[gmx-users] Fwd: Force field for urea and urea-TMAO mixture

field? Any suggestions regarding this will be highly appreciated. Thank you Regards -- Ishrat Jahan Research Scholar Department Of Chemistry A.M.U Aligarh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting

[gmx-users] Force field for urea and urea-TMAO mixture

suggestions regarding this will be highly appreciated. Thank you Regards -- Ishrat Jahan Research Scholar Department Of Chemistry A.M.U Aligarh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post

[gmx-users] Force field for urea and urea-TMAO mixture

suggestions regarding this will be highly appreciated. Thank you Regards -- Ishrat Jahan Research Scholar Department Of Chemistry A.M.U Aligarh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post

Re: [gmx-users] RDF calculation from surface of protein

isit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Ishrat Jahan Research Scholar Department Of Chemistry A.M.U Aligarh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mai

Re: [gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation

> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://

Re: [gmx-users] Position Restraints MD

wrote: > > > On 9/24/19 12:09 AM, ISHRAT JAHAN wrote: > > Thanks Justin Sir for the response. Actually I have done the MD > simulation > > of protein in presence of metal w.o.t. applying any position restraints > and > > during the trajectory analysis I found

Re: [gmx-users] Position Restraints MD

of metal on that protein so , I applied position restraint on that metal atom. Is is better to do so or I should apply distance restraint? Any help would be appreciated. Thanks and regards On Tue, Sep 24, 2019 at 9:32 AM ISHRAT JAHAN wrote: > Thanks Justin Sir for the response. > > On Mo

Re: [gmx-users] Position Restraints MD

Thanks Justin Sir for the response. On Mon, Sep 23, 2019 at 4:18 PM Justin Lemkul wrote: > > > On 9/20/19 2:10 AM, ISHRAT JAHAN wrote: > > Dear all, > > I am doing MD simulation of protein and metal atom. I had applied > position > > restraints on metal ato

[gmx-users] Position Restraints MD

or on the whole system. Am I doing it correct or not? Any help related to this will be appreciated. Thanks in advance -- Ishrat Jahan Research Scholar Department Of Chemistry A.M.U Aligarh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Regarding reliability of MD simulation

or multiple simulation only in water in order to say that all the simulation including protein-osmolytes produces reliable results? Kindly help. Thanks in advance Best regards Ishrat Jahan Research Scholar Department Of Chemistry A.M.U Aligarh -- Gromacs Users mailing list * Please search the archive

Re: [gmx-users] Fwd: atoms are not part of any of the T-Coupling groups

Thank you Justin sir for the reply. I have resolved my problem. On Wed, May 8, 2019, 5:57 PM Justin Lemkul wrote: > > > On 5/7/19 1:41 AM, ISHRAT JAHAN wrote: > > -- Forwarded message - > > From: ISHRAT JAHAN > > Date: Tue, May 7, 2019 at

[gmx-users] Fwd: atoms are not part of any of the T-Coupling groups

-- Forwarded message - From: ISHRAT JAHAN Date: Tue, May 7, 2019 at 11:05 AM Subject: atoms are not part of any of the T-Coupling groups To: Dear all, I am trying to calculate the lennard Jones interaction energy between protein and urea in the first solvation shell. I have

[gmx-users] Multiple MD simulation

conformations of protein and how to check the convergence of the results? Any help regarding this will be highly appreciated. Thanks in advance Ishrat Jahan Research Scholar Department Of Chemistry A.M.U Aligarh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org

[gmx-users] Hydrogen bond calculation

molecule in the first hydration shell? How do I make the index? kindly advise the proper steps. Thank you -- Ishrat Jahan Research Scholar Department Of Chemistry A.M.U Aligarh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

[gmx-users] Preferential interaction coefficient (PIC)

Dear all, I have calculated the PIC of osmolytes using the following steps. Please correct me if i m wrong at any point. 1. First i have calculated no. Of water and osmolytes molecule within 0.4 nm of protein using gmx select command and named it as W-local and O- local. 2. Then subtracted the

