AMBER Archive (2006)

Subject: AMBER: how to restrain some residues in a NPT MD?

From: Zhihong Yu (computation_at_mail.nankai.edu.cn)
Date: Mon Oct 30 2006 - 09:20:38 CST

Dear All,

        I have a system containing several protein fragments, because I extract all residues within the distance of 20A of an inhibitor, I want to do NPT MD with very weakly restraint (1.0 kcal/mol*A^2) to those residues in the 15~20A shell, so I did the MD in following four steps, and everything is OK.

1. mpirun -np 8 pmemd.MPI -O -i min1.in -o min1.out -p system.prmtop -c system.inpcrd -r system_min1.rst -ref system.inpcrd (restrain solute minimize water)
2. mpirun -np 8 pmemd.MPI -O -i min2.in -o min2.out -p system.prmtop -c system_min1.rst -r system_min2.rst (minimize the whole system)
3. mpirun -np 8 pmemd.MPI -O -i heat.in -o heat.out -p system.prmtop -c system_min2.rst -r system_heat.rst -x system_heat.mdcrd -ref system_min2.rst (weakly restrain solute and heat the system from 0K to 300K in 20ps)
4. mpirun -np 8 pmemd.MPI -O -i equ_product.in -o equ_product.out -p system.prmtop -c system_heat.rst -r system_equ2_product.rst -x system_equ2_product.mdcrd -ref system_heat.rst (do NPT MD at 300K for 1ns)

When I analysis the MD trajectory, I found the backbone RMSD is not very stable in 1ns simulation, so I want to do another 1ns MD simulation based on the step 4 as follows:

mpirun -np 8 pmemd.MPI -O -i equ_product.in -o product_2.out -p system.prmtop -c system_heat.rst -r system_product_2.rst -x system_product_2.mdcrd -ref system_heat.rst

at this moment, I found a problem that the temperature increased to very high, while in step 4 the temperature is very stable, average temperature is 300.03K, temperature RMS fluctuations is 1.84K. At the same time, "Density" decreased to the value almost equal to the initial value in step 4(0.9571)

 NSTEP = 50 TIME(PS) = 1020.100 TEMP(K) = 483.64 PRESS = 3604.9
                                            -------------------
 Etot = -45928.6887 EKtot = 29393.8883 EPtot = -75322.5770
 BOND = 1159.7388 ANGLE = 3198.1474 DIHED = 3618.2022
 1-4 NB = 1283.6419 1-4 EEL = 11045.3955 VDWAALS = 9122.6836
 EELEC = -111006.6701 EHBOND = 0.0000 RESTRAINT = 6256.2836
 EAMBER (non-restraint) = -81578.8606
 EKCMT = 15282.0460 VIRIAL = -8022.8348 VOLUME = 299419.6738
                                                    Density = 0.9879
                                                    ---------------------------

 NSTEP = 100 TIME(PS) = 1020.200 TEMP(K) = 483.56 PRESS = 3562.6
                                            -------------------
 Etot = -48449.6942 EKtot = 29388.6835 EPtot = -77838.3777
 BOND = 1155.9994 ANGLE = 3288.6053 DIHED = 3788.3022
 1-4 NB = 1279.2409 1-4 EEL = 11012.7785 VDWAALS = 9584.3672
 EELEC = -109772.8083 EHBOND = 0.0000 RESTRAINT = 1825.1371
 EAMBER (non-restraint) = -79663.5149
 EKCMT = 15907.0210 VIRIAL = -7323.8078 VOLUME = 302009.3056
                                                    Density = 0.9900
                                                    ---------------------------

but when I didn't restrain those residues within 15~20A shell and restart MD based on step 4 as follows:

mpirun -np 8 pmemd.MPI -O -i equ_product.in -o product_2.out -p system.prmtop -c system_heat.rst -r system_product_2.rst -x system_product_2.mdcrd

everything looks good:

 NSTEP = 50 TIME(PS) = 1020.100 TEMP(K) = 300.26 PRESS = -45.9
 Etot = -65782.2433 EKtot = 18248.4030 EPtot = -84030.6463
 BOND = 988.3259 ANGLE = 2784.8558 DIHED = 3480.3918
 1-4 NB = 1207.0591 1-4 EEL = 11079.5310 VDWAALS = 7853.6265
 EELEC = -111424.4364 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 7287.8821 VIRIAL = 7583.4197 VOLUME = 298489.4102
                                                    Density = 1.0137
 Ewald error estimate: 0.1396E-03
 

 NSTEP = 100 TIME(PS) = 1020.200 TEMP(K) = 301.29 PRESS = -290.3
 Etot = -65747.3646 EKtot = 18311.4818 EPtot = -84058.8464
 BOND = 988.4036 ANGLE = 2795.8995 DIHED = 3576.7810
 1-4 NB = 1208.2661 1-4 EEL = 11100.0828 VDWAALS = 7787.7048
 EELEC = -111515.9842 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 7325.2614 VIRIAL = 9195.5766 VOLUME = 298360.9939
                                                    Density = 1.0141
 Ewald error estimate: 0.1364E-04

So I think these two problems (temperature and density) are related to the restrain in NPT MD, which rst file should I use as reference coordinates in restart NPT MD? or I can't make use of the finished 1ns MD and must do a new MD completely for 2ns as step4? Moreover it seems that it's not correct using "system_heat.rst" as reference coordinates in step4? then how to restrain some residues in a NPT MD?

    Any advice will be greatly appreciated! Thanks in advance & Best regards!

    yours sincerely, Zhihong Yu

PS: "equ_product.in" file is attached for your information

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu