Re: [gmx-users] Rupture force definition

Thanks Justin, I want to see the change statistically by using same parameter (velocity and same spring constant) Hence, I think it will be better to pull the same system by choosing its different conformation. Eg. I had taken the the last conformation of production md ( 50 ns) for pulling.

Re: [gmx-users] Rupture force definition

On 5/17/19 6:15 AM, Rakesh Mishra wrote: Dear Justin After long time again I want to ask one question. If suppose I want to repeat the same production simulation ( final md simulation) for different seeds, then how to do. Because as from the knowledge of gromacs there is no manual way to put

Re: [gmx-users] Rupture force definition

Dear Justin After long time again I want to ask one question. If suppose I want to repeat the same production simulation ( final md simulation) for different seeds, then how to do. Because as from the knowledge of gromacs there is no manual way to put different seeds in the .mdp files. On Mon,

Re: [gmx-users] Rupture force definition

On 6/25/18 8:48 AM, Rakesh Mishra wrote: Dear Justin. I have observed one thing that during pulling (Constant velocity pulling ) of dsDNA/dsRNA ( globally say Nucleic acid ) along helical direction, we observe that in the force/time .xvg file, some time force value is +ve and some time

Re: [gmx-users] Rupture force definition

Dear Justin. I have observed one thing that during pulling (Constant velocity pulling ) of dsDNA/dsRNA ( globally say Nucleic acid ) along helical direction, we observe that in the force/time .xvg file, some time force value is +ve and some time force value is -ve. So why it happens. In my

Re: [gmx-users] Rupture force definition

On 6/8/18 2:52 AM, Rakesh Mishra wrote: Dear Justin . I have two query 1-What can be the optimized value of rate can be taken for pulling of dsDNA/dsRNA using gromacs format where solvent is aqua. From your umbrella sampling manual, rate is very high like (0.01 nm/ps), which is equal to

Re: [gmx-users] Rupture force definition

Dear Justin . I have two query 1-What can be the optimized value of rate can be taken for pulling of dsDNA/dsRNA using gromacs format where solvent is aqua. >From your umbrella sampling manual, rate is very high like (0.01 nm/ps), which is equal to 0.0001Angstrom/fs. 2- In pulling mdp file

Re: [gmx-users] Rupture force definition

On 5/15/18 2:46 AM, Rakesh Mishra wrote: Dear Justin, In all the respect that you have suggested is absolutely correct. But I have a question that just like a constant rate pulling like - [pull_coord1_rate= 0.01 ; 0.01 nm per ps = 10 nm per 1 ns ( which was from your

Re: [gmx-users] Rupture force definition

Dear Justin, In all the respect that you have suggested is absolutely correct. But I have a question that just like a constant rate pulling like - [pull_coord1_rate= 0.01 ; 0.01 nm per ps = 10 nm per 1 ns ( which was from your umbrella sampling)] Is there any formate in

Re: [gmx-users] Rupture force definition

On 5/10/18 8:17 AM, Rakesh Mishra wrote: Thanks to ur quick response Would you please shed some light on my query no. 1 about the box size. Please go through that. I don't know exactly what you'd like me to say. Your interpretation of GROMACS' requirements is correct. I don't know what

Re: [gmx-users] Rupture force definition

Thanks to ur quick response Would you please shed some light on my query no. 1 about the box size. Please go through that. On Thu, May 10, 2018 at 5:35 PM, Justin Lemkul wrote: > > > On 5/10/18 1:24 AM, Rakesh Mishra wrote: > >> Dear Justin, >> >> I have discussed a lot

Re: [gmx-users] Rupture force definition

On 5/10/18 1:24 AM, Rakesh Mishra wrote: Dear Justin, I have discussed a lot regarding the pulling of dsRNA/dsDNA using gromacs about your protocol. Thanks for those discussion. But I faced two more basic problem in gromacs. 1- I need double size box if I need to pull half distance of

Re: [gmx-users] Rupture force definition

Dear Justin, I have discussed a lot regarding the pulling of dsRNA/dsDNA using gromacs about your protocol. Thanks for those discussion. But I faced two more basic problem in gromacs. 1- I need double size box if I need to pull half distance of box (Which makes time demanding ). Eg.

Re: [gmx-users] Rupture force definition

On 2/15/18 4:13 AM, Rakesh Mishra wrote: Dear Justin thanks for your advise. I will check for longer run for getting response according to you. I would like to explain my system,which is siRNA of chain A and B. Here, after doing all formalities, I had run 10 ns then try to apply the pull

Re: [gmx-users] Rupture force definition

Dear Justin thanks for your advise. I will check for longer run for getting response according to you. I would like to explain my system,which is siRNA of chain A and B. Here, after doing all formalities, I had run 10 ns then try to apply the pull protocol. See, here for pulling this system, I

Re: [gmx-users] Rupture force definition

On 2/14/18 7:31 AM, Rakesh Mishra wrote: Dear Justin, Can you explain something regarding this issue. I couldn't get resolve one problem. Though now I am able to make restrict (immobile ) the needed residue and pulled another one. But the contradiction that i am facing is that, when I am

