[gmx-users] Simulated annealing problem

Hi, I am trying to anneal two protein molecules. The usual protocol for a MD simulation was followed. But the problem arises that at high temperatures, the number of hydrogen bonds are increasing instead of getting decreased. The GROMOS43a1 force field was used and the mdp file for the simulation

[gmx-users] simulated annealing

your tau_t is 1 ps and you want to increase the temperature by 300 K in 10 ps. I doubt that this is possible. Try heating over a longer period of time. The longer the period, the closer you will get to your target temperature. Why do you need to do the heating over 10 ps? Also, when using any de

Re: [gmx-users] Simulated annealing in implicit solvent

On 8/7/12 8:10 PM, Ольга Кононова wrote: Hello, I got a problem, trying to make preparation (in particular, heating from 0 to 300 K) of my system in implicit solvent (GBSA OBC model). For gradual heating I use simulated annealing (see mdp below) and sd integrator, which allows me do not use th

[gmx-users] Simulated annealing in implicit solvent

Hello, I got a problem, trying to make preparation (in particular, heating from 0 to 300 K) of my system in implicit solvent (GBSA OBC model). For gradual heating I use simulated annealing (see mdp below) and sd integrator, which allows me do not use thermostat. I also set up gen_vel = yes and

Re: [gmx-users] simulated annealing mdp

Thank you for reply -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface

Re: [gmx-users] simulated annealing mdp

On 6/12/12 9:09 AM, rama david wrote: Hello Justin and Ravi, Lets explain me Why I did simulated anealing?? .. I synthesise peptide and I have experimental data for its self assembly, I just want to reproduced these data. I arranged the 32 protein in axis to petide fibre, in antiparrallel

Re: [gmx-users] simulated annealing mdp

Hello Justin and Ravi, Lets explain me Why I did simulated anealing?? .. I synthesise peptide and I have experimental data for its self assembly, I just want to reproduced these data. I arranged the 32 protein in axis to petide fibre, in antiparrallel Beta sheet structure. I dont have crystal

Re: [gmx-users] simulated annealing mdp

On 6/12/12 8:20 AM, Lord RaviRaj .. wrote: On Tue, Jun 12, 2012 at 4:42 PM, rama david mailto:ramadavidgr...@gmail.com>> wrote: THANK YOU Justin, -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-use

Re: [gmx-users] simulated annealing mdp

On Tue, Jun 12, 2012 at 4:42 PM, rama david wrote: > THANK YOU Justin, > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don'

Re: [gmx-users] simulated annealing mdp

THANK YOU Justin, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or

Re: [gmx-users] simulated annealing mdp

On 6/12/12 3:39 AM, rama david wrote: Hi Gromacs Friends, I planed to do simulated annealing... My protocol is as follow ( forcefield G96 53a6 spc water model) 1. nvt at 310 k for 100 ps 2. Sa (mdp is posted below ) 3. NPT at 310 k for 100 ps Is it right ?? There are two levels of "righ

[gmx-users] simulated annealing mdp

Hi Gromacs Friends, I planed to do simulated annealing... My protocol is as follow ( forcefield G96 53a6 spc water model) 1. nvt at 310 k for 100 ps 2. Sa (mdp is posted below ) 3. NPT at 310 k for 100 ps Is it right ?? Please suggest me improvements... Sa mdp file title= gromacs de

Re: [gmx-users] Simulated Annealing Protocol...

bipin singh wrote: Hello users, I have also got a doubt regarding SA. My doubt is, whether it is correct to do SA in NVT? I mean increasing the temperature to desired temperature during SA (with position restraints) with no pressure coupling. Afterwards NPT(with position restraints) then final

Re: [gmx-users] Simulated Annealing Protocol...

Hello users, I have also got a doubt regarding SA. My doubt is, whether it is correct to do SA in NVT? I mean increasing the temperature to desired temperature during SA (with position restraints) with no pressure coupling. Afterwards NPT(with position restraints) then final production run in NPT

Re: [gmx-users] Simulated Annealing Protocol...

rama david wrote: Hi Gromacs Specialist, Thank you Justin For your reply. I run one Simulated Annealing) MD after your reply. My aim is to find protein conformation and study protein self assembly study .. the protocol I follow is as.. 1. Upto energy minimisation I followed th

[gmx-users] Simulated Annealing Protocol...

