? Best, grita -- View this message in context: http://gromacs.5086.x6.nabble.com/GPU-version-of-Gromacs-tp5010581.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -

[gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?

Dear Richard, many thanks for this clarification. Best, grita -- View this message in context: http://gromacs.5086.x6.nabble.com/what-is-sigma-in-gromacs-the-radius-of-a-sphere-or-the-diameter-of-a-sphere-tp5010517p5010580.html Sent from the GROMACS Users Forum mailing list archive at Nabble.