Re: [gmx-users] temperature problem

rules for particular force field ...Or Some thing more than that needed to be done to define their interaction in non-bonded file !!! Thanks and Regards Lovika On Mon, Jun 22, 2015 at 6:16 PM, Lovika Moudgil lovikamoud...@gmail.com wrote: Thanks Justin Regrads Lovika On Mon, Jun 22

Re: [gmx-users] temperature problem

)* I am not being able to find this gro file . Thanks and Regards Lovika On Fri, Jun 19, 2015 at 7:45 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/19/15 10:13 AM, Lovika Moudgil wrote: Hi .. Can anybody tell me about *nrdf* (*radial distribution functions*) value that is in log

Re: [gmx-users] temperature problem

Hi .. Can anybody tell me about *nrdf* (*radial distribution functions*) value that is in log file . How it effect our system !! Any link that I can follow to understand its role more clearly !!! Thanks and Regards Lovika On Wed, Jun 17, 2015 at 10:54 AM, Lovika Moudgil lovikamoud

Re: [gmx-users] temperature problem

Thanks Justin . Your suggestions helped me a lot I got it . Regards Lovika On Sun, Jun 7, 2015 at 7:23 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/6/15 2:03 AM, Lovika Moudgil wrote: Hi Justin ... Thanks for being so supportive . I tried things as you said and figured out

Re: [gmx-users] temperature problem

...@vt.edu wrote: On 6/5/15 8:09 AM, Lovika Moudgil wrote: Hi Justin... Yes I agree my system is behaving absurdly . But I am wondering why !!I have done minimization without any error ..here is the result ... Steepest Descents converged to Fmax 1000 in 1004 steps Potential Energy = -9.6667906e

Re: [gmx-users] temperature problem

behaving weird . If system is wrong why its working even for one step ?? Thanks and Regards Lovika On Thu, Jun 4, 2015 at 6:27 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/4/15 8:52 AM, Lovika Moudgil wrote: HiiiHere is my .mdp file below ... title= OPLS Lysozyme NVT equilibration

Re: [gmx-users] temperature problem

Thanks and Regards Lovika On Thu, Jun 4, 2015 at 5:09 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/4/15 12:39 AM, Lovika Moudgil wrote: Hi...Justin Thanks for explaining .. I just want to ask could there be any other reasons too?? ...Because I have tried it with PME too

Re: [gmx-users] temperature problem

is the only useful feature of cutoff electrostatics. Use an actual model physics. Mark On Tue, Jun 2, 2015 at 10:19 AM Peter Kroon p.c.kr...@rug.nl wrote: On 02/06/15 09:43, Lovika Moudgil wrote: Hi everyone I am having some problem in my md run .In my system temperature

Re: [gmx-users] temperature problem

: On 6/3/15 3:46 AM, Lovika Moudgil wrote: Hi...thanks for reply Peter and Mark I tried with temperature coupling . But things are still same ... Hi ... Mark would you like to explain this factor to me ?? Using a plain cutoff in the condensed phase is outdated methodology

[gmx-users] temperature problem

Hi everyone I am having some problem in my md run .In my system temperature of system is abruptly increasing .I have done nvt for 50 picoseconds ..nd then using it for further md simulation .I am not getting any error for this temperature increase .But when I plot temperature graph ,

[gmx-users] nvt problem

Hi Everyone , I am having a problem in NVT of system . In my system I have Gold and aminoacid . For Gold I am using GolP forcefield and for aminoacid using OPLSAA forcefield . I have done energy minimization of my system but when I am doing NVT I am getting error of water is not getting settled .