Re: [gmx-users] Rupture force definition

Dear Justin, Can you explain something regarding this issue. I couldn't get resolve one problem. Though now I am able to make restrict (immobile ) the needed residue and pulled another one. But the contradiction that i am facing is that, when I am pulling with -rate (in negative z direction,

Re: [gmx-users] Rupture force definition

Thank you very much Justin. Here it is working but having some problem. pull_group2_name = chain_B35 is moving in the + z direction & pull_group4_name= chain_B26 is moving oppositely in the -z direction While I have given pull in +z direction for both the above group. Note -

Re: [gmx-users] Rupture force definition

On 2/1/18 7:59 AM, Rakesh Mishra wrote: Dear Justin Here I am applying pull for two groups with respect to two reference group as following. ; Pull code pull= yes pull_ngroups= 4 pull_ncoords= 1 pull_group1_name= chain_A8 (reference

Re: [gmx-users] Rupture force definition

Dear Justin Here I am applying pull for two groups with respect to two reference group as following. ; Pull code pull= yes pull_ngroups= 4 pull_ncoords= 1 pull_group1_name= chain_A8 (reference also immobile ) pull_group2_name=

Re: [gmx-users] Rupture force definition

Thank you Justin. I got it and did it also. On Thu, Jan 25, 2018 at 7:04 PM, Justin Lemkul wrote: > > > On 1/25/18 2:41 AM, Rakesh Mishra wrote: > >> Thanks for reply. >> >> Dear Justin >> >> Is it possible to transform .xtc file in the form of .pdb formate >> excluding

Re: [gmx-users] Rupture force definition

On 1/25/18 2:41 AM, Rakesh Mishra wrote: Thanks for reply. Dear Justin Is it possible to transform .xtc file in the form of .pdb formate excluding solvent and ion molecules simultaneously. I am familiar to do this with "trjconv" command. But by using this we can transform .xtc file in the

Re: [gmx-users] Rupture force definition

Thanks for reply. Dear Justin Is it possible to transform .xtc file in the form of .pdb formate excluding solvent and ion molecules simultaneously. I am familiar to do this with "trjconv" command. But by using this we can transform .xtc file in the form of .pdb formate, where water molecules and

Re: [gmx-users] Rupture force definition

On 1/24/18 5:02 AM, Rakesh Mishra wrote: Dear Justin Thank you very much for removing the doubts . Let me extend my query in this respect again. As according to pull code formate which is discussed in your testing work of umbrella sampling . Please have a rough look. Pull code pull

Re: [gmx-users] Rupture force definition

Dear Justin Thank you very much for removing the doubts . Let me extend my query in this respect again. As according to pull code formate which is discussed in your testing work of umbrella sampling . Please have a rough look. Pull code pull= yes pull_ngroups=

Re: [gmx-users] Rupture force definition

On 1/23/18 3:01 AM, Rakesh Mishra wrote: Ok, thanks for learifivcation. Dear Justin I have one another query regarding pulling using umbrella sampling. See these two lines below. Eg.Pull group natomspbc atom distance at startreference at t=0 131

Re: [gmx-users] Rupture force definition

Ok, thanks for learifivcation. Dear Justin I have one another query regarding pulling using umbrella sampling. See these two lines below. Eg.Pull group natomspbc atom distance at startreference at t=0 131 1387 231

Re: [gmx-users] Rupture force definition

On 1/19/18 12:52 AM, Rakesh Mishra wrote: Dear Justin Thanks for your explanation . Yes I am agree that it will depend on the k value and path direction. Let suppose we map the experimental spring constant and rate then it will be some how relevant for my study. My another query is the same

Re: [gmx-users] Rupture force definition

Dear Justin Thanks for your explanation . Yes I am agree that it will depend on the k value and path direction. Let suppose we map the experimental spring constant and rate then it will be some how relevant for my study. My another query is the same from umbrella sampling of puling code. If I

Re: [gmx-users] Rupture force definition

On 1/17/18 7:09 AM, Rakesh Mishra wrote: Dear, ​Justin​ I have one query regarding pulling of si-rNA (having chain-a and chain-b). Here, I am pulling 3' end of chain-a and fixed 3' end of chain-b (diagonally apposite ). I am doing pulling using gromacs with constant velocity rate using

[gmx-users] Rupture force definition

Dear, ​Justin​ I have one query regarding pulling of si-rNA (having chain-a and chain-b). Here, I am pulling 3' end of chain-a and fixed 3' end of chain-b (diagonally apposite ). I am doing pulling using gromacs with constant velocity rate using Umbrella sampling. after finalization of pulling

[gmx-users] Rupture force definition

Dear, all I have one query regarding pulling of si-rNA (having chain-a and chain-b). Here, I am pulling 3' end of chain-a and fixed 3' end of chain-b (diagonally apposite ). I am doing pulling using gromacs with constant velocity rate using Umbrella sampling. after finalization of pulling before