Re: [gmx-users] Protein fragments during production simulation

6:26 AM, SAPNA BORAH sapnauser...@gmail.com wrote: Dear all, I am trying to simulate a globular protein predicted by Ab-initio method using web servers, Robetta and Itasser. I am currently using Gromacs 4.6.5. A problem has occured during the production md run, when my protein starts

Re: [gmx-users] Protein fragments during production simulation

of fragments has reduced comparatively to the 1ns equilibration run. Is this also a pbc related issue, and can someone please put some light on what exactly is the problem going on? Regards, Sapna On Wed, Apr 29, 2015 at 10:46 AM, SAPNA BORAH sapnauser...@gmail.com wrote: Hi Tsjerk, Thank your

[gmx-users] Protein fragments during production simulation

Dear all, I am trying to simulate a globular protein predicted by Ab-initio method using web servers, Robetta and Itasser. I am currently using Gromacs 4.6.5. A problem has occured during the production md run, when my protein starts to break into fragments while it remains inside the water box.

Re: [gmx-users] Protein fragments during production simulation

Dear Justin, Thanks for the clarification. :) Regards, Sapna On 4/30/15, Justin Lemkul jalem...@vt.edu wrote: On 4/30/15 10:12 AM, SAPNA BORAH wrote: Dear all, I have some doubts regarding pbc being new to gromacs. Since my protein was breaking into fragments, I introduced pbc options

Re: [gmx-users] Force-field bias???

-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of SAPNA BORAH sapnauser...@gmail.com Sent: Wednesday, August 05, 2015 10:20 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Force-field bias??? Dear all, Thank you for your answers which

[gmx-users] Force-field bias???

Dear all, I have a general query about unfolding simulations. Is there a bias among force-fields selected for unfolding, i.e. is it possible that unfolding of the protein may be different with a change in force fields applied? Literature has given some support on this, however, I am not sure how

Re: [gmx-users] Force-field bias???

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: Wednesday, August 05, 2015 7:31 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Force-field bias??? On 8/5/15 6:24 AM, SAPNA

[gmx-users] Simulation of post translationally modified peptide

Dear All, I am trying to simulate nisin containing modified amino acids, DAL(D- ALANINE), DBU (Z-DEHYDROBUTYRINE), DHA(2,3-DIDEHYDROALANINE) and DBB (D-ALPHA-AMINOBUTYRIC ACID). Can anyone suggest me from where I can obtain the forcefields for the above entities? Thanks in advance. Regards,

Re: [gmx-users] Construction of silver nanoparticles

Thank you Justin Sapna Mayuri Borah c/o Dr. A. N. Jha Research student Tezpur University, India On Tue, Oct 13, 2015 at 7:21 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/13/15 9:45 AM, SAPNA BORAH wrote: > >> Thank you Justin. >> >> I have mailed

[gmx-users] Construction of silver nanoparticles

Dear All, I am trying to perform silver nanoparticles simulations. Since I found articles performing such simulations in gromacs, I have a query against how do I incorporate the silver atoms in the simulation box? Thanks in Advance. Sapna Mayuri Borah c/o Dr. A. N. Jha Research student Tezpur

Re: [gmx-users] Construction of silver nanoparticles

wrote: > > > On 10/12/15 7:20 AM, SAPNA BORAH wrote: > >> Dear All, >> >> I am trying to perform silver nanoparticles simulations. Since I found >> articles performing such simulations in gromacs, I have a query against >> how >> do I incorporate the silve

Re: [gmx-users] how to make 8M solutions??

molecules that is, and then add that many molecules. Decide whether you care about the volume excluded by the protein when considering what that molality means. Mark On Wed, Jul 8, 2015 at 6:51 AM SAPNA BORAH sapnauser...@gmail.com wrote: Dear all, I am trying to add gdmcl to a protein

[gmx-users] how to make 8M solutions??

Dear all, I am trying to add gdmcl to a protein, however I am unable to make molal solutions. I can add gdmcl by -nmol command but to make molal solutions is giving me a hard time. This is a basic query but it has been bugging me for quite a long time. Please put some light on doing this... I

Re: [gmx-users] simulation_time[Nikita Bora]

hi... So there is no direct way to know the values to be used . however the last line is still unclear... Sapna Mayuri Borah c/o Dr. A. N. Jha Research student Tezpur University, India On Fri, May 20, 2016 at 12:00 PM, Tsjerk Wassenaar wrote: > Hi Nikita, > > It's not like

Re: [gmx-users] Extending the MD

:) Sapna Mayuri Borah c/o Dr. A. N. Jha Research student Tezpur University, India On Thu, May 26, 2016 at 6:01 PM, sun <sun.i...@gmail.com> wrote: > Allright Sapna. Thank you very much. > > Sent from my iPhone > > > On 26-May-2016, at 4:59 pm, SAPNA BORAH <sa