Hi Gromacs Specialist, Thank you Justin For your reply. I run one Simulated Annealing) MD after your reply. My aim is to find protein conformation and study protein self assembly study .. the protocol I follow is as.. 1. Upto energy minimisation I followed the general way 2. I di

Re: [gmx-users] Simulated Annealing Protocol...

rama david wrote: Dear Gromacs Specialists, I am very novice to Molecular Simulation study. I am using GROMACS 4.5.4 version . I completed some GROMACS tutorials , I not found any tutorial on Simulated Annealing.. If Any one know the link please give me it.. I make my protoco

[gmx-users] Simulated Annealing Protocol...

Dear Gromacs Specialists, I am very novice to Molecular Simulation study. I am using GROMACS 4.5.4 version . I completed some GROMACS tutorials , I not found any tutorial on Simulated Annealing.. If Any one know the link please give me it.. I make my protocol to work on simulated

[gmx-users] Simulated annealing with implicit water model

Hi There, I am going to run a simulated annealing simulation on a system with implicit water model. I have tried running simulated annealing with explicit water model. Please suggest and comment if anybody have tried such simulation in gromacs. with thanks, Vivek -- gmx-users mailing listgmx-

Re: [gmx-users] Simulated Annealing parameters

On 17/12/2010 3:38 AM, Ehud Schreiber wrote: Dear fellow GROMACS users, I am using the simulated annealing option in gromacs 4.5.2 (in an implicit solvent all-vs-all setting, by the way), i.e. using the annealing, annealing_npoints, annealing_time, annealing_temp parameters in the mdp file.

[gmx-users] Simulated Annealing parameters

Dear fellow GROMACS users, I am using the simulated annealing option in gromacs 4.5.2 (in an implicit solvent all-vs-all setting, by the way), i.e. using the annealing, annealing_npoints, annealing_time, annealing_temp parameters in the mdp file. I also specify the tcoupl, tc_grps and tau_t par

Re: [gmx-users] simulated annealing (SA)

- Original Message - From: shahab shariati Date: Tuesday, May 18, 2010 23:36 Subject: [gmx-users] simulated annealing (SA) To: gmx-users@gromacs.org > Hi gromacs users >   > 1) after doing simulated annealing simulation, who can I understand that > obtained structure

[gmx-users] simulated annealing (SA)

Hi gromacs users 1) after doing simulated annealing simulation, who can I understand that obtained structure is in global minimum and not in local minimum? 2) who can I understand that parameters used in mdp file (annealing_npoints, annealing_time, annealing_temp) are true? Any help will highly

Re: [gmx-users] simulated annealing (SA)

shahab shariati wrote: Hi gromacs users about SA simulation, I saw in some papers that annealing _time is very short. fpr example [The temperature was increased from 0 to 600 K over the first 4 ps, held at 600 K for 2 ps, and then slowly cooled to 0 K over 14 ps in simulation of protein-d

[gmx-users] simulated annealing (SA)

Hi gromacs users about SA simulation, I saw in some papers that annealing _time is very short. fpr example [The temperature was increased from 0 to 600 K over the first 4 ps, held at 600 K for 2 ps, and then slowly cooled to 0 K over 14 ps in simulation of protein-dna]. Is there limitation in ele

Re: [gmx-users] simulated annealing

On 25/04/2010 10:17 PM, leila karami wrote: Hi gromacs users (1) Simulated annealing method is as two forms: single and periodic. I want to do Simulated annealing for obtaining global minimum in protein structure. No procedure is assured of finding a global minimum with less than infinite ef

[gmx-users] simulated annealing

Hi gromacs users (1) Simulated annealing method is as two forms: single and periodic. I want to do Simulated annealing for obtaining global minimum in protein structure. Which one of them is better? (in point of view obtaining to global minimum). Thank you so much for any help! -- gmx-users m