Re: [gmx-users] itp file

the .itp file from GROMOS for other forcefield. Which kind of molecule are you studying? For generating the .itp file is usually use the pdb2gmx tool. Regards Lalita Message: 1 Date: Thu, 11 Sep 2014 10:22:39 +0530 From: Lovika Moudgil lovikamoud...@gmail.com To: gmx-us...@gromacs.org

Re: [gmx-users] itp file

Thanks Justin ... I will try as you said!! Regards Lovika On Thu, Sep 11, 2014 at 6:08 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/11/14 6:09 AM, Lovika Moudgil wrote: Thanks for reply Lalit , Actually my system have citrate anion and I want .itp for citrate and further I will use

[gmx-users] Integrator problem

Hi everyoneI want to ask one question...In my .mdp file if I use md intergrator for energy minimisation .then system is fine...but if I use steep integrator...my system got error of more force on one atomI not clear why this is happeingcan any body guide me please.. Regards

Re: [gmx-users] Status of MD simulation

Hi...I think the best way is to check log file If I m wrong please do correct me!! Regards Lovika On 8 Sep 2014 19:21, ankit agrawal aka...@gmail.com wrote: hi I am running a 5ns simulation using mdrun command. So this will take a day to complete. So I want to know that how to check the

Re: [gmx-users] Integrator problem

Oo.thanks for guiding Mark !!! Regards Lovika On 8 Sep 2014 19:45, Mark Abraham mark.j.abra...@gmail.com wrote: The md integrator does MD, not EM... Mark On Sep 8, 2014 4:11 PM, Lovika Moudgil lovikamoud...@gmail.com wrote: Hi everyoneI want to ask one question...In my .mdp file

Re: [gmx-users] non-zero charge

with certainty always say that a fractional charge is wrong (and hence an error). -Justin With regards, Indu On Fri, Sep 5, 2014 at 11:14 AM, Lovika Moudgil lovikamoud...@gmail.com wrote: Hi Everyone , I want to ask one question , that my system have non-zero total charge and its

[gmx-users] water not getting settle

Hi everyone , I am getting an error about water i.e step 168: Water molecule starting at atom 5226 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. I have already tried reducing timestep ..but it didn't worked . If I freeze water things work fine . But what

Re: [gmx-users] coordinates don't match

Thanks Lalita and Rinu for reply ...I got the point!!! Regards lovika On Wed, Aug 27, 2014 at 3:51 PM, RINU KHATTRI nickname.mi...@gmail.com wrote: firstly check your topology file i think you forgot to add either ligand or any molecule which is present in your pdb . in maximum steps of

[gmx-users] coordinates don't match

Hi everyone , I have a question , If coordinates of my .pdb file and .top file are not matching than what is the right way to correct it ! Like if I have one coordinate more in .pdb than in .top and I delete one from .pdb ...and it get fine !!! Will it be a problem in future or its fine to do

Re: [gmx-users] mdrun error

is constituent of a molecule (e.g. H2O), then you could also try moving the molecule coordinates and see how it goes. I had a similar issue, but moving the molecule by an angstrom worked in my case. Good luck! Regards, Kester - 원본 메일 - *보낸사람* : Lovika Moudgil lovikamoud

[gmx-users] mdrun error

Hi everyone , Need some help .I have got an error in my mdrun . Upto grompp every thing was fine but when I give command for mdrun ,It stops with this ... Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=1 Step= 14, Dmax= 1.2e-06 nm, Epot= 2.08534e+18

Re: [gmx-users] mdrun error

into atom 19 specifically? Perhaps, changing the coordinate of atom 19 manually, and let it do another minimisation run would solve the issue? Regards, Kester - 원본 메일 - *보낸사람* : Lovika Moudgil lovikamoud...@gmail.com *받는사람* : gmx-us...@gromacs.org *받은날짜* : 2014년 8월 24일(일) 18

[gmx-users] pH simulation

Hi everyone... I want to do pH simulation in gromacs . I didn't found any specific link that I can follow for calculation regarding pH . Can you please guide me ..Any link that can help me... Thanks in advance Regards Lovika -- Gromacs Users mailing list * Please search the archive at

[gmx-users] merge two .top file

Hi everyone Can anybody tell me that how can I merge two different .top (topology) files Thanks and Regards Lovika -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] merge two .top file

Thanks Justin:) On Tue, May 27, 2014 at 5:26 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/27/14, 7:39 AM, Lovika Moudgil wrote: Hi everyone Can anybody tell me that how can I merge two different .top (topology) files A .top file is a system topology, so it's hard

