From: Shulin Zhuang (shulin.zhuang_at_gmail.com)
Date: Sun Nov 25 2007 - 16:43:40 CST

Dear All,

Now I want to use VMD1.86 to solvate my protein in a long box, using VMD
Main -> Extentions -> Modeling -> Add Solvation Box.
In this solvate plugin, there are two choice for the solvation: using
Molecule Dimensions or not using Molecule Dimensions.

For my protein, the minmax is {13.6169996262 13.2609996796 13.8509998322}
{63.3330001831 43.0810012817 45.9640007019}

1. If not using Molecule Dimensions, I should put the minmax value of my
protein as the minmax of box padding value, then I should give the minmax
value for Box Size,for example:box min: 13.62 13.26 13.85,box box 47
12 12. After performing the solvation, a log file generated :

E:/temp/protein.psf E:/temp/protein.pdb -o solvate -s WT -minmax {{13.62
13.26 13.85} {47 12 12}} -x 13.6169996262 -y 13.2609996796 -z 13.8509998322+x
63.3330001831 +y 43.0810012817 +z 45.9640007019 -b 2.4

replicating 2 by 1 by 1
Solvate 1.2 completed successfully.

After the solvation, the total atom of the system is 33083
For the system, the minmax is : {0.00499999988824 0.00200000009499
0.00300000002608} {110.322998047 55.077999115 57.9580001831}
                        the center is : 55.5037269592 27.5927238464
29.0032558441

2. If using Molecule Dimensions, the box size value is not set, and for the
Box Padding, I use: min: 13.6169996262 13.2609996796 13.8509998322; max: 47
12 12
After solvation, a log file generated:

E:/temp/protein.psf E:/temp/protein.pdb -o solvate -s WT -x 13.6169996262-y
13.2609996796 -z 13.8509998322 +x 47 +y 12 +z 12 -b 2.4

replicating 2 by 1 by 1
Solvate 1.2 completed successfully.

After the solvation, for the system, the total atom is 33083
the minmax : {0.00200000009499 0.00300000002608 0.00400000018999} {
110.319999695 55.0789985657 57.9589996338}
the center : 55.5009384155 27.5936813354 29.0042133331

Comparison of these two methods, I do not find any difference, for the total
atoms is the same, the box size, system minmax and system center are almost
the same. Here, I want to ask a question is that, when I use each of these
two methods to setup the system, then minimize, heat and equilibrate the
syetem, then pull the protein with constant velocity(10m/s), however, during
the pulling, the force increases large( on the reported papers, with a 10m/s
pulling speed,the unfolding force is about 1400pN, however, after 250ps, my
force is above 4000pN) as if during the pulling the water box is also
pulled, although I just fix the first residue CA atom (set B column of this
CA atom 1), and pull the last CA atom(set this CA atom occupancy 1).

For this protein, I use a already setup file by others, however, I minimize,
heat, equilibrate and do constant velocity pulling, the force is just 1600.
All the configuration file for NAMD run is almost the same, for the
difference is that, I just use a media box size above.

I guess that for my abnormal SMD, it is due to the systemsetup, but I could
not find the problem. Using VMD to check the protein and the box, no
problem, the distance between protein and water box boundaries is more than
12 angstrom.

Here, I want to know, for SMD simulation, how to solvate the protein in a
long water box. Wish anyone can give me some advice about the system setup
for SMD. For this problem, I worked on it for one and a half month and still
could not tackle it.

Best regards
Shulin