[gmx-users] free energy of complex system

lambda=0 to 1 state ? If that be the case then please suggest a way to customize the procedure. Please provide some suggestions. I'm really willing to apply this method in my scenario. Thank you. -- Abhisek Mondal *Senior Research Fellow* *Protein Crystallography Group* *Structural Biology

[gmx-users] protein dna pulling

/0B6O-L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU ). Shouldn't the both strands be moving together (as the COM was determined using residues from both strand of DNA) ? Some suggestions in this regard would be highly appreciated. Thank you. -- Abhisek Mondal *Senior Research

Re: [gmx-users] residue not found

the .rtp file for > the actual nomenclature. Most force fields use DT instead of THY, DA for > (deoxy)ADE, RA for ADE (RNA), etc. AMBER uses special residue names for > 5'- and 3'-nucleotides, as well. > > -Justin > > > On Wed, 8 Aug 2018, 6:54 pm abhisek Mondal, >

[gmx-users] residue not found

the residue name instead of the name of the bases I can't understand. A little suggestion would be terrific here. Thank you. -- Abhisek Mondal *Senior Research Fellow* *Protein Crystallography Group* *Structural Biology and Bioinformatics Division* *CSIR-Indian Institute of Chemical Biology*

[gmx-users] conversion issue from .str to .itp

mx.py", line 799, in m.read_charmm_rtp(rtplines,atomtypes) File "cgenff_charmm2gmx.py", line 540, in read_charmm_rtp self.G.add_node(self.natoms, atm[self.natoms]) TypeError: add_node() takes exactly 2 arguments (3 given) Help me out here. Thanks. -- Abhisek Mondal *Se

Re: [gmx-users] error in index file

of gromacs are you using and what selection string are you using? > > On Tue, Apr 3, 2018 at 11:32 AM, abhisek Mondal <abhisek.m...@gmail.com> > wrote: > > > Location of the files: > > https://drive.google.com/drive/u/0/folders/0B6O- > > L5Y7BiGJfmQ4N2FpblBEcFNxaDZn

Re: [gmx-users] error in index file

ue, Apr 3, 2018 at 11:20 AM, abhisek Mondal <abhisek.m...@gmail.com> > wrote: > > > Hi, > > > > I'm just having some issue creating index file for umbrella sampling. > > > > I have a ligand: > > Group20 (NAP) has73 elements > > > > No

[gmx-users] error in index file

. NAP is clearly showing is of 73 elements, but how come it is showing me 6 elements when added to index file ? Please help me out here. Thanks. -- Abhisek Mondal *Senior Research Fellow* *Structural Biology and Bioinformatics Division* *CSIR-Indian Institute of Chemical Biology* *Kolkata 700032

[gmx-users] non-matching atom names

out of this. Thank you. -- Abhisek Mondal *Senior Research Fellow* *Structural Biology and Bioinformatics Division* *CSIR-Indian Institute of Chemical Biology* *Kolkata 700032* *INDIA* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] conversion of str to itp

Thanks a lot for the support... Solved it ! On Mon, Feb 19, 2018 at 6:27 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 2/19/18 7:26 AM, abhisek Mondal wrote: > >> Hi, >> I have generated a .str file from .pdb file using CGenFF server. But >> whe

[gmx-users] conversion of str to itp

. Is this all happening because of the version conflict of CGenFF ? If it is so then please suggest me how can I make it work in gromacs. Thank you. -- Abhisek Mondal *Senior Research Fellow* *Structural Biology and Bioinformatics Division* *CSIR-Indian Institute of Chemical Biology* *Kolkata 700032

[gmx-users] determining the unbinding path

(regarding choosing such unbinding path) for elaborate understanding. Thank you. -- Abhisek Mondal *Senior Research Fellow* *Structural Biology and Bioinformatics Division* *CSIR-Indian Institute of Chemical Biology* *Kolkata 700032* *INDIA* -- Gromacs Users mailing list * Please search

Re: [gmx-users] convergence of PMF

11-17 14:38, Justin Lemkul wrote: > >>> > >>> On 11/17/17 6:28 AM, abhisek Mondal wrote: > >>>> Hello, > >>>> > >>>> I understand the invariant trend is the key feature to look out for > >>>> in this > >>>&

Re: [gmx-users] convergence of PMF

_ > 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: Thursday, November 16, 2017 8:04 AM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] convergence of PMF

[gmx-users] convergence of PMF

Hi, I have derived a PMF (protein-ligand) using umbrella sampling method. But how can I comment if the obtained PMF has converged well ? What are the ways to check the convergence of a PMF ? Please help me out here. Thank you. -- Abhisek Mondal *Senior Research Fellow* *Structural

