VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Thu Jul 20 2017 - 17:18:55 CDT

Hi Arthur,

Each SCSE particle is meant to represent a complete CH2 group, so there
are no hydrogens in the solvent. Its like a partial coarse-graining of
the system, since adding in explicit hydrogens was not going to add any
benefit in terms of structure, but was going to make parameterization
more difficult.

-Josh

On 07/20/2017 04:14 PM, Arthur Vale wrote:
> Dear Joshua Vermaas,
>
> Thank you for the prompt response and for providing us with the script. We ran it on our system and it worked great. One thing we were wondering is that when we use it to generate a SCSE system the script generates C - C molecules with no hydrogens. After checking the top_scs.top file we saw that the hydrogen atoms are not specified. Is it supposed to be so or we should add the hydrogens some other way?
>
> Thank you once more,
>
> Arthur Vale
>
>
> ________________________________________
> From: Vermaas, Joshua [Joshua.Vermaas_at_nrel.gov]
> Sent: Thursday, July 20, 2017 4:35 PM
> To: Arthur Vale; vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: Building HMMM using patch files
>
> Hi Arthur,
>
> There was a goof during submission and publication, in that I forgot to include the script that goes along with the patch files and cuts the tails down for you. I've attached it here, as well as putting it on github for the folks that stumble into this thread at a later date (https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fjvermaas%2Fhmmmsolvents&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C67ec826212664e8c6bc508d4cfbc95b1%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636361856312850596&sdata=rl%2B5JE8bWmc2TcinEKGk1gwRamZ8rOUw6H598SOWqTM%3D&reserved=0). Hopefully it is fairly self-explanatory, but basically you source the tcl script and use the "hmmmize" procedure.
>
> -Josh
>
> On 07/20/2017 03:23 PM, Arthur Vale wrote:
> Dear All,
>
> Me and my group are attempting to turn a regular lipid membrane into an HMMM as described in this article: doi: 10.1021/acs.jpcb.6b11378. We have previously built HMMM membranes using CHARMM-GUI but we want to use the enhanced version of it described in the aforementioned paper. We have a pre-equilibrated regular lipid membrane generated through CHARMM-GUI lipid generator, as well as the files provided in the article. From reading the topology files we are under the impression that we can use the patches topology file to both cut the lipid tails and generate the SCSE solvent. Since previously we were successful doing the standard procedure with the autoPSF in VMD, we don't know how to actually proceed to apply these patches in order to achieve this. We tried doing it with the add patches in autoPSF as well as the patch command in psfgen but we were unsuccessful. Could anyone describe the steps to achieve this? I attached the contents of the topology and parameter files provided in the article below for ref
erence.
>
> Thank you in advance,
>
> Arthur Vale
>
> ==> patches.top <==
> !Patch to terminate C2 tail at carbon 5.
> PRES C25T
> ATOM C25 CTL3 -0.27
> ATOM H5R HAL3 0.09
> ATOM H5S HAL3 0.09
> ATOM H5T HAL3 0.09
> BOND C25 H5T
>
> !Patch to terminate C3 tail at carbon 5.
> PRES C35T
> ATOM C35 CTL3 -0.27
> ATOM H5X HAL3 0.09
> ATOM H5Y HAL3 0.09
> ATOM H5Z HAL3 0.09
> BOND C35 H5Z
>
> ==> top_scs.top <==
> MASS 1 SCSM 14.027000 SC ! "Simple Carbon Solvent Methane"
> MASS 2 SCSE 14.027000 SC ! "Simple Carbon Solvent Ethane"
>
> DEFA FIRS none LAST none
> AUTOGENERATE ANGLES DIHEDRALS
>
> RESI SCSM 0.00
> ATOM C SCSM 0.00
>
> RESI SCSE !Simple Carbon Solvent ethane
> ATOM C1 SCSE 0.00
> ATOM C2 SCSE 0.00
> BOND C1 C2
>
> END
>
> ==> par_scs.prm <==
> BONDS
> SCSE SCSE 222.500 1.5300 ! CTL2-CTL2 bond parameter.
>
>
> NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch -
> cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
> !adm jr., 5/08/91, suggested cutoff scheme
> !
> !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
> !
> !epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
> !Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
> !
> !atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4
> !
>
> SCSM 0.0 -0.350 2.080
> SCSE 0.0 -0.112 2.080
>
> NBFIX
> SCSM SCSM -0.625 3.15
> SCSE SCSE -0.274 3.15
>
> END
>
>