[gmx-users] negative steps from tpbconv

Hi, I am trying to extend the run time in tpr file to include more steps using tpbconv… This has worked well for a while, but now I get two errors… One is that it writes “now -207466 steps”, which doesn’t make sense – why is this number negative… Also, “You've simulated long enough. Not

RE: [gmx-users] negative steps from tpbconv

extension you need ... you can give trr and edr files to grompp so the tpr file is a continuation of earlier one ... XAvier. On Feb 24, 2011, at 11:50 AM, Jesper Sørensen wrote: Hi, I am trying to extend the run time in tpr file to include more steps using tpbconv… This has worked well

RE: [gmx-users] negative steps from tpbconv

assle with extensions. > > Cheers, > > Tsjerk > > 2011/2/24 Jesper Sørensen : >> Hi Xavier, >> >> >> >> That worked, thanks… Would it also work if I just gave the old >> state.cpt file to mdrun? >> >> >> >> Jesper >&g

Re: [gmx-users] Simulation of POPC in water using CHARMM27

I would say looking at the CHARMM force field website would be the first thing to do. Google: CHARMM FORCE FIELD, and you should get the relevant pages... The articles are listed on the website... /Jesper On May 11, 2012, at 9:19 PM, Shima Arasteh wrote: > Dear gmx users, > > Anybody can gui

[gmx-users] switching and shifting in GMX 4.6 on GPUs

Dear GMX developers, Thanks so much for the GMX 4.6 release. Testing on GPUs has shown impressive speed-ups. I have a question however, regarding the missing "switching and shifting" for non-bonded interactions. I looked at the developer zone website and saw this comment below: http://www.grom

Re: [gmx-users] switching and shifting in GMX 4.6 on GPUs

Hi Berk, I am running membrane simulations using both the CHARMM36 and MARTINI v. 2.1 parameters. So both those cut-off treatments are important to me, but if there are ways around it I'd be happy to explore them to be able to use the GPUs. The place it would be most effective would probably be

Re: [gmx-users] switching and shifting in GMX 4.6 on GPUs

Hi Berk and others, Sorry it has been a long time since this issue was posted, but I got side-tracked from this issue with other projects. And I want to make sure I understand this correctly before venturing into more simulations. So this gets a little long winded, but I hope you will help me f

Re: [gmx-users] switching and shifting in GMX 4.6 on GPUs

Hi Richard, Thanks for the reply. It was very helpful. I've looked at the updated manual regarding the x-modifiers and that cleared it up for me. Best regards, Jesper On Apr 13, 2013, at 4:48 AM, "Broadbent, Richard" wrote: > > > On 12/04/2013 21:50, "Jesp

Re: [gmx-users] ATP/Mg+2 parameters

HI George, For AMBER you can use the parameters by Meagher, Redman, and Carlson they were developed with this force field in mind. They are available on the Bryce group amber parameter database below, although you will have to port them to Gromacs format yourself. http://www.pharmacy.manchester

Re: [gmx-users] where can be obtain circled lipids bilayer?

The shape is a sphere not a circle, what the picture is showing is a cut through the vesicle. Have you googled lipid vesicles? I don't know of a place that will have template systems like this for you. But you should be able to get these by making a large enough system with enough lipids to form

Re: [gmx-users] where can be obtain circled lipids bilayer?

Is it really fair to call this a circle? A circle is a 2D object. What you are describing here is a disc. Jesper On May 2, 2013, at 1:13 PM, Mirco Wahab wrote: > There are indeed "circular lipid bilayer structures" possible, but they are > not found very frequently. See here for example: >

Re: [gmx-users] constant protonation state MD

Shahid, This must be system dependent then because there are experimental methods, e.g. NMR and CD, that can help determine the secondary structure of proteins/peptides are various pH ranges. What is your system? A peptide? A globular protein? Best, Jesper On May 3, 2013, at 7:33 PM, shahid na

Re: [gmx-users] constant protonation state MD

invalidate your modeling observations. Best of luck! Jesper On May 5, 2013, at 9:47 PM, shahid nayeem wrote: > It is a peptide. > Shahid > > > On Mon, May 6, 2013 at 4:46 AM, Jesper Sørensen wrote: > >> Shahid, >> >> This must be system dependent then be

Re: [gmx-users] question about energygrps

Huyjin, If you look in your log file from the rerun you will see that when running using the GPU, energy groups are ignored or unused for energy reporting. Thus for this to work you need to run it on the CPUs. This is what I get in my output md.log when trying the same thing... >> NOTE: With GP

Re: [gmx-users] version 4.5.5 GPU with gtx670 and cuda 4.2

Hi Sebastian, This may just be my take, but the Keppler Cards are not supported yet as far as I understand it. They are at least not mentioned on the GROMACS GPU page in the Supported Cards section - granted that page has not been updated in quite a while. Specifically, does this work when you

Re: [gmx-users] version 4.5.5 GPU with gtx670 and cuda 4.2

t forcing the device does work but it does not seem to > be the case. > Probably I have to wait for an update or the 4.6 version. > > All the best, > > Sebastian > > On 10/29/2012 05:50 PM, Jesper Sørensen wrote: >> Hi Sebastian, >> >> This may just