[gmx-users] Measuring distance to the nearest image

Hi all, I am trying to measure the distance between the COM of two side chain functional groups across the periodic boundary to their nearest image rather than across the unit cell itself. I have tried several gromacs distance commands with no success and more at random as I trawl through the

Re: [gmx-users] Measuring distance to the nearest image

se on behalf of Anthony Nash" wrote: Hi all, I am trying to measure the distance between the COM of two side chain functional groups across the periodic boundary to their nearest image rather than across the unit cell itself. I have tried several gromacs distance comman

Re: [gmx-users] Measuring distance to the nearest image

Hi Alexandr, Those were my thoughts also. I was just hoping there was something out there already written to save me time. Thanks Anthony Dr Anthony Nash BSc (Hons) MSc MSc PhD MRSC Department of Physiology, Anatomy & Genetics Oxford University OX1 3PT UK On 19/12/2017 1

Re: [gmx-users] Measuring distance to the nearest image

ehalf of Mark Abraham" wrote: Hi This is exactly what two well chosen selections should produce, given a tpr and the PBC option. What have you tried that didn't work as you expected? Mark On Mon, Dec 18, 2017, 5:23 PM Anthony Nash wrote:

Re: [gmx-users] Measuring distance to the nearest image

ple where the structure comes from a single frame would be a useful thing to explore whether the code is working correctly. I don't think the composition of the index groups should matter, but I can't see how the code wouldn't work correctly. Mark

Re: [gmx-users] Speed up simulations with GROMACS with virtual interaction sites

https://distributedscience.wordpress.com/2017/06/19/speeding-up-md-simulations-in-explicit-solvent/ Kind regards Anthony Nash PhD MRSC Department of Physiology, Anatomy, and Genetics University of Oxford From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.or

Re: [gmx-users] Speed up simulations with GROMACS with virtual interaction sites

Hi Stephane, I hope it is useful. I am afraid I have very little charmm experience. I used the approach posted for an amber ff. I hope someone can help with the charmm aspect. Kind regards Anthony Nash PhD MRSC Department of Physiology, Anatomy, and Genetics University of Oxford

Re: [gmx-users] Predict Physical Properties of Novel Proteins

just as time consuming (and sometimes more so) and fraught with just as many difficulties as the in vivo aspects to table top molecular biology (growing cells, cloning, expressing and performing a particular assay). Thus, using MD as a filter is quite bold. Dr Anthony Nash PhD MRSC

[gmx-users] Performing energy minimisation for an alanine scan

ters sufficient for modelling stateB upon immediate execution of an energy minimisation (and NPT/NVT dynamics)? I've had very little experience with the lambda implementation in gromacs and I turn to more experience. Many thanks Anthony Kind regards Anthony Nash PhD MRSC Department of Physiolog

Re: [gmx-users] Performing energy minimisation for an alanine scan

't be pushing each structure for very long after equilibrium. Thanks both Anthony Kind regards Anthony Nash PhD MRSC Department of Physiology, Anatomy, and Genetics University of Oxford From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of

Re: [gmx-users] Performing energy minimisation for an alanine scan

Thanks Mark, sounds like a good idea. Kind regards Anthony Nash PhD MRSC Department of Physiology, Anatomy, and Genetics University of Oxford From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark Abraham Sent: 08 July 2018 22:38:41 To: gmx

Re: [gmx-users] Performing energy minimisation for an alanine scan

e, is this a concern? Thanks Anthony Kind regards Anthony Nash PhD MRSC Department of Physiology, Anatomy, and Genetics University of Oxford From: Anthony Nash Sent: 08 July 2018 22:45:39 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Performing energy minimis

Re: [gmx-users] Performing energy minimisation for an alanine scan

ck between five projects today with little room to think. Thanks Anthony Kind regards Anthony Nash PhD MRSC Department of Physiology, Anatomy, and Genetics University of Oxford From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Abhishek Ach

Re: [gmx-users] Performing energy minimisation for an alanine scan

enion, solvate etc., steps immediately with the provided .pdb file. Are you suggesting I run a pdb2gmx over the 600+ .pdb files using a modified (as per your emails below) FF? If so I would imagine that would be easy enough to automate. Thanks Anthony Kind regards Anthony Nash PhD

Re: [gmx-users] Performing energy minimisation for an alanine scan

Thanks for your help. I completely agree with your points raised. I've dropped the pmx developers and email, hopefully there will be a little bit of wiggle room for me to move forward on this project some time soon. Thanks again, and to Mark and Justin. Anthony Kind regards Anthony

[gmx-users] Segmentation fault using gmx solvent

sure why. Suggestions are hugely appreciated. Please let me know what information I can provide to help. Thanks Anthony Kind regards Dr Anthony Nash PhD MRSC Senior Research Scientist Nuffield Department of Clinical Neurosciences RMCR Kellogg College University of Oxford http://www.kellogg.ox.ac.