Re: [gmx-users] rlist, rcolumb, and rvdw

Hi, No, you need to design it correctly in the first place. See eg http://manual.gromacs.org/documentation/2016.1/user-guide/cutoff-schemes.html Mark On Thu, 12 Jan 2017 05:31 #SUKRITI GUPTA# wrote: > Hi Mark, > > > If I am using the older version of gromacs with

Re: [gmx-users] rlist, rcolumb, and rvdw

Hi Mark, If I am using the older version of gromacs with group cutoff, what do you mean by "you always want a buffer"? Do we have to do some extra step after md simulation? Regards Sukriti

Re: [gmx-users] Specs for GPU box

Szilárd, I think I am starting to understand and appreciate your argument. In essence, you are warning me against building a beast of stupidity. : ) Sounds like you're in a situation that's not too bad. Just for the $5-10k extra you'd get decent MD server! ;) (Have you considered donating

Re: [gmx-users] protein XYZ dimension function of time

Thanks a lot Justin!  -Atanu On Wednesday, 11 January 2017 6:56 AM, Justin Lemkul wrote: On 1/11/17 3:16 AM, atanu das wrote: > Hi All, > Is there a simple way to calculate a protein's X, Y, and Z dimensions from a > trajectory as a function of time (not the box

Re: [gmx-users] Fwd: LJ cut-offs

PS is the one type of lipid that doesn't work all that well in the CHARMM36 force field, even with the reparameterisation of the ion interactions that was done. I'd be tempted to go with a difference force field unless there is a real reason for needing CHARMM36. Slipids, for example, should

Re: [gmx-users] Fwd: LJ cut-offs

On 1/11/17 1:57 PM, Mohsen Ramezanpour wrote: Thanks Justin, Good to know. I used version 5.0 as Lee et al. 2015. I agree with you in general about keeping cut-offs the same. My systems are pure PS lipid membranes. The study by Klauda in 2016 shows that the higher order in PS membranes

Re: [gmx-users] domain decomposition error in the energy minimization step

Dear Carsten, Thanks. The forward state simulations works properly with mdrun -ntmpi 8 -ntomp 2 or mdrun -ntmpi 4 -ntomp 4 as you suggested. For the backward state GROMACS still gives too many lincs warning error with those mdrun commands in the md step, indicating the system is far from

Re: [gmx-users] rlist, rcolumb, and rvdw

Hi, On Wed, Jan 11, 2017 at 8:11 PM Mohsen Ramezanpour < ramezanpour.moh...@gmail.com> wrote: > I found the discussion and the links inside very useful. Thanks! > > I agree with was discussed above. I should not mess around with cut-offs > :-) > > Regarding the main question on this post (Just

Re: [gmx-users] rlist, rcolumb, and rvdw

I found the discussion and the links inside very useful. Thanks! I agree with was discussed above. I should not mess around with cut-offs :-) Regarding the main question on this post (Just for curiosity): If one wish to use 0.8-0.1 (mess around :-) ), shall we change the rlist and rcolumb to 0.1

Re: [gmx-users] Fwd: LJ cut-offs

Thanks Justin, Good to know. I used version 5.0 as Lee et al. 2015. I agree with you in general about keeping cut-offs the same. My systems are pure PS lipid membranes. The study by Klauda in 2016 shows that the higher order in PS membranes might be because of PS-PS or PS-K+ interactions.

Re: [gmx-users] Fwd: LJ cut-offs

On 1/11/17 1:34 PM, Mohsen Ramezanpour wrote: I found these two links from other post of mine which might be useful for this discussion too: People have used 11-12 switching range as well. So, if it works, there is no restriction to not choose such numbers with 0.1 nm difference in cutoffs.

Re: [gmx-users] Fwd: LJ cut-offs

Since I join this discussion, this is perhaps a good moment to ask following questions. I use Gromacs 5.0.4 and the file.mdp options that I found here http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM , so: 1. The bug that was described here

Re: [gmx-users] Fwd: LJ cut-offs

I found these two links from other post of mine which might be useful for this discussion too: People have used 11-12 switching range as well. So, if it works, there is no restriction to not choose such numbers with 0.1 nm difference in cutoffs. http://pubs.acs.org/doi/abs/10.1021/jp101759q

Re: [gmx-users] Fwd: LJ cut-offs

On 1/11/17 12:46 PM, Mohsen Ramezanpour wrote: Hi Guys, Thanks for your comments. My question was exactly what Dawid clarified. Sure, I will read those as you suggested. Dawid, regarding this: "You need to keep in mind however that each force field was optimized for given set of cut-offs and