Re: [gmx-users] simulated annealing (SA)

shahab shariati wrote: Hi all Simulated annealing consists of heating and gradually cooling steps. What is maximum temperature that we can use for heating in SA simulation of protein. The better question is not if there is a maximum, but rather if whatever you're doing is neces

[gmx-users] simulated annealing (SA)

Hi all Simulated annealing consists of heating and gradually cooling steps. What is maximum temperature that we can use for heating in SA simulation of protein. Any help will highly appreciate. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gm

Re: [gmx-users] simulated annealing (SA)

shahab shariati wrote: Dear Justin thanks for your attention In mdp file, if annealing_temp and annealing_time values are as follow: annealing_temp = 200 700 600 500 400 300 annealing_time =03040 506070 so, dt and nsteps have to determine such that time of

[gmx-users] simulated annealing (SA)

Dear Justin thanks for your attention In mdp file, if annealing_temp and annealing_time values are as follow: annealing_temp = 200 700 600 500 400 300 annealing_time =03040 506070 so, dt and nsteps have to determine such that time of SA simulation be 70. is it true? -

Re: [gmx-users] simulated annealing (SA)

shahab shariati wrote: Hi all For simulated annealing simulation, except things mentioned as follow,what things should be in mdp file? Specify anything you need to. If a default value isn't what you want, change it. There are many settings beyond what you've listed below that you need

Re: [gmx-users] simulated annealing (SA)

shahab shariati wrote: Hi all I have some questions about simulated annealing (SA): 1) Is SA a optimization method? or a minimization method? It is probably best described as optimization. 2) Steps in md simulation are as follow: (a) minimization (b) equilibration (c) production run

[gmx-users] simulated annealing (SA)

Hi all For simulated annealing simulation, except things mentioned as follow,what things should be in mdp file? integrator dt nsteps annealing annealing npoints annealing time annealing temp tcoupl tc_ grps tau_t ref_ t Any help will highly appreciated! -- gmx-users mailing listgm

[gmx-users] simulated annealing (SA)

Hi all I have some questions about simulated annealing (SA): 1) Is SA a optimization method? or a minimization method? 2) Steps in md simulation are as follow: (a) minimization (b) equilibration (c) production run (d) analysis so, where do SA lie in previous line? (before or after minimizatio

Re: [gmx-users] simulated annealing

On 21/04/2010 10:19 PM, leila karami wrote: Dear Justin thanks for your accuracy. I want to use simulated annealing to obtain global minimum for protein-dna structure. I will do first heating and then slowly cooling and I will my full md simulation in 300K. is my manner true? if so, is my mdp fil

[gmx-users] simulated annealing

Dear Justin thanks for your accuracy. I want to use simulated annealing to obtain global minimum for protein-dna structure. I will do first heating and then slowly cooling and I will my full md simulation in 300K. is my manner true? if so, is my mdp file true, now? Tcouple = berendsen ref_t = 300

Re: [gmx-users] simulated annealing

leila karami wrote: Dear Justin thanks for your attention I want to use simulated annealing to obtain global minimum for protein-dna structure. I will do first heating and then slowly cooling. is my mdp file true, now? T-couple = brendsen ref-t = 300 annealing: single annealing_npo

[gmx-users] simulated annealing

Dear Justin thanks for your attention I want to use simulated annealing to obtain global minimum for protein-dna structure. I will do first heating and then slowly cooling. is my mdp file true, now? T-couple = brendsen ref-t = 300 annealing: single annealing_npoints: 5 annealing_time: 0 3

Re: [gmx-users] simulated annealing

leila karami wrote: Hi gromacs users it is my mdp file: annealing: single annealing_npoints: 5 annealing_time: 0 3 6 9 12 annealing_temp: 500 450 400 350 300 300 is my ref-t. is it true? The value of ref_t doesn't matter so much, since, according to the manual: "The actual a

