Re: [gmx-users] mdp option periodic molecules

Perfect, Thanks! On 06.03.20 09:00, Christian Blau wrote: Hi Johannnes, That is correct. Another confirmation of what you already suspect is found in the manual in http://manual.gromacs.org/documentation/current/reference-manual/topologies/molecule-definition.html

Re: [gmx-users] mdp option periodic molecules

Hi Johannnes, That is correct. Another confirmation of what you already suspect is found in the manual in http://manual.gromacs.org/documentation/current/reference-manual/topologies/molecule-definition.html

Re: [gmx-users] how to generate average structure from trajectory

Hi, For discarding first 1ns , modify the trajectory with *trjconv* with *-b* flag. Use the modified trajectory for cluster analysis with *gmx cluster* to get an average structure from a highly populated cluster. Thanks & Regards, -- *Subhomoi Borkotoky, Ph. D.* Kusuma

Re: [gmx-users] GMX 2020 - COMM Removal Issue

On 3/6/20 10:00 AM, Daniel Kozuch wrote: [Somehow my response got put in a different thread - hopefully this works] Justin, Thanks for your reply. I agree that some COM motion is normal. However, this was a very short simulation (1 ns), so the size of the drift (several nm) was

[gmx-users] Minimize energy of protein in CCl4

Hi! I am trying to minimize two proteins in CCl4 solvent. When I do mdrun -v -deffnm em, gromacs says too many LINCS warnings I have tried the following: 1. use smaller time step 2. turn off temperature/pressure coupling 3. play around the lincs entries Does this mean the minimization is just

Re: [gmx-users] GMX 2020 - COMM Removal Issue

[Somehow my response got put in a different thread - hopefully this works] Justin, Thanks for your reply. I agree that some COM motion is normal. However, this was a very short simulation (1 ns), so the size of the drift (several nm) was unexpected. To test, I repeated the simulation with

Re: [gmx-users] 12 bead mapping of lipid

Hi Dave, Thanks for your reply. I have seen the new topology file. But I am wondering how can I get the mapping of the new POPS. Is there any way that I can do it myself? Rabeta Yeasmin -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] GMX 2020 - COMM Removal Issue

Additional (good) news, the problem appears to be resolved in the 2020.1 update (at least for the membrane only system). I'll conduct some additional tests to see if there is any lingering problems. Dan -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On

Re: [gmx-users] 12 bead mapping of lipid

Hi, I have run some coarse-grained simulations in GROMACS and now I am trying to learn converting back the system to all-atom. I have set up the coarse-grained system in CHARMM-GUI, They did not provide the mapping files and the mapping files all I found in MARTINI website has 13 beads for POPS,

Re: [gmx-users] GMX 2020 - COMM Removal Issue

Hello, we resolved some issues with COM removal in the latest release (please see the patch notes for more details). So it might be that you where affected by this before. Please let us know if the issue shows up again. Cheers Paul On 06/03/2020 18:58, Daniel Kozuch wrote: Additional

Re: [gmx-users] 12 bead mapping of lipid

Hello, Do you want to include the 12 bead POPS model in your Martini CG simulations? That is straightforward : Download the "itp" file to the directory with the "top" file and enter #include "martini_v2.0_POPS_02.itp" with the hash in the header of the ".top" file. That should be enough to be

Re: [gmx-users] how to generate average structure from trajectory

On 3/6/20 3:21 PM, Sadaf Rani wrote: Dear Subhomoi Thanks for your reply. I was doing the following:- discarding 1 ns trajectory by the following command:- gmx trjconv -f md.xtc -s md.gro -n index.ndx -b 1000 -e 2000 -o md_1000ps.xtc If your simulation is longer than 2 ns, you are not just

Re: [gmx-users] GMX 2020 - COMM Removal Issue

Yes, a smaller system with only membrane/solvent (no protein) causes the same issue. Best, Dan -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Justin Lemkul Sent: Friday, March 6, 2020 11:02 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users]

Re: [gmx-users] how to generate average structure from trajectory

Dear Subhomoi Thanks for your reply. I was doing the following:- discarding 1 ns trajectory by the following command:- gmx trjconv -f md.xtc -s md.gro -n index.ndx -b 1000 -e 2000 -o md_1000ps.xtc Extracting average structure by the following command:- gmx rmsf -s md.tpr -f md_1000ps.xtc -o

[gmx-users] Can drude shell positions be minimized with keeping atoms positions restrained?

Hi everybody. Since my first email seemed to be not following the list's nettiquete rules (sorry for that), I'm trying again. First, I was not successful in solving this issue on gromacs versions 2018.4, 2019.6 and 2020.1: so, it is consistent among them. What we are trying to do is to

Re: [gmx-users] GMX 2020 - COMM Removal Issue

Thanks Paul! Unfortunately while 2020.1 seems to work for the membrane system (no protein), for the protein-membrane system I am still having significant COM motion in the xy plane (i.e. the membrane translates several nm/ns sideways in its own plane). This happens regardless of coupling the

Re: [gmx-users] 12 bead mapping of lipid

Hello, I see the problem now. You are right, the backmapping files have the 13 bead POPS rather that the latest 12 bead POPS. As far as I know the backmapping files have not been publicly updated but you could try the Martini forum. If the exact lipid coordinates are absolutely essential to your