Re: [gmx-users] Fwd: LJ cut-offs

Hi Guys, Thanks for your comments. My question was exactly what Dawid clarified. Sure, I will read those as you suggested. Dawid, regarding this: "You need to keep in mind however that each force field was optimized for given set of cut-offs and they virtually become part of that FF (just like

Re: [gmx-users] Specs for GPU box

Hi, On Sat, Jan 7, 2017 at 3:20 AM, Alex wrote: > Hi Szilárd, > > Thanks for responding. Yes, those systems are indeed expensive, and our main > objective here wasn't really bang for the buck. What we want is the fastest > possible single node for the money, and if that

Re: [gmx-users] [gmx-developers] executing mdp file--error

This is a usage question and is not related to development; I am CC'ing this over to gmx-users. Please continue the discussion there. On 1/11/17 8:40 AM, Kulkarni R wrote: Hi gromacs users, I am using Gromacs version 5.1.1 and em.mdp is #em.mdp ; to test ; grompp -f em.mdp -c

Re: [gmx-users] protein XYZ dimension function of time

On 1/11/17 3:16 AM, atanu das wrote: Hi All, Is there a simple way to calculate a protein's X, Y, and Z dimensions from a trajectory as a function of time (not the box vector, the protein dimensions as in how the protein spreads itself in the 3 directions as the simulation progresses i.e.

Re: [gmx-users] rlist, rcolumb, and rvdw

On 1/11/17 2:57 AM, Mark Abraham wrote: Hi, Those ancient comments pertain only to the deprecated "group" cutoff scheme. You should look at the extensive documentation of both schemes in the current reference manuals. Particularly vdw cutoffs are baked into the forcefield and should not be

Re: [gmx-users] Fwd: LJ cut-offs

Also, you could try to find something in these articles: http://apps.webofknowledge.com/Search.do?product=WOS=P2QP4ybhv2TW78yMOMx_mode=GeneralSearch=9bcb8bea-c281-4524-a7de-e664898a322b 2017-01-11 13:48 GMT+01:00 Dawid das : > You might also want to read the Default

Re: [gmx-users] Fwd: LJ cut-offs

Hi, I believe that Mohsen here did not ask about what you are writing about Mark. He asks about cut-offs not the exponents in the LJ formula. I am no expert in that but I reviewed Andrew Leach's book on that and also other resources and I did not find any reason why lower and upper cut-off for

[gmx-users] Group vs Verlet cutoff scheme

Hi all, I have a system containing few small ions in water and I was running it on Gromacs 4.5.6 version. However I have run all these simulations with PME electrostatics using group cutoff scheme, as that is only available in older version of Gromacs. Will I be getting different result if I

Re: [gmx-users] gromacs in cgywin

Hi, Had included a few more lines in .mdp file and now it is working well. Thanks, Subashini.K From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of liming_52 Sent:

Re: [gmx-users] domain decomposition error in the energy minimization step

Dear Qasim, those kinds of domain decomposition 'errors' can happen when you try to distibute an MD system among too many MPI ranks. There is a minimum cell length for each domain decomposition cell in each dimension, which depends on the chosen cutoff radii and possibly other inter-atomic

[gmx-users] protein XYZ dimension function of time

Hi All, Is there a simple way to calculate a protein's X, Y, and Z dimensions from a trajectory as a function of time (not the box vector, the protein dimensions as in how the protein spreads itself in the 3 directions as the simulation progresses i.e. XX, YY, ZZ)? I see that GROMACS has an

Re: [gmx-users] gromacs in cgywin

Delete the ";", and it maybe bring some surprise. For example, run "grompp -f em.mdp -c test_GMX.gro -p test_GMX.top -o em.tpr -v" or "mdrun -v -deffnm em". -- With my best wishes, Ming Li, PhD Chinese Academy of Agricultural Sciences, Beijing, China At 2017-01-11 16:24:16, "Subashini

[gmx-users] gromacs in cgywin

Hi, I have installed gromacs in cgywin. I want to run these commands #em.mdp ; to test ; grompp -f em.mdp -c test_GMX.gro -p test_GMX.top -o em.tpr -v ; mdrun -v -deffnm em I had sourced gmrx before typing these commands. source /usr/local/gromacs/bin/GMXRC But, it says, -bash: syntax