Re: [gmx-users] simulated annealing

leila karami wrote: Hi gromacs users I want to use simulated annealing. I have a question: 1) in mdp file, T-couple = no. is that true? No. You need a thermostat to control the temperature of your system. -Justin -- Justin A. Lemkul Ph.D. Ca

[gmx-users] simulated annealing

Hi gromacs users it is my mdp file: annealing: single annealing_npoints: 5 annealing_time: 0 3 6 9 12 annealing_temp: 500 450 400 350 300 300 is my ref-t. is it true? Thank you so much for any help! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/lis

[gmx-users] simulated annealing

Hi gromacs users I want to use simulated annealing. I have a question: 1) in mdp file, T-couple = no. is that true? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! P

Re: [gmx-users] Simulated annealing

jayant james wrote: Hi! I have two phosphorylated serines which form part of peptide that I want to perform simulated annealing. But the catch is the SEP group is read as a Non-Protein and so it is present in two T-coupling groups, the Non-Potein and the protein group I want to heat. I need

Re: [gmx-users] Simulated annealing

Hi! I have two phosphorylated serines which form part of peptide that I want to perform simulated annealing. But the catch is the SEP group is read as a Non-Protein and so it is present in two T-coupling groups, the Non-Potein and the protein group I want to heat. I need to remove this group (SEP-p

Re: [gmx-users] Simulated annealing

jayant james wrote: Hi ! I am attempting to do a simulated annealing and running into problem. Let me give a introduction to my system. I have a segment of a protein that was not crystallographyically resolved, but was later resolved by NMR. So I ligated the NMR structure to the crystal struct

[gmx-users] Simulated annealing

Hi ! I am attempting to do a simulated annealing and running into problem. Let me give a introduction to my system. I have a segment of a protein that was not crystallographyically resolved, but was later resolved by NMR. So I ligated the NMR structure to the crystal structure and in an attempt to

Re: [gmx-users] Simulated annealing

jayant james wrote: Hi! So the part of my pr.mdp files that handles pressure and temperature looks like as below and if I were to create an index file by name "N-extension" an type it next in the tc-grps as N-extension along with the existing Protein Non-Protein groups is this how I get to h

Re: [gmx-users] Simulated annealing

Hi! So the part of my pr.mdp files that handles pressure and temperature looks like as below and if I were to create an index file by name "N-extension" an type it next in the tc-grps as N-extension along with the existing Protein Non-Protein groups is this how I get to handle the simulated anneali

Re: [gmx-users] Simulated annealing

jayant james wrote: Hi! I have appended the NMR structure to a part of the protein that was not resolved to the protein and now I want to perform simulated annealing of the 40 amino acids (NMR structure had 33 amino acids and to link I needed another 7 aa) that have been thrown into the crys

Re: [gmx-users] Simulated annealing

Hi! I have appended the NMR structure to a part of the protein that was not resolved to the protein and now I want to perform simulated annealing of the 40 amino acids (NMR structure had 33 amino acids and to link I needed another 7 aa) that have been thrown into the crystal structure. I am new to

Re: [gmx-users] Simulated annealing

jayant james wrote: Hi! I have a question with regard to a system that I am attempting to model. The N-terminal of chain of the protein was not resolved crystallographically but was later solved by NMR. Now my plan is to append the NMR structure on to chain A of the protein and perform simula

[gmx-users] Simulated annealing

Hi! I have a question with regard to a system that I am attempting to model. The N-terminal of chain of the protein was not resolved crystallographically but was later solved by NMR. Now my plan is to append the NMR structure on to chain A of the protein and perform simulated annealing only for the

Re: [gmx-users] SIMULATED ANNEALING

sharada wrote: *Thankyou for the reply Mark. In fact I started another simulated annealing job for my peptide with Tcoupl = Berendsen using the same annealing protocol. I didnot get any warnings. However the temperature increases from 0 to 53K and fluctuates around that through out till the

Re: Re: [gmx-users] SIMULATED ANNEALING

000e+00 Other-Other2.54858e+015.55314e+027.27596e+000.0e+00 0.0e+00 T-ProteinT-Other 4.00791e+002.87110e+00 -- Original Message -- From: Mark Abraham To: Discussion list for GROMACS users Date: Fri, 13 Feb 2009 00:13:23 +1100 Subject: Re: [gmx-us

