[gmx-users] Error in Coarse Graining the atomistic trajectory

of how to troubleshoot the above problem. Any help will be highly appreciated. *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged

Re: [gmx-users] Martini Website is not accessible

Okay, Thank You *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* On Mon, May 22, 2017 at 5:17 PM, Peter Kroon <p.c.kr...@rug.nl> wrote: > Hi, > > > we are aware of it and will probably fix it later today. It's an u

[gmx-users] Martini Website is not accessible

*Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission

[gmx-users] Error In Umbrella sampling.

iven in the tutorial. Is is safe to use maxwarn in this case ? or is their any solution to overcome this warning ? Any help will be highly appreciated. Thank you *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* -- *DISCLAIMER:* *This communicat

Re: [gmx-users] Potential Energy is positive on minimizing the system

Thanks a lot! *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Thu, Feb 23, 2017 at 9:10 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 2/23/17 9:07 AM, Anurag Dobhal wrote: > >&

Re: [gmx-users] Potential Energy is positive on minimizing the system

*Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Thu, Feb 23, 2017 at 7:23 PM, Anurag Dobhal < anurag.dob...@nano-medicine.co.in> wrote: > Thank you ! > > > > > *Anurag Dobhal* > *G

Re: [gmx-users] Potential Energy is positive on minimizing the system

Thank you ! *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Thu, Feb 23, 2017 at 7:09 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 2/23/17 8:29 AM, Anurag Dobhal wrote: > >> Tha

Re: [gmx-users] Potential Energy is positive on minimizing the system

Thank you. Should I not use PME and PBC while performing simulations in Vaccum ? -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or

[gmx-users] Potential Energy is positive on minimizing the system

Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) Any help will be appreciated. Thank you *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* -- *DISCLAIMER:* *This communication is intended only for the person or ent

[gmx-users] Potential Energy is positive on minimizing the system

Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) Any help will be appreciated. Thank you *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* -- *DISCLAIMER:* *This communication is intended only for the person or ent

Re: [gmx-users] Neutralization of the non solvated system

Thank you *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* On Thu, Dec 22, 2016 at 6:26 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 12/22/16 5:24 AM, Anurag Dobhal wrote: > >> Dear Gromacs users, >>

[gmx-users] Neutralization of the non solvated system

Dear Gromacs users, I am simulating a polyemer chain having positive charge. I am running the simulation without any solvent, in this sitiuation how can I neutralize my system ? Thank You *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai

Re: [gmx-users] Regarding tc-grps

Thank you Justin and Peter for the valuable inputs. *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* On Thu, Sep 29, 2016 at 8:25 PM, Peter Kroon <p.c.kr...@rug.nl> wrote: > Hi, > > please see http://www.gromacs.or

Re: [gmx-users] Regarding tc-grps

is stoping, showing error of segmentation fault. Thank You *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* On Thu, Sep 29, 2016 at 8:26 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/29/16 10:31 AM, Anurag Dobhal wrote: &g

Re: [gmx-users] changing the location of a molecule in a box

of the protien. Thank You *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* On Fri, Sep 9, 2016 at 4:24 PM, Anurag Dobhal < anurag.dob...@nano-medicine.co.in> wrote: > Dear Gromacs users, > > I am working on a biphasic system where I have taken chloroform and water >

[gmx-users] changing the location of a molecule in a box

of the protien. Thank You *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other

[gmx-users] Parameters file for CHARMM 27 Force Field

-Vz79yKJWFgwYVN3cUJHSUE Thank You *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any

Re: [gmx-users] Energy minimization has stopped

Thanks a lot Justinn and Mark for the valuable suggestions. I will start over again by choosing a force field which is suitable for the RNA molecules. *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Thu, Jun

Re: [gmx-users] Energy minimization has stopped

for RNA molecules. I was suggested (Link Below) earlier that I can take the charges from any other forcefield. (http://permalink.gmane.org/gmane.science.biology.gromacs.user/85228) please enlight me where I am going wrong. Thank You *Anurag Dobhal* *Graduate Student (Bioprocess Technology

Re: [gmx-users] Energy minimization has stopped

I am using OPLS AA force field. parameters (charges) for the atoms are taken from the charmm27 force field. *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Thu, Jun 23, 2016 at 4:15 PM, Justin Lemkul <ja

[gmx-users] Energy minimization has stopped

f rvdw= 1.0 ; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions (yes/no) any suggestions ? *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* -- *DISCLAIMER:* *This communication is intended only for the

[gmx-users] WARNING: Duplicate line found in or between hackblock and rtp entries

Dear Gromacs Users, I Simulated a Nucleotide pair using OPLS AA force field. while running " gmx pdb2gmx" I am getting the following warning. WARNING: Duplicate line found in or between hackblock and rtp entries How to address this warning ? Thank You *Anurag Dobhal* *Gradua

Re: [gmx-users] Total Charge on Guanine molecule by OPLS AA force field is negative

Thank You *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Fri, Jun 17, 2016 at 5:02 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 6/17/16 6:26 AM, Anurag Dobhal wrote: > >> D

Re: [gmx-users] Total Charge on Guanine molecule by OPLS AA force field is negative

Dear Justin, I have already added the H to the guanine molecule striped from the nucleotide. The charges given in the ffnonbonded.itp for all the atoms of guanine (Including the H on N9) do not add to zero. *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical

[gmx-users] Total Charge on Guanine molecule by OPLS AA force field is negative

at guanine has negative charge ? should I continue with thae same parameters or change them to bring the total charge of the molecule to zero. Thank You for your help *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* -- *

