Date: Wed, 16 Mar 2016 10:29:58 +0000 (UTC)
Dear Loeffler,I can understand y axis value deviation. I have attached my rmsd plot here. Kindly have a look and tell me how can I change this.
Thank you. Best Regards, Saman Yousuf AliJunior Research Fellow,
| Lab No. P-133, Computational Chemistry Laboratory
Dr. Panjwani Center for Molecular Medicine & Drug Research,
International Center for Chemical & Biological Sciences,
University of Karachi – 75270.Karachi-Pakistan.
Contact No:
Office (92-21) 111222292 (Ext 309)
Email ID: saman.yousufali64.yahoo.com
saman.ali.iccs.edu
|
On Wednesday, March 16, 2016 3:08 PM, Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk> wrote:
You haven't quite told us how you have actually arrived at your
plot... All we know is that you write 1000 frames per trajectory and
have created 30 of those.
On Wed, 16 Mar 2016 09:55:35 +0000
Saman Yousuf ali <saman.yousufali64.yahoo.com> wrote:
> Dear Amber Users,I have run total 30 ns md simulation and then I have
> plotted rmsd graph. Number of frames per files is 1000 ps, my rmsd
> plot y axis end on 60000 ps. I was expected it ends on 30000 ps. I
> face this problem every time, whenever I run md simulation. Kindly
> guide me regarding this problem and give me useful suggestion. My
> production input file in pasted below. irest=1, ntx=5, min = 0, ntb =
> 2, ntp=1, ntc=2, ntf=2, ntpr = 5000, ntwx = 500, ntwe = 0,ntwr =
> 5000, ntt = 3, gamma_ln = 3.0, tempi = 300.0, temp0 = 300.0, nstlim =
> 500000, dt = 0.002, cut = 12.0/
> Thank you.
> Best Regards, Saman Yousuf AliJunior Research Fellow,
> | Lab No. P-133, Computational Chemistry Laboratory
> Dr. Panjwani Center for Molecular Medicine & Drug Research,
> International Center for Chemical & Biological Sciences,
> University of Karachi – 75270.Karachi-Pakistan.
>
> Contact No:
> Office (92-21) 111222292 (Ext 309)
> Email ID: saman.yousufali64.yahoo.com
> saman.ali.iccs.edu
>
> |
>
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