[gmx-users] constraint error

Hi everyone... Can any body help me ...As i have an .itp file in which I have defined constraint and then I am defining this .itp file in my .top fileAnd with grompp command I got this error . I think I have defined constraints on right place. Than why this error ??Where I need to move

Re: [gmx-users] constraint error

Thanks for reply Justin . Yes ...I get your point . Regards Lovika On Sat, May 24, 2014 at 4:57 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/24/14, 4:46 AM, Lovika Moudgil wrote: Hi everyone... Can any body help me ...As i have an .itp file in which I have defined constraint

[gmx-users] how to generate .top file

Hi everyone.. I have a .pdb file with protein and gold slab .Problem is I can generate .top file for my protein with pdb2gmx but I want my slab in the same system .I can generate .gro file for both but what about .top file . Can any body help me with this issue .Thanks in advance. Regards Lovika

Re: [gmx-users] how to generate .top file

UA 1 0196.96655 [ system ] Protein with gold [ molecules ] ... Hmm, I wonder, should one account for the gravitational effects of gold. Pretty heavy stuff :p Cheers, Tsjerk On Fri, May 23, 2014 at 11:39 AM, Lovika Moudgil lovikamoud...@gmail.com wrote

Re: [gmx-users] how to generate .top file

Thanks Tsjerk [?] Regards Lovika On Fri, May 23, 2014 at 4:17 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Lovika, Yes, you can #include gold.itp or something along those lines. Cheers, Tsjerk On Fri, May 23, 2014 at 12:44 PM, Lovika Moudgil lovikamoud...@gmail.com

Re: [gmx-users] mdrun error

Thanks for help Justin. Regards Lovika On Tue, May 20, 2014 at 2:49 AM, Justin Lemkul jalem...@vt.edu wrote: On 5/19/14, 11:24 AM, Lovika Moudgil wrote: Hiii Everyone I need some helpAs in my grompp command I am getting warning about charge group and rlist Can any body

[gmx-users] Need guidance

Hi Everyone, Need guidance and help. As I am doing md simulation for Lysozyme in presence of gold i.e Au(111) with force field oplsaa and Golp parameters . What I am doing is first generating .top file for protein with oplsaa force field and then using Golp gold .itp and .gro file parameters

Re: [gmx-users] mdrun error

guide me .. Regards and Thanks Lovika On Sun, May 18, 2014 at 9:54 AM, Lovika Moudgil lovikamoud...@gmail.comwrote: Mark thanks for your reply and support . [?] Regards Lovika On Sat, May 17, 2014 at 5:23 PM, Mark Abraham mark.j.abra...@gmail.comwrote: No, the .mdp file mostly

Re: [gmx-users] mdrun error

information to be sure. Mark On May 17, 2014 7:33 AM, Lovika Moudgil lovikamoud...@gmail.com wrote: Hi Everyone I need some help. With my mdrun command I am getting this following error . Program mdrun, VERSION 4.6.5 Source code file: /home/itlab/Documents/gromacs/gromacs

Re: [gmx-users] mdrun error

AM, Lovika Moudgil lovikamoud...@gmail.com wrote: Thanks for quick reply Mark...what information you are asking for?Should I search for this my .mdp file?? Thanks Lovika On Sat, May 17, 2014 at 11:35 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Your simulation seems

[gmx-users] mdrun error

Hi Everyone I need some help. With my mdrun command I am getting this following error . Program mdrun, VERSION 4.6.5 Source code file: /home/itlab/Documents/gromacs/gromacs-4.6.5/src/mdlib/domdec_con.c, line: 722 Fatal error: DD cell 0 0 1 could only obtain 1 of the 2 atoms that are

[gmx-users] need guidance

Hi Everyone , I need some help . gromacs software is new for me . I want to know how can I run my protein in presence of gold atoms . What force field should be there that is compatible with gold atoms and what changes i need to do .Is there any link that I can follow ? Please guide me . Thanks