Re: [gmx-users] Water molecule in the first hydration shell

Thank you Mark sir. On Mon, Jan 21, 2019, 8:27 AM Mark Abraham Hi, > > I suggest you don't ask for "within 0.5 of com of protein" if what you want > is e.g. "within 0.5 of protein" > > Mark > > On Mon, Jan 21, 2019 at 3:51 AM ISHRAT JAHAN wrote: > >

Re: [gmx-users] Water molecule in the first hydration shell

I have calculated it and from there i got the forst hydration layer. On Mon, Jan 21, 2019, 8:29 AM Bratin Kumar Das <177cy500.bra...@nitk.edu.in wrote: > Calculate the rdf first > > On Mon 21 Jan, 2019, 8:22 AM ISHRAT JAHAN > > Thanks for the reply Justin sir.Please tell me

Re: [gmx-users] Water molecule in the first hydration shell

Thanks for the reply Justin sir.Please tell me the right command as i have to calculate it from the surface of protein. On Mon, Jan 21, 2019, 1:39 AM Justin Lemkul > > On 1/20/19 1:01 AM, ISHRAT JAHAN wrote: > > Dear all, > > I want to calculate the number of water molecule wit

[gmx-users] Water molecule in the first hydration shell

-b 110 -tu ns Please tell me whether I have calculated it correctly or not. Thanks -- Ishrat Jahan Research Scholar Department Of Chemistry A.M.U Aligarh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * C

[gmx-users] Fwd: Query regarding Preferential Interaction Coefficient Calculation

in this regard. Thanks in advance -- Forwarded message - From: ISHRAT JAHAN Date: Wed, Jan 16, 2019, 11:23 AM Subject: Query regarding Preferential Interaction Coefficient Calculation To: Dear all, I have done the MD simulation of protein in osmolytes, now i want to calculate

[gmx-users] Query regarding Preferential Interaction Coefficient Calculation

Dear all, I have done the MD simulation of protein in osmolytes, now i want to calculate the preferential interaction coefficient of osmolytes from protein surface.Will anyone please guide me the proper steps of the calculation? Thanks and regards -- Ishrat Jahan Research Scholar Department

[gmx-users] Preferential Binding Coefficient

Will any Please guide me how to calculate the preferential binding coefficient for cosolvent molecule from protein surface? -- Ishrat Jahan Research Scholar Department Of Chemistry A.M.U Aligarh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support

[gmx-users] Population Density Plot

Dear all, Can anyone tell me the command used for calculating the population density plot between Ree and Rg? As I have calculated the Ree and Rg value from gmx polystat command now, i want to plot population density between Ree and Rg. Your help will be appreciated. Thank u - Ishrat Jahan

Re: [gmx-users] Related to energy minimization

Thank u for your instant reply. What changes you have done in mdp file to remove core dump error? On Tue, Sep 11, 2018, 1:26 PM Bratin Kumar Das <177cy500.bra...@nitk.edu.in> wrote: > Ya > > On Tue, Sep 11, 2018, 12:45 PM ISHRAT JAHAN wrote: > > > Did your problem o

Re: [gmx-users] Related to energy minimization

Did your problem of core dumped was solved? On Tue, Sep 11, 2018, 12:23 PM Bratin Kumar Das <177cy500.bra...@nitk.edu.in> wrote: > No problem...I did for other proteins also...during NVT ensemble it's > concentration will be fixed. > > On Tue, Sep 11, 2018 at 11:22 AM, ISH

Re: [gmx-users] Related to energy minimization

ep 11, 2018, 10:29 AM ISHRAT JAHAN wrote: > > > Why should we delete all the water from protein surface. Actually i am > > doing this in simulation in a urea box. How do i remove water from > protein > > surface? > > > > On Tue, Sep 11, 2018, 10:19 AM Bratin

