Re: [gmx-users] Umbrella Sampling tutorial

2013-11-10 Thread Justin Lemkul
On 11/10/13 9:14 AM, shahab shariati wrote: Dear Justin Very thanks for your reply. What you described earlier should not be attempted with "distance" geometry. It won't work very well. The use of restraints is almost NEVER necessary, especially in the case where the reference group > is mu

[gmx-users] Umbrella Sampling tutorial

2013-11-10 Thread shahab shariati
Dear Justin Very thanks for your reply. > What you described earlier should not be attempted with "distance" > geometry. It won't work very well. The use of restraints is almost > NEVER necessary, especially in the case where the reference group > is much more massive than the pulling group. I w

Re: [gmx-users] Umbrella Sampling tutorial

2013-11-10 Thread Justin Lemkul
On 11/10/13 5:31 AM, shahab shariati wrote: Dear Justin Thanks for your reply. You are right. I should not extrapolate too literally from your tutorial to my system. But, I have a general question: There is 2 groups in COM pulling method (reference group + pull group). If I want to use pu

[gmx-users] Umbrella Sampling tutorial

2013-11-10 Thread shahab shariati
Dear Justin Thanks for your reply. You are right. I should not extrapolate too literally from your tutorial to my system. But, I have a general question: There is 2 groups in COM pulling method (reference group + pull group). If I want to use pull_geometry = distance, so, I should fix referen

Re: [gmx-users] Umbrella Sampling tutorial

2013-11-09 Thread Justin Lemkul
On 11/9/13 9:38 AM, shahab shariati wrote: Dear Justin Thanks for your explanation. My system contains lipid bilayer + drug + water molecules. I want to calculate Potential of mean force as a function of the distance between the centers of mass of drug and the lipid bilayer. Box vector alon

[gmx-users] Umbrella Sampling tutorial

2013-11-09 Thread shahab shariati
Dear Justin Thanks for your explanation. My system contains lipid bilayer + drug + water molecules. I want to calculate Potential of mean force as a function of the distance between the centers of mass of drug and the lipid bilayer. Box vector along which the pulling is being conducted is Z. 1

Re: [gmx-users] Umbrella Sampling tutorial

2013-11-09 Thread Justin Lemkul
On 11/9/13 8:22 AM, shahab shariati wrote: Daer Justin I studied your tutorial (Umbrella Sampling). It is very beneficial for me. The system you considered was the dissociation of a single peptide from the growing end of an protofibril. You considered following parameters: Chain_B: referenc

[gmx-users] Umbrella Sampling tutorial

2013-11-09 Thread shahab shariati
Daer Justin I studied your tutorial (Umbrella Sampling). It is very beneficial for me. The system you considered was the dissociation of a single peptide from the growing end of an protofibril. You considered following parameters: Chain_B: reference group for pulling. Chain_A: group to which pu

Re: [gmx-users] umbrella sampling tutorial

2013-04-29 Thread Justin Lemkul
On 4/29/13 6:42 AM, Shima Arasteh wrote: Dear Justin, About Umbrella sampling tutorial, would you please let me know why you created an index file contains of chain A and chain B? Also, what's the meaning of 19 and 20 created by a text editoras groups.txt file? I can not understand this.

[gmx-users] umbrella sampling tutorial

2013-04-29 Thread Shima Arasteh
Dear Justin, About Umbrella sampling tutorial, would you please let me know why you created an index file contains of chain A and chain B? Also, what's the meaning of 19 and 20 created by a text editoras groups.txt file? I can not understand this. Thanks in advance. Sincerely, Shima  --

Re: [gmx-users] umbrella sampling tutorial quastion

2012-01-09 Thread Dariush Mohammadyani
As I know, it is not necessary to restrain neither reference nor pulled group. When you apply pulling force, it means you have restrained both of them. Dariush On Mon, Jan 9, 2012 at 4:15 PM, przemek bartha wrote: > Hello, > According to Justin's tutorial on umbrella sampling, > link: > http://w

Re: [gmx-users] umbrella sampling tutorial quastion

2012-01-09 Thread Justin A. Lemkul
przemek bartha wrote: Hello, According to Justin's tutorial on umbrella sampling, link: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/06_umbrella.html could anyone explain, if the molecules are restrained in any way in the umbrella sampling part? The umbrel

[gmx-users] umbrella sampling tutorial quastion

2012-01-09 Thread przemek bartha
Hello, According to Justin's tutorial on umbrella sampling, link: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/06_umbrella.html could anyone explain, if the molecules are restrained in any way in the umbrella sampling part? What I mean, is when we pull molecule A

Re: [gmx-users] Umbrella Sampling tutorial

2011-11-24 Thread Justin A. Lemkul
Steven Neumann wrote: Hey Gmx Users, I went through Justin tutorial of umbrella sampling with spacing of 0.2 nm: Time COM distance 0 - 0.5 208 - 0.7 218 - 0.92 225 - 1.119 231 - 1.41 235 - 1.61 239 - 1.81 246 - 2.09 253 - 2.3 261 - 2.51 268 - 2.71 276 - 2.91 289 - 3.11 307 - 3.3 325

[gmx-users] Umbrella Sampling tutorial

2011-11-24 Thread Steven Neumann
Hey Gmx Users, I went through Justin tutorial of umbrella sampling with spacing of 0.2 nm: Time COM distance 0 - 0.5 208 - 0.7 218 - 0.92 225 - 1.119 231 - 1.41 235 - 1.61 239 - 1.81 246 - 2.09 253 - 2.3 261 - 2.51 268 - 2.71 276 - 2.91 289 - 3.11 307 - 3.3 325 - 3.5 348 - 3.7 359 - 3.93 3