[gmx-users] Calculate total non-bonded contacts in gromacs

Dear all, Is there any protocol in gromacs that can help me get the total number of non-bonded contacts in a protein, or protein-ligand with respect to time? Thanks in advance. Regards, Sapna. Sapna Mayuri Borah c/o Dr. A. N. Jha Research student Tezpur University, India -- Gromacs Users

Re: [gmx-users] Extending the MD

Hi!! After converting the tpr, while initiating mdrun, try adding the previous cpt file as well.. mdrun -s next.tpr -cpi previous.cpt Thanks! Sapna Mayuri Borah c/o Dr. A. N. Jha Research student Tezpur University, India On Thu, May 26, 2016 at 4:31 PM, sun wrote: >

Re: [gmx-users] Extending the MD

r missing or renamed" > > > > Sent from my iPhone > > > On 26-May-2016, at 4:35 pm, SAPNA BORAH <sapnauser...@gmail.com> wrote: > > > > Hi!! > > > > After converting the tpr, while initiating mdrun, try adding the previous > > cpt file as we

Re: [gmx-users] Extending the MD

0 ns > simulation. > > Sent from my iPhone > > > On 26-May-2016, at 4:43 pm, SAPNA BORAH <sapnauser...@gmail.com> wrote: > > > > Well that's kinda new i must say. Can you please paste the entire command > > you have used. I think you have mis-named the file :

Re: [gmx-users] Extending the MD

University, India On Thu, May 26, 2016 at 4:57 PM, SAPNA BORAH <sapnauser...@gmail.com> wrote: > It may be a case. You can rename the files to what they were and try > again. Since here, the error simply implies the files are renamed or > missing. > > Sapna Mayuri Bora

Re: [gmx-users] simulation_time[Nikita Bora]

the > people who show why their parameter choices work. The models didn't arrive > by divine inspiration :-) > > Mark > > On Thu, May 26, 2016 at 8:42 AM SAPNA BORAH <sapnauser...@gmail.com> > wrote: > > > hi... > > So there is no direct way to know the

Re: [gmx-users] topology and coordinate file not matching after grompp

Dear Swagata, You have to include the benzene molecules in your topology section. [ molecules ] ; Compound#mols Protein_chain_A 1 PDB 250*6 SOL 7217 BENZENE xyz It should solve your problem. Sapna. Sapna Mayuri Borah c/o Dr. A. N. Jha

[gmx-users] Different results for same protein's simulation in 4.6.5 and 5.0.4

Dear all, I have tried running the same protein in the two versions of gromacs 4.6.5 and 5.0.4. Now, both the runs are producing entirely different results. The results till equilibration are same. After the run however, there is a total change in the production results. I have used the same

Re: [gmx-users] Different results for same protein's simulation in 4.6.5 and 5.0.4

gy/Reproducibility. You > should see a similar range of variation in the trajectories produced in the > two versions that are incompletely sampling the same ensemble, but one can > say very little about two single observed trajectories sampled from them. > > Mark > > On

Re: [gmx-users] Different results for same protein's simulation in 4.6.5 and 5.0.4

thing we'd be able to see from the RMSD > plot anyway, whether you removed jumps or not. Otherwise it does not > contain useful information (in this regard). > > Cheers, > > Tsjerk > On Feb 11, 2016 05:28, "SAPNA BORAH" <sapnauser...@gmail.com> wrote: > > >

Re: [gmx-users] Different results for same protein's simulation in 4.6.5 and 5.0.4

be needed. > > Kind regards > > Dries > On 29 Feb 2016 5:25 a.m., "SAPNA BORAH" <sapnauser...@gmail.com> wrote: > > > Dear Mark, > > > > I have still not been able to solve my problem. A whole new problem has > now > > arisen. I am list

[gmx-users] g_cluster analysis

Dear all, I am trying to use g_cluster protocol to get representative snapshots of the simulations. I have concatenated 9 set of simulations and run g_cluster for the same. The result shows a total of 198 clusters. Is this correct? Following is the command I have used: g_cluster -s models.gro

[gmx-users] Zinc Oxide Simulation

Hi! We are working with ZnO nanoparticle structures generated from Virtual NanoLab Software, using the Wulff constructor. We are using gromos54a7ff for the simulation, and introduced ZnO parameters from literature. Partial charges for Zn= 1.026. For O= -1.026. (Surface Science 602 (2008)

Re: [gmx-users] Zinc Oxide Simulation

but you need to > check if they can reproduce the phases you're interested in. For instance: > http://pubs.acs.org/doi/full/10.1021/la9022739 > > best > > Andre > > > > On Thu, Apr 20, 2017 at 9:32 AM, SAPNA BORAH <sapnauser...@gmail.com> > wrote: > > >