Re: [gmx-users] Related to energy minimization

ters from protein surface > > On Tue, Sep 11, 2018 at 10:06 AM, ISHRAT JAHAN > wrote: > > > I am getting the same error as u have posted today. Segmentation fault > core > > dumped. Although my minimization runs properly. > > > > On Mon, Sep 10, 2018, 6:30 PM Br

Re: [gmx-users] Related to energy minimization

> initial configuration of your .pdb file. Please upload all the lines > written in your terminal during mdrun operation > > On Mon, Sep 10, 2018, 4:13 PM ISHRAT JAHAN wrote: > > > Thank u for your reply sir. I have changed the -Dflexible to -DPosres but > > still gets the

Re: [gmx-users] Related to energy minimization

e 1000 force constant. Don't > give large force costant. > > On Mon, Sep 10, 2018, 3:14 PM ISHRAT JAHAN wrote: > > > Dear all, > > I am trying to do energy minimization of two docked protein. At the > energy > > minimization step during MD simulation process, th

[gmx-users] Related to energy minimization

der = 4 ewald_rtol = 1e-5 constraints = none ; Bond types to replace by constraints pbc = xyz ; Periodic Boundary Conditions (yes/no) [image: Screenshot_from_2018-09-10_14_59_11.jpg] -- Ishrat Jahan Research Scholar Department Of Chemistry A.M.U Aligarh -- Grom

Re: [gmx-users] How to center my complex in the box?

ling_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Ishr

Re: [gmx-users] Related to g_enemat command

Abraham wrote: > Hi, > > You probably ran your simulation on a GPU, which doesn't implement energy > groups. (You probably missed that your log file has noted that.) You can > use mdrun -rerun yourtrajectory to recompute these on the CPU. > > Mark > > On Sat, Aug 11, 2018

[gmx-users] Related to g_enemat command

fault (core dumped) As i know energy.edr file does not contains groups like null: protein-protein interaction Any help regarding this will be appreciated. Thanks in advance -- Ishrat Jahan Research Scholar Department Of Chemistry A.M.U Aligarh -- Gromacs Users mailing list * Please search

[gmx-users] Fwd: Hydration Property of protein

Dear all, Can anyone tell me how to calculate the number of water molecule at particular distance from the surface of protein? Thanks Ishrat Jahan Research Scholar Department Of Chemistry A.M.U Aligarh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support

[gmx-users] Hydration Property of protein

Dear all, Can anyone tell me how to calculate the number of water molecule at particular distance from the surface of protein? Thanks -- Ishrat Jahan Research Scholar Department Of Chemistry A.M.U Aligarh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org

Re: [gmx-users] Error in full MD

here is my log and mdp file. On Tue, Apr 17, 2018 at 3:22 PM, RAHUL SURESH <drrahulsur...@gmail.com> wrote: > Hi > > Please add your log file as well as your mdp settings. > > On Tue, Apr 17, 2018 at 3:10 PM, ISHRAT JAHAN <jishra...@gmail.com> wrote: > > >

[gmx-users] Error in full MD

no error appears in energy minimization and equillibration steps. Thanks -- Ishrat Jahan Research Scholar Department Of Chemistry A.M.U Aligarh -- 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

[gmx-users] Fwd: REMD Simulation

it will effect the results? Thankyou -- Ishrat Jahan Research Scholar Department Of Chemistry A.M.U Aligarh -- 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 http://www.gromacs.org/Support

[gmx-users] REMD Simulation

it will effect the results? Thankyou -- Ishrat Jahan Research Scholar Department Of Chemistry A.M.U Aligarh -- 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 http://www.gromacs.org/Support

Re: [gmx-users] Related to REMD

C/o. Prof. S. Balasubramanian > Molecular Simulations Lab > Chemistry and Physics of Materials Unit (CPMU) > Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR) > Bangalore, India > > On Thu, Jan 4, 2018 at 12:20 PM, ISHRAT JAHAN <jishra...@gmail.com> wrote

