Re: [AMBER] Trying to perform a heating MD in increments

From: Abelak, Kavin <kabelak.rvc.ac.uk>
Date: Tue, 4 Aug 2015 10:13:19 +0000

Dear Alaa,

I think you need to read through the manual (AMBER15, starting chapter 18.4) and look closely at what all the flags and parameters mean. I’m also fairly new to AMBER and the manual has proved very helpful.

I direct you to http://ambermd.org/tutorials/basic/tutorial3/section4.htm where a progressive heating script can be found. Although you have to be careful as this is for GB implicit solvent and you have to modify your parameters accordingly. To answer your specific question, it seems you need to put ntx=5 and irest=1.

As for “cut", I don’t think you’re meant to change it between sequential runs, but maybe someone with more experience can chip in here. And I think changing ntpr/ntwx will make analysing the results a bit tricky (also, writing every 5000 steps for a 25000 step run will only give you 6 data-points) unless you are analysing each heating segment individually.

Best of luck!

Regards,
Kavin







On 4 Aug 2015, at 09:39, Amber mail <amber.auc14.gmail.com<mailto:amber.auc14.gmail.com>> wrote:

Dear AMBER users,

I performed a minimization for a protein, and I want to perform 50ps of
heating MD at 100K. Then I will heat up the system in increments of 25K
with 50ps of MD simulation at each temperature increment until the desired
temperature of 310K is established.

I just want to make sure that I am on the right track!

What I have done to perform this run is that I created the heat input files
as follows

heat100.in

Heat100K
&cntrl
 imin=0,
 ntx=1,
 irest=0,
 nstlim=25000,
 dt=0.002,
 ntf=2,
 ntc=2,
 tempi=0.0,
 temp0=100.0,
 ntpr=100,
 ntwx=100,
 cut=8.0,
 ntb=2,
 ntp=1,
 ntt=3,
 gamma_ln=1.0,
 tautp=1.0,
 taup=1.0,
 pres0=1.01325,
 nmropt=0
/

heat125.in

Heat125K
&cntrl
 imin=0,
 ntx=1,
 irest=0,
 nstlim=25000,
 dt=0.002,
 ntf=1,
 ntc=2,
 tempi=100.0,
 temp0=125.0,
 ntpr=5000,
 ntwx=5000,
 cut=10.0,
 ntb=2,
 ntp=1,
 ntt=3,
 gamma_ln=1.0,
 tautp=1.0,
 taup=1.0,
 pres0=1.01325,
 nmropt=0,
/

The running commands from the script are

mpirun -np 40 ${DIR_NAME} -O -i heat100.in -o ${FILENAME}_100K.out -p
${TOPNAME}.top -c ${FILENAME}_min.res -r ${FILENAME}_100K.res -x
${FILENAME}_100K.crd -ref ${FILENAME}_min.res

mpirun -np 40 ${DIR_NAME} -O -i heat125.in -o ${FILENAME}_125K.out -p
${TOPNAME}.top -c ${FILENAME}_100K.res -r ${FILENAME}_125K.res -x
${FILENAME}_125K.crd -ref ${FILENAME}_100K.res

mpirun -np 40 ${DIR_NAME} -O -i heat150.in -o ${FILENAME}_150K.out -p
${TOPNAME}.top -c ${FILENAME}_125K.res -r ${FILENAME}_150K.res -x
${FILENAME}_150K.crd -ref ${FILENAME}_125K.res

mpirun -np 40 ${DIR_NAME} -O -i heat175.in -o ${FILENAME}_175K.out -p
${TOPNAME}.top -c ${FILENAME}_150K.res -r ${FILENAME}_175K.res -x
${FILENAME}_175K.crd -ref ${FILENAME}_150K.res

mpirun -np 40 ${DIR_NAME} -O -i heat200.in -o ${FILENAME}_200K.out -p
${TOPNAME}.top -c ${FILENAME}_175K.res -r ${FILENAME}_200K.res -x
${FILENAME}_200K.crd -ref ${FILENAME}_175K.res

mpirun -np 40 ${DIR_NAME} -O -i heat225.in -o ${FILENAME}_225K.out -p
${TOPNAME}.top -c ${FILENAME}_200K.res -r ${FILENAME}_225K.res -x
${FILENAME}_225K.crd -ref ${FILENAME}_200K.res

mpirun -np 40 ${DIR_NAME} -O -i heat250.in -o ${FILENAME}_250K.out -p
${TOPNAME}.top -c ${FILENAME}_225K.res -r ${FILENAME}_250K.res -x
${FILENAME}_250K.crd -ref ${FILENAME}_225K.res

mpirun -np 40 ${DIR_NAME} -O -i heat275.in -o ${FILENAME}_275K.out -p
${TOPNAME}.top -c ${FILENAME}_250K.res -r ${FILENAME}_275K.res -x
${FILENAME}_275K.crd -ref ${FILENAME}_250K.res


Am I doing right? I am not sure If I have to put ntx=5, irest=1 in my
heat input files in order to make my heating MD simulation sequential? What
I am thinking of is that the commands above already will be performed in
sequential manner since the files flaged with -c will get every coordinate
file from the previous run.

I appreciate If you could help me
Thanks in advance!
_______________________________________________
AMBER mailing list
AMBER.ambermd.org<mailto:AMBER.ambermd.org>
http://lists.ambermd.org/mailman/listinfo/amber


[http://www.rvc.ac.uk/media/default/images/social-media/change.gif]

[RVC Logo - link to RVC Website]<http://www.rvc.ac.uk> [Twitter icon - link to RVC (Official) Twitter] <http://twitter.com/RoyalVetCollege> [Facebook icon - link to RVC (Official) Facebook] <http://www.facebook.com/theRVC> [YouTube icon - link to RVC YouTube] <http://www.youtube.com/user/RoyalVetsLondon?feature=mhee> [Pinterest icon - link to RVC Pinterest] <http://pinterest.com/royalvetcollege/> [Instagram icon - link to RVC Instagram] <http://instagram.com/royalvetcollege>

This message, together with any attachments, is intended for the stated addressee(s) only and may contain privileged or confidential information. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Royal Veterinary College (RVC). If you are not the intended recipient, please notify the sender and be advised that you have received this message in error and that any use, dissemination, forwarding, printing, or copying is strictly prohibited. Unless stated expressly in this email, this email does not create, form part of, or vary any contractual or unilateral obligation. Email communication cannot be guaranteed to be secure or error free as information could be intercepted, corrupted, amended, lost, destroyed, incomplete or contain viruses. Therefore, we do not accept liability for any such matters or their consequences. Communication with us by email will be taken as acceptance of the risks inherent in doing so.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Aug 04 2015 - 03:30:03 PDT
Custom Search