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bay__gulf金虫 (著名写手)
刘苏州
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【在线答疑】关于NAMD/VMD已有27人参与
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上面问题的.conf文件
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小木虫(金币+0.5):给个红包，谢谢回帖交流
小木虫(金币+0.5):给个红包，谢谢回帖交流
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############################################################# ## JOB DESCRIPTION ## ############################################################# # Simulate the 4-nanotube system with induced pressure difference ############################################################# ## ADJUSTABLE PARAMETERS ## ############################################################# structure cnt.psf coordinates cnt.pdb set temperature 300 set outputname sim_short # Continuing a job from the restart files Bincoordinates initial.coor Binvelocities initial.vel ############################################################# ## SIMULATION PARAMETERS ## ############################################################# # Input paraTypeCharmm on parameters par_all27_prot_lipid.prm # Periodic Boundary conditions cellBasisVector1 23 0. 0. cellBasisVector2 0. 19.919 0. cellBasisVector3 0. 0 30.3962 wrapAll on # Force-Field Parameters exclude scaled1-4 1-4scaling 1.0 cutoff 12. switching on switchdist 10. pairlistdist 14.5 # Integrator Parameters timestep 1 ;# 1fs/step nonbondedFreq 2 fullElectFrequency 4 stepspercycle 20 # Constant Temperature Control langevin on ;# do langevin dynamics langevinDamping 5 ;# damping coefficient (gamma) of 5/ps langevinTemp $temperature langevinHydrogen no ;# don't couple langevin bath to hydrogens # Output outputName $outputname restartfreq 1000 ;# 1000steps = every 1ps dcdfreq 1000 outputEnergies 1000 # Fixed Atoms Constraint (set PDB occupancy-column to 1) fixedAtoms on # IMD Settings (can view sim in VMD) if {0} { IMDon on IMDport 3000 ;# port number (enter it in VMD) IMDfreq 1 ;# send every 1 frame IMDwait no ;# wait for VMD to connect before running? } ############################################################# ## EXTRA PARAMETERS ## ############################################################# tclForces on tclForcesScript { set cellLengthZ 30.3962 ;# The length of the unit cell in the z-direction, should be the same as the value in "cellBasisVector3" set LowerBoundary -12.5 set UpperBoundary 12.5 set force {0 0 0.4} set watIdList {} for {set i 577} {$i<1320} {incr i 3} { lappend watIdList $i addatom $i } proc calcforces {} { global cellLengthZ LowerBoundary UpperBoundary force watIdList loadcoords coorList foreach i $watIdList { set z [lindex $coorList($i) 2] set z [expr $z-round($z/$cellLengthZ)*$cellLengthZ] ;# Translate this coordinate into its corresponding value in the original unit cell if {$z>$UpperBoundary || $z<$LowerBoundary} { addforce $i $force } } } } ############################################################# ## EXECUTION SCRIPT ## ############################################################# run 40000 ;# 40ps |
107楼2009-11-16 17:03:39
2楼2009-05-02 11:58:42
bay__gulf
金虫 (著名写手)
刘苏州
- 模拟EPI: 8
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lei0736(金币+4,VIP+0):谢谢 又添猛将 5-3 16:09
lei0736(金币+4,VIP+0):谢谢 又添猛将 5-3 16:09
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【回2楼】 可以，比如下面这篇文献 Bryan J. Johnson, Jordi Cohen, Richard W. Welford, Arwen R. Pearson, Klaus Schulten, Judith P. Klinman, and Carrie M. Wilmot. Exploring molecular oxygen pathways in Hanseluna Polymorpha copper-containing amine oxidase. Journal of Biological Chemistry, 282:17767-17776, 2007. [ Last edited by bay__gulf on 2009-5-2 at 13:21 ] |
3楼2009-05-02 13:13:06
4楼2009-05-02 13:45:28