Re: [gmx-users] Related to REMD

temperature. Will you please tell me what to do as i am unable to understand? Thanks in advance On Tue, Jan 2, 2018 at 4:55 PM, Sudip Das <das.sudi...@gmail.com> wrote: > Hi Ishrat, > > > On Tue, Jan 2, 2018 at 4:14 PM, ISHRAT JAHAN <jishra...@gmail.com> wrote: > &g

Re: [gmx-users] Related to REMD

My system contains only 95 protein atom and 750 sol molecule. On Tue, Jan 2, 2018 at 4:55 PM, Sudip Das <das.sudi...@gmail.com> wrote: > Hi Ishrat, > > > On Tue, Jan 2, 2018 at 4:14 PM, ISHRAT JAHAN <jishra...@gmail.com> wrote: > > > Dear all, > > I

[gmx-users] Related to REMD

Dear all, I am trying to do REMD simulation. I had equillbrated the system for 5ns and extracted the seed conformation at 3ns using the command- gmx trjconv -f traj.trr -o 3ns.gro -s topol.tpr -dump 3000 -pbc mol I had used temperature generator for REMD simulation from folding.bmc.uu.se/remd with

[gmx-users] osmolytes box generation in gromacs

Dear all, I want to make 3M glycine box of size 6,6,6 in gromacs.can anyone tell me how to find the number of glycine molecule required for making 3M glycine box. Thanks in advance. -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Fwd: Related to PCA

-- Forwarded message -- From: ISHRAT JAHAN <jishra...@gmail.com> Date: Fri, Oct 6, 2017 at 12:08 PM Subject: Related to PCA To: gromacs.org_gmx-users@maillist.sys.kth.se Dear all If we plot the Free Energy Landscapes of proteins from First two principal components a

Re: [gmx-users] Protein break after simulation

no grompp not gives any warning neither i have used -maxwarn option. On Mon, Sep 11, 2017 at 5:26 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/11/17 2:43 AM, ISHRAT JAHAN wrote: > >> how can i check whether the structure is whole or not in .tpr file? After >

Re: [gmx-users] Protein break after simulation

Here i am providing you the link of protein structure https://we.tl/X4yEyZq2aR On Sun, Sep 10, 2017 at 8:59 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/10/17 3:27 AM, ISHRAT JAHAN wrote: > >> Dear Justin >> I have used all the commands given in the l

Re: [gmx-users] Protein break after simulation

r the > trjconv -whole stage? Is the structure in that .tpr whole? > > Mark > > On Sun, Sep 10, 2017 at 9:27 AM ISHRAT JAHAN <jishra...@gmail.com> wrote: > > > Dear Justin > > I have used all the commands given in the link provided by you but unable > > to get

Re: [gmx-users] Protein break after simulation

<jalem...@vt.edu> wrote: > > > On 9/9/17 1:50 AM, ISHRAT JAHAN wrote: > >> Dear all, >> I have done 100ns md simulation of protein with drug using amber99sb.ff >> with gromacs-5.1.4 version. After simulation i found my protein broken >> into >> smaller

Re: [gmx-users] Protein break after simulation

Actually my final .gro file is totally broken into smaller parts when i load it in vmd, for this what will i do? On Sat, Sep 9, 2017 at 7:36 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/9/17 10:05 AM, ISHRAT JAHAN wrote: > >> Dear Justin >> commands whic

Re: [gmx-users] Protein break after simulation

protein_pbc.xtc -pbc whole -center -n protein_drg.ndx On Sat, Sep 9, 2017 at 7:04 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/9/17 1:50 AM, ISHRAT JAHAN wrote: > >> Dear all, >> I have done 100ns md simulation of protein with drug using amber99sb.ff >> with groma

[gmx-users] Protein break after simulation

Dear all, I have done 100ns md simulation of protein with drug using amber99sb.ff with gromacs-5.1.4 version. After simulation i found my protein broken into smaller parts in .gro file but when i load the final xtc file to pr.gro molecule does not break. I have applied -pbc nojump ,cluster and

