# [gmx-users] Hole in the membrane during initial equilibration

anu chandra anu80125 at gmail.com
Fri Aug 7 17:04:34 CEST 2015

```Dear Gromacs users,

I am trying to run a membrane protein simulation with  slab geometry along
Z-axis, due to ion asymmetry. The simulation box was well equilibrated
before implementing the slab geometry. The box dimension before the
addition of slab was -  ' 112.347  112.347  126.531  90.00  90.00  90.00'
and I added a 2 nm vacuum slab along Z-axis by using 'editconf' command -
editconf -f input.pdb -o ouput.pdb -c -box 11.2347  11.2347  14.6531.
Later, I tried to carry out NVT equilibration after 1000 steps initial
minimization. Unfortunately, a number holes formed in the membrane which
eventually leads the mixing up of water from top and bottom layer. Below, I
copied the NVT mdp file used for equilibration. Please help me to figure
out error with my simulation.

###############################################################

define                  = -DREST_ON -DNVT  ; restrain the protein here
integrator              = md
dt                      = 0.001
nsteps                  = 25000
nstlog                  = 1000
nstxout                 = 1000
nstvout                 = 1000
nstfout                 = 1000
nstcalcenergy           = 100
nstenergy               = 1000
;
cutoff-scheme           = Verlet
nstlist                 = 20
rlist                   = 1.2
verlet-buffer-tolerance = -1
coulombtype             = pme
rcoulomb                = 1.2
vdwtype                 = Cut-off
vdw-modifier            = Force-switch
rvdw_switch             = 1.0
rvdw                    = 1.2
;
ewald-geometry          = 3dc
pbc                     = xy
;
nwall                    = 2
wall-type                = 10-4
wall-r-linpot            = -1
wall-atomtype            = CT3 CT3
wall-density             = 5 5
wall-ewald-zfac          = 3
;
tcoupl                  = V-rescale
tc_grps                 = Protein POPC Cal_CL_SOL
tau_t                   = 0.5    0.5     0.5
ref_t                   = 305.0    305.0    305.0
;
constraints             = h-bonds
constraint_algorithm    = LINCS
;
nstcomm                 = 100
comm_mode               = linear
comm_grps               = Protein_POPC Cal_CL_SOL
;
gen-vel                 = yes
gen-temp                = 305.0
gen-seed                = -1
;
refcoord_scaling        = com

##############################################################

Many thanks in advance
Anu
```
{"ft_lang_label":"__label__en","ft_lang_prob":0.6949354,"math_prob":0.9881968,"size":1924,"snap":"2019-35-2019-39","text_gpt3_token_len":625,"char_repetition_ratio":0.1484375,"word_repetition_ratio":0.0,"special_character_ratio":0.37681913,"punctuation_ratio":0.13636364,"nsfw_num_words":0,"has_unicode_error":false,"math_prob_llama3":0.9791107,"pos_list":[0],"im_url_duplicate_count":[null],"WARC_HEADER":"{\"WARC-Type\":\"response\",\"WARC-Date\":\"2019-09-16T03:26:04Z\",\"WARC-Record-ID\":\"<urn:uuid:59a01378-709c-4c32-8224-71a1202cbc22>\",\"Content-Length\":\"5281\",\"Content-Type\":\"application/http; msgtype=response\",\"WARC-Warcinfo-ID\":\"<urn:uuid:56f89b7d-bf51-4724-9bf0-c63fc7d57364>\",\"WARC-Concurrent-To\":\"<urn:uuid:2c580e92-dac0-446b-93d3-a1f1d74329f7>\",\"WARC-IP-Address\":\"130.237.48.102\",\"WARC-Target-URI\":\"https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-August/099763.html\",\"WARC-Payload-Digest\":\"sha1:P3WLRYFRZJWSEF6JL3HZMXTO5QNTSD4U\",\"WARC-Block-Digest\":\"sha1:RRWA3PZQFDPX5VJYFZT4RIW2PHLQMHLF\",\"WARC-Identified-Payload-Type\":\"text/html\",\"warc_filename\":\"/cc_download/warc_2019/CC-MAIN-2019-39/CC-MAIN-2019-39_segments_1568514572471.35_warc_CC-MAIN-20190916015552-20190916041552-00439.warc.gz\"}"}