Re: [gmx-users] Grompp error

Thanks a lot for your insight. I will redefine them. *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Mon, May 30, 2016 at 8:26 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 5/30/16 1

Re: [gmx-users] Grompp error

Thanks a lot for your reply. I have set tc-groups as tc-grps = Other acetone ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each *Anurag Dobhal* *Graduate Student (Bioprocess Technology

[gmx-users] Grompp error

300 K Removing all charge groups because cutoff-scheme=Verlet Fatal error: Atom 79 in multiple T-Coupling groups (1 and 2) " The error means that T-coupling is treating both the polymer (other) and solvent (acetone) as other molecules. How can I rectify the error ? *Anurag Dobhal* *Gradua

[gmx-users] uninstall gromacs 5.0

Dear Users: I want to uninstall gromacs 5.0 and replace it with gromacs 5.1. The link provided in the gromacs website (Removing a GROMACS installation) does not give any solution with the same. how can i uninstall gromacs 5.0 ?? Thanks in advance. Anurag Dobhal -- *DISCLAIMER

[gmx-users] Grompp Error No default Ryckaert-Bell. types

Dear gromacs users. I am simulating a molecule in opls-aa force field. While running energy minimization I did get the error No default Ryckaert-Bell. types. I checked the line in topol.top and it says that dihedral for ( C-CT-OH-HO) has No default Ryckaert-Bell. types. but on checking

[gmx-users] Grompp error No default Ryckaert-Bell. types

Hello all How can I address the No default Ryckaert-Bell. types error. The error is also in between the atoms which are not bonded with each other. Thank you -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential

[gmx-users] Fatal error: Atom type Zn2+ (residue ZN) not found in atomtype database

Dear all I am running pdb2gmx to creat the topology file of my structure, But I did get the error Fatal error: Atom type Zn2+ (residue ZN) not found in atomtype database Although my .pdb file does not contain Atom type Zn2+ (residue ZN) *Anurag DobhalJuniour Research fellowSupervisor:

Re: [gmx-users] regarding GROMACS Tutorial KALP15 in DPPC

) and what will be the command ??? looking for your kind reply. please help. Thank you On Thu, Oct 2, 2014 at 10:22 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/2/14 12:51 PM, Anurag Dobhal wrote: how will I get to know that the system have shrunken enough, and which file I need to solvate

Re: [gmx-users] regarding GROMACS Tutorial KALP15 in DPPC

you On Tue, Sep 30, 2014 at 8:05 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/30/14 10:30 AM, Anurag Dobhal wrote: Dear justin Thank you for your rely and precious time. I am aware that .gro file is to be visualized in VMD and its content can be checked in text editor. all the previous

Re: [gmx-users] regarding GROMACS Tutorial KALP15 in DPPC

how will I get to know that the system have shrunken enough, and which file I need to solvate. On Thu, Oct 2, 2014 at 9:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/2/14 8:50 AM, Anurag Dobhal wrote: Thanks Justin I m running the command mdrun -s em.tpr and I did get

[gmx-users] regarding GROMACS Tutorial KALP15 in DPPC

Hello gromacs users. I am running GROMACS Tutorial of KALP15 in DPPC. I am in the step define box and solvate. after the command perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat i am getting an error as Use of uninitialized value $box_x in multiplication

Re: [gmx-users] regarding GROMACS Tutorial KALP15 in DPPC

again for your time. On Tue, Sep 30, 2014 at 4:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/30/14 5:51 AM, Anurag Dobhal wrote: Hello gromacs users. I am running GROMACS Tutorial of KALP15 in DPPC. I am in the step define box and solvate. after the command perl inflategro.pl

Re: [gmx-users] regarding GROMACS Tutorial KALP15 in DPPC

it is actually .trr format, which can not be visualised in VMD or checked in text editor. Please help. On Tue, Sep 30, 2014 at 4:41 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/30/14 7:06 AM, Anurag Dobhal wrote: Thank you Justin for your reply as per your suggestion i verified the contents

Re: [gmx-users] Regarding GROMACS Tutorial KALP15 in DPPC

hello justin Can you please tell me how will i solvate my system. which command will i use and what will be my input and output file. Thanks for your help Anurag dobhal On Sun, Sep 28, 2014 at 6:58 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/28/14 9:14 AM, Anurag Dobhal wrote: Hey

[gmx-users] Regarding GROMACS Tutorial KALP15 in DPPC

. Please help Anurag Dobhal -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received

Re: [gmx-users] Regarding GROMACS Tutorial KALP15 in DPPC

please help how to proceed and where I am wrong. Thank you Anurag Dobhal On Sun, Sep 28, 2014 at 5:37 PM, Anurag Dobhal anurag.dob...@nano-medicine.co.in wrote: Dear users. I am doing the tutorial KALP15 in DPPC. I heve done till the command genrestr -f KALP_newbox.gro -o

Re: [gmx-users] Regarding GROMACS Tutorial KALP15 in DPPC

28, 2014 at 6:33 PM, Anurag Dobhal anurag.dob...@nano-medicine.co.in wrote: Dear users. I am doing the tutorial KALP15 in DPPC. I heve done till the command perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat and then i minimised the the system by running the command

[gmx-users] Regarding error in grompp while running the tutorial of KALP15 in DPPC

I am getting an error while running the commmand gmx grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr Fatal error: Unknown bond_atomtype MNH3 -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain

[gmx-users] Regarding error in grompp while running the tutorial of KALP15 in DPPC

I am getting an error while running the commmand gmx grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr Fatal error: Unknown bond_atomtype MNH3 please help -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may