Re: [gmx-users] SIMULATED ANNEALING

sharada wrote: Dear Nuno Azoia, I followed one of the replies given at gmx-users list which I quote here...I donot know whether this is right ? In that case the temperature has truly changed from 0 to 60 how is it possible if Tcoupl = no...?I am in doubt. You're actually running in an NVE

Re: Re: [gmx-users] SIMULATED ANNEALING

Dear Nuno Azoia, I followed one of the replies given at gmx-users list which I quote here...I donot know whether this is right ? In that case the temperature has truly changed from 0 to 60 how is it possible if Tcoupl = no...?I am in doubt. Kindly comment. sharada Re: [gmx-users] how to write a

Re: Re: [gmx-users]Simulated annealing

Dear Xavier and Jochen, Thank you for the suggestions: it works well now. Jes. On Mon, 27 Oct 2008 Xavier Periole wrote : >On 27 Oct 2008 06:36:09 - > "JMandumpal" <[EMAIL PROTECTED]> wrote: >> Dear GROMACS users, >> >>I have got a problem while running a simulated anealing simulations,

Re: [gmx-users]Simulated annealing

On 27 Oct 2008 06:36:09 - "JMandumpal" <[EMAIL PROTECTED]> wrote: Dear GROMACS users, I have got a problem while running a simulated anealing simulations, using GROMACS 3.3.3 version, of pure water: the task: I want to cool the system (water- 500 molecules) from 360 K to 0K in 100ps

Re: [gmx-users]Simulated annealing

JMandumpal wrote: > > Dear GROMACS users, > > I have got a problem while running a simulated anealing simulations, using > GROMACS 3.3.3 version, of pure water: > > the task: > > I want to cool the system (water- 500 molecules) from 360 K to 0K in 100ps > time ( fast cooling). For that I us

[gmx-users]Simulated annealing

Dear GROMACS users, I have got a problem while running a simulated anealing simulations, using GROMACS 3.3.3 version, of pure water: the task: I want to cool the system (water- 500 molecules) from 360 K to 0K in 100ps time ( fast cooling). For that I used the following script: title

Re: [gmx-users] Simulated Annealing problem

On Sat, 22 Mar 2008, Mark Abraham wrote: Hello, Thanks for reply. I am sorry for typo here, but just checked the .mdp file. Its correct in the input file. In the log file, it says for annealing as: grpopts: nrdf: 8093.62 55326.4 ref_t:300 300 ta

Re: [gmx-users] Simulated Annealing problem

Hello, Thanks for reply. I am sorry for typo here, but just checked the .mdp file. Its correct in the input file. In the log file, it says for annealing as: grpopts: nrdf: 8093.62 55326.4 ref_t:300 300 tau_t:0.1 0.1 anne

Re: [gmx-users] Simulated Annealing problem

[EMAIL PROTECTED] wrote: Dear All, I am trying to do simulated annealing for solvated protein system. the excerpts of the file is as: energygrps = protein non-protein ;Temperature coupling tcoupl = Berendsen tc-grps = protein non-protein tau_t

[gmx-users] Simulated Annealing problem

Dear All, I am trying to do simulated annealing for solvated protein system. the excerpts of the file is as: energygrps = protein non-protein ;Temperature coupling tcoupl = Berendsen tc-grps = protein non-protein tau_t= 0.1 0.1

[gmx-users] Simulated Annealing-SINGLE precession

Dear GMX users, We are interested in Simulated Annealing MD for Spep in the tutorial. We tried using single precession (GMX version 3.2.1 in Lunux), we got segmentation fault. But in double precession, there is no error obtained. Do we need to run in only double precession? Is it possible to t

[gmx-users] Simulated annealing MD

Dear GMX users, I am interested in doing Simulated Annealing MD using GROMACS. Does any body have any tutorial or protocol for doing? With thanks Dr.C.Karunakaran __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around