Re: [gmx-users] Fwd: Unusual bonding between residues in vmd

will you please tell me the method of generating the pdb file from the .xtc file as i have generated it from trjconv after applying pbc but when i open it in vmd , protein totally broken down. On Tue, Aug 22, 2017 at 12:37 PM, Nikhil Maroli wrote: > Hi, > You have to load

[gmx-users] Related to fluctuation in Pressure

Dear all, I have done md simulation at 1 bar pressure but after the simulation when i plot the pressure graph, plot shows fluctuation range from -200 to 200 bar. Is this fluctuation is acceptable? Thanks in advance -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Fwd: Unusual bonding between residues in vmd

re's a mismatch between the coordinate file you loaded in VMD > and what's in the XTC. For example, you didn't write the ligand to the XTC. > > Mark > > On Tue, Aug 22, 2017 at 8:10 AM ISHRAT JAHAN <jishra...@gmail.com> wrote: > > > -- Forwarded mess

Re: [gmx-users] Fwd: Unusual bonding between residues in vmd

, 2017 at 12:10 PM, ISHRAT JAHAN <jishra...@gmail.com> wrote: > I have selected the whole system while writing the .xtc file and from that > .xtc file i wrote the gro file, then how there is mismatch b/w the > coordinates of .xtc and .gro file. > > On Tue, Aug 22, 2017 at 1

[gmx-users] Fwd: Unusual bonding between residues in vmd

-- Forwarded message -- From: ISHRAT JAHAN <jishra...@gmail.com> Date: Tue, Aug 22, 2017 at 11:35 AM Subject: Unusual bonding between residues in vmd To: gromacs.org_gmx-users@maillist.sys.kth.se Dear all, I was trying to do the simulation of 100 ns of protein and drug in g

[gmx-users] Fwd: tetrahedral order parameter

-- Forwarded message -- From: ISHRAT JAHAN <jishra...@gmail.com> Date: Fri, Jun 2, 2017 at 10:29 AM Subject: Re: [gmx-users] tetrahedral order parameter To: gmx-us...@gromacs.org I have used gmx hydorder but unable to understand the output as it gives two .xpm and two .ou

Re: [gmx-users] tetrahedral order parameter

I have used gmx hydorder but unable to understand the output as it gives two .xpm and two .out file. what these file describe please help. On Thu, Jun 1, 2017 at 6:14 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 6/1/17 3:42 AM, ISHRAT JAHAN wrote: > >> Dear all

[gmx-users] tetrahedral order parameter

Dear all, I want to calculate tetrahedral order parameter of water molecule.can anyone tell me how to calculate it. Thanks in advance -- 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

[gmx-users] Tetrahedral orientational order parameter

Dear All, I am trying to calculate the tetrahedral orientational order parameter using command g_hydorder. I get two output with option -or option which is of the type - 0 0 2.92500 0 1 2.92500 0 2 2.92500 0 3 2.92500 0 4 2.92500 0 5 2.92500 0 6 2.92500 0 7 2.92500 0 8

[gmx-users] core dumped during equilibration in gromacs

Dear all, I am trying to simulate protein in urea box using "amber99sb-ildn" force field.During the equilibration following error occur-Step 8, time 0.016 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.27, max 0.000527 (between atoms 2089 and 2094) bonds that rotated

Re: [gmx-users] Fwd: analysis of osmolyte at particular distance from backbone

t;mark.j.abra...@gmail.com> wrote: > Hi, > > So, you want to make a selection according to a geometric criterion, which > is what gmx select does. > > Mark > > On Mon, Apr 3, 2017 at 10:12 AM ISHRAT JAHAN <jishra...@gmail.com> wrote: > > > i want to calcul

