Re: [gmx-users] Citrate parameters

2019-04-12 Thread Pandya, Akash
Thank you Justin and Mark, it worked. I will bare all this in mind. Akash -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Justin Lemkul Sent: 12 April 2019 16:59 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Citrate parameters On 4/12/19

Re: [gmx-users] Citrate parameters

2019-04-12 Thread Justin Lemkul
On 4/12/19 11:57 AM, Pandya, Akash wrote: How would I find out if there are duplicates or not? grompp has told you what it is finding as duplicates. You need to look into the parent force field files and compare the values you are supplying vs. what are in the existing force field,

Re: [gmx-users] Citrate parameters

2019-04-12 Thread Pandya, Akash
How would I find out if there are duplicates or not? Akash -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Mark Abraham Sent: 12 April 2019 16:47 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Citrate parameters Hi, It seems

Re: [gmx-users] Citrate parameters

2019-04-12 Thread Mark Abraham
Hi, It seems that all/most things before the [moleculetype] definition duplicates the standard contents of the forcefield, as you can see from the contents of the itp file and the original warnings you mentioned. Unfortunately you now have the problem of determining whether all of it is

Re: [gmx-users] Citrate parameters

2019-04-12 Thread Pandya, Akash
Sorry but I don't quite understand where the duplicates come from? I've pasted my itp file below: [ defaults ] 1 2 yes 1.0 1.0 [ atomtypes ] OC 8 15. -0.760 A 0.302906 0.50208 CC 6 12.0110 0.620 A 0.356359 0.29288 HA 1 1.0080 0.090 A 0.235197 0.09205 CT2 6 12.0110 -0.180 A 0.387541

Re: [gmx-users] Citrate parameters

2019-04-12 Thread Justin Lemkul
On 4/12/19 10:52 AM, Pandya, Akash wrote: Hi all, My simulation contains citrate molecules. When I try to solvate the system, I get this error. Can anybody help with this? Your citrate topology is introducing duplicate parameters that already exist in the force field. In this instance,

Re: [gmx-users] Citrate parameters

2019-04-12 Thread Pandya, Akash
I'm using the CHARMM27 FF and I obtained the parameters from literature. Akash -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Soham Sarkar Sent: 12 April 2019 16:05 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Citrate parameters Which

Re: [gmx-users] Citrate parameters

2019-04-12 Thread Soham Sarkar
Which force field you are using and how you made the itp of the citrate molecule? On Fri, 12 Apr 2019, 8:23 pm Pandya, Akash, wrote: > Hi all, > > My simulation contains citrate molecules. When I try to solvate the > system, I get this error. Can anybody help with this? > > WARNING 1 [file

[gmx-users] Citrate parameters

2019-04-12 Thread Pandya, Akash
Hi all, My simulation contains citrate molecules. When I try to solvate the system, I get this error. Can anybody help with this? WARNING 1 [file CITff.itp, line 3]: Overriding atomtype OC WARNING 2 [file CITff.itp, line 4]: Overriding atomtype CC WARNING 3 [file CITff.itp, line 5]:

Re: [gmx-users] Energy from a subgroup of molecules

2019-04-12 Thread paul buscemi
Thank you Justin. Using energy groups is not really that bad. By using gmx select ‘atomname Cx and resname ADSORBATE and within 0.5 of resname SURFACE’ -on near.ndx I can find the atom/s of the adsorbate that is proximal to the surface and can track the LJ pot’l by frame and use VMD

Re: [gmx-users] Tpr version check

2019-04-12 Thread Erik Marklund
Hi, Thanks Mark. See https://redmine.gromacs.org/issues/2924. Kind regards, Erik __ Erik Marklund, PhD, Associate Professor of Biochemistry Associate Senior Lecturer in Computational Biochemistry Department of Chemistry – BMC, Uppsala University +46