Re: [gmx-users] g_order for all-atom simulations for double bonds

-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Mohsen Ramezanpour [ramezanpour.moh...@gmail.com] Sent: 12 January 2018 05:21 To: Discussion list for GROMACS users; Discussion list for GROMACS users Subject: [gmx-users] g_order for all-atom

[gmx-users] g_order for all-atom simulations for double bonds

Dear Gromacs users, I have a bilayer composed of lipids with two unsaturated bonds in each tail. I did my simulations in Gromacs v. 2016.3 in Charmm36FF. BUT, I am doing the analysis in Gromacs v. 2016.2. I want to calculate the order parameter for this lipid. Here is what I do: 1) I calculate

[gmx-users] g_order

I have a molecule with a carbon chain attached to a ring. I want to use g_order to generate the ordering parameter across the simulation box. I've read the manual entry for g_order, and it said to create an index file with only the "relevant" atoms included, so I made a group with just the atoms

Re: [gmx-users] g_order

On 9/10/15 6:58 PM, Stella Nickerson wrote: I'm simulating an ionic liquid/water liquid-liquid interface. The IL has an alkyl chain hanging off a ring, and previous simulations have found ordering of the IL at the liquid-liquid surface as the molecules essentially lay themselves flat against

Re: [gmx-users] g_order

I'm simulating an ionic liquid/water liquid-liquid interface. The IL has an alkyl chain hanging off a ring, and previous simulations have found ordering of the IL at the liquid-liquid surface as the molecules essentially lay themselves flat against the interface. I though Sz might illustrate that.

Re: [gmx-users] g_order

On 9/10/15 1:58 PM, Stella Nickerson wrote: I have a molecule with a carbon chain attached to a ring. I want to use g_order to generate the ordering parameter across the simulation box. I've read the manual entry for g_order, and it said to create an index file with only the "relevant" atoms

[gmx-users] g_order and gromacs 5.0

Hi All, I would like to compute the SCD parameters of the DOPC sn1 and sn2 chains in membrane simulated with the CHARMM36 force field with gmx order tool of GMX5.0. To know how to do that, I have searched on the mailing list and came across the thread of T. Piggot about problems with g_order and

[gmx-users] g_order (warning)

Hi all I have DOPC lipid in my system. After preparing index file exactly based on how-to on the g_order page, I used following command to obtain order parameters of acyl chains: g_order -s md.tpr -f final.xtc -n sn1.ndx -d z -od deuter_sn1.xvg -o order_sn1.xvg I encountered following warnings:

Re: [gmx-users] g_order (warning)

On 1/15/14, 9:30 AM, shahab shariati wrote: Hi all I have DOPC lipid in my system. After preparing index file exactly based on how-to on the g_order page, I used following command to obtain order parameters of acyl chains: g_order -s md.tpr -f final.xtc -n sn1.ndx -d z -od deuter_sn1.xvg -o