Re: [gmx-users] Fwd: analysis of osmolyte at particular distance from backbone

ob. Look at > http://manual.gromacs.org/documentation/2016/user-guide/cmdline.html and > find something useful. > > Mark > > On Mon, Apr 3, 2017 at 9:46 AM ISHRAT JAHAN <jishra...@gmail.com> wrote: > > > -- Forwarded message -- > > From: ISHRAT JAHAN <

[gmx-users] Fwd: analysis of osmolyte at particular distance from backbone

-- Forwarded message -- From: ISHRAT JAHAN <jishra...@gmail.com> Date: Fri, Mar 31, 2017 at 12:51 PM Subject: analysis of osmolyte at particular distance from backbone To: gmx-us...@gromacs.org Dear all, I want to calculate the number of osmolyte molecule at particular di

Re: [gmx-users] wt% of the solvent

Hi, You have to calculate the number of alcohol and water molecules in the box and use genbox command with -nmol option.In -nmol put number of alcohol molecule and from the output of genbox command remove the extra number of water molecules with the calculated one. On Sun, Apr 2, 2017 at 12:34

[gmx-users] analysis of osmolyte at particular distance from backbone

Dear all, I want to calculate the number of osmolyte molecule at particular distance from backbone with respect to residue.I have tried the command trjorder but it gives the number of osmolytes w.r.t time and i want it w.r.t residue. Can anyone help me how to calculate this. Thanks in advance --

Re: [gmx-users] core dumped during equilibration in gromacs

at happens when you simulate your solvent box alone? > And your protein in vacuum? Or choose a smaller PR time step? You have a > problem with a complex system, so simplify things in order to find your > problem. > > Mark > > On Wed, Mar 22, 2017 at 12:30 PM ISHRAT JAHAN <jish

Re: [gmx-users] core dumped during equilibration in gromacs

, > > All of the advice there still applies to trying to move from a successful > energy minimization to a dynamical simulation. Without knowing all the > details of how you prepared everything, that advice is all anybody can say. > > Mark > > > > > On Wed, Mar

Re: [gmx-users] core dumped during equilibration in gromacs

, > > Your initial structure seems to be horribly broken, e.g. clashing atoms. > Consider the advice at > http://www.gromacs.org/Documentation/Terminology/Blowing_Up > > Mark > > On Wed, Mar 22, 2017 at 10:27 AM ISHRAT JAHAN <jishra...@gmail.com> wrote: > > > Dear al

[gmx-users] core dumped during equilibration in gromacs

Dear all, I am trying to simulate protein in urea box using "amber99sb-ildn" force field.when i do the energy minimization step with emtol 1000 it shows many lincs warning then i increase the emtol to 1500 minimization occur in 1 step but in pr run it shows segmentation fault as- step 13: Water

[gmx-users] segmentation fault in md

Dear all I am trying to simulate 3M urea in a water box.when i do the mdrun of pr , i get too many LINCS warning and also segmentation fault(core dumped). I am pasting my em.mdp and pr.mdp file below- em.mdp ; ;User spoel (236) ;Wed Nov 3 17:12:44 1993 ;Input file ; cpp

[gmx-users] gromacs mdrun problem

Dear all I am trying to simulate 3M urea in a water box.when i do the mdrun of pr , i get too many LINCS warning and also segmentation fault(core dumped). I am attaching my em.mdp and pr.mdp file below- Thanks in advance -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Temperature interval in REMD simulations

Dear all I am trying to perform REMD simulation of small peptide. I am doing REMD first time. I am not sure how to decide the temperature interval in a given range. I have used temperature generator for REMD-simulations for 290 K to 500 K with exchange probability of 0.25. It gives 18 replicas.

[gmx-users] Error in installing gromacs

Dear all I have installed gromacs on cygwin 64 bit computer and it has installed successfully but when i run the command -pdb2gmx.exe following error occued C:/cygwin64/usr/local/gromacs/bin/pdb2gmx.exe: error while loading shared libraries: cyggmxpreprocess-6.dll: cannot open shared object file: