<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt"><div>Hi<br><br>When i subjected the complex to EM, it gave following warning:<br>"1-4 interaction between 3063 and 3068 at distance 1.436 which is larger than the 1-4 table size 1.000 nm. These are ignored for the rest of the simulation. This usually means your system is exploding,"<br><br>These atoms are oxygens of 2 phosphate grps ofATP. Later if i continue, with SD it converges with less precision. so i applied CG. It converged. But when I carry out position-restrained dynamics, it gave # of LINCS warnings in both cases. Does this mean EM is not done properly ? How should I address this ?<br><br>Regards,<br>Nikhil<br></div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><br><div style="font-family: arial,helvetica,sans-serif; font-size: 13px;"><font face="Tahoma"
size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Mark Abraham <Mark.Abraham@anu.edu.au><br><b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Tuesday, 23 June, 2009 9:10:15 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] simulation of protein in presence of ATP<br></font><br>nikhil damle wrote:<br>> OK till here done ! the pdb file generated for EM should have ATP molecule @proper position as input .top file has the ATP.itp included. It did not have. If I do -ci it would randomly replace the solvent. I want ATP @ its proper location. how do i do this ?<br><br>Like I implied several emails ago, you should order the [molecules] entries according to the coordinate file, as normal.<br><br>Mark<br>_______________________________________________<br>gmx-users mailing list
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