[gmx-users] reliability of PMF

/mol in PMF ? I mean, with this error rate, how precise I can consider my PMF curve ? Any comments and/or references would be highly appreciated. Thank you -- Abhisek Mondal *Senior Research Fellow* *Structural Biology and Bioinformatics Division* *CSIR-Indian Institute of Chemical Biology

Re: [gmx-users] plot force vs time

for the force on the spring. Thank you. On Fri, Oct 27, 2017 at 8:04 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/27/17 5:27 AM, abhisek Mondal wrote: > >> Hi, >> >> I'm performing an umbrella sampling simulation with a protein ligand >&g

[gmx-users] plot force vs time

Hi, I'm performing an umbrella sampling simulation with a protein ligand system. For starter, I'm trying to pull the ligand with different rates. How can I obtain the Force-vs-Time plot for each individual rate of pulling performed ? Thank you. -- Abhisek Mondal *Senior Research

[gmx-users] transmembrane protein simulation

a thermodynamically favorable tertiary structure of the same protein ? I mean generating the folds based on the membrane environment provided. Being a beginner in membrane protein simulation, any given advice will be highly appreciated. Thank you. -- Abhisek Mondal *Senior Research Fellow

Re: [gmx-users] Doubt about gmx wham analysis

Mailing_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. > -- Abh

Re: [gmx-users] gromacs-5.1.4 installation issue

t; > On Wed, May 24, 2017 at 2:13 PM abhisek Mondal <abhisek.m...@gmail.com> > wrote: > > > Hi, > > > >I have been trying to install latest version of gromacs > (Gromacs-5.1.4) > > in my cluster. > > > > Installation went without any error.

[gmx-users] gromacs-5.1.4 installation issue

/libgromacs_mpi.so.1) gmx_mpi: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /app/gromacs-5.1.4/lib64/libgromacs_mpi.so.1) Can you please help me out here, regarding what is going wrong here. Thank you. -- Abhisek Mondal *Senior Research Fellow* *Structural

Re: [gmx-users] ligand moving out during umbrella sampling

confused regarding whether this approach will work out. Giving it a try though. On Sun, May 21, 2017 at 8:39 PM, abhisek Mondal <abhisek.m...@gmail.com> wrote: > Beg your pardon, I have not ignored your comment entirely regarding using > specific residue COM. I just recently succeede

Re: [gmx-users] ligand moving out during umbrella sampling

ior. > > -Justin > > > Thank you. >> >> On Fri, May 19, 2017 at 5:18 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 5/19/17 5:56 AM, abhisek Mondal wrote: >>> >>> On Thu, May 18, 2017 at 6:48 PM, Justin

Re: [gmx-users] ligand moving out during umbrella sampling

you. On Fri, May 19, 2017 at 5:18 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 5/19/17 5:56 AM, abhisek Mondal wrote: > >> On Thu, May 18, 2017 at 6:48 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 5/17/17 8:55 AM,

Re: [gmx-users] ligand moving out during umbrella sampling

On Thu, May 18, 2017 at 6:48 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 5/17/17 8:55 AM, abhisek Mondal wrote: > >> This time I think I got ligand restrained successfully during the umbrella >> sampling. I have removed the restrain from protein, as per y

Re: [gmx-users] ligand moving out during umbrella sampling

x compared to the protein structure from the beginning. Please suggest me a way out. On Mon, May 15, 2017 at 5:48 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 5/15/17 2:45 AM, abhisek Mondal wrote: > >> On Thu, May 11, 2017 at 9:03 PM, Justin Lemkul <jalem...@vt.edu>

Re: [gmx-users] ligand moving out during umbrella sampling

On Thu, May 11, 2017 at 9:03 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 5/11/17 9:21 AM, abhisek Mondal wrote: > >> On Thu, May 11, 2017 at 11:02 AM, abhisek Mondal <abhisek.m...@gmail.com> >> wrote: >> >> Hi, >>> >>&

Re: [gmx-users] ligand moving out during umbrella sampling

On Thu, May 11, 2017 at 9:03 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 5/11/17 9:21 AM, abhisek Mondal wrote: > >> On Thu, May 11, 2017 at 11:02 AM, abhisek Mondal <abhisek.m...@gmail.com> >> wrote: >> >> Hi, >>> >>&

Re: [gmx-users] ligand moving out during umbrella sampling

> > > On 5/11/17 9:21 AM, abhisek Mondal wrote: > >> On Thu, May 11, 2017 at 11:02 AM, abhisek Mondal <abhisek.m...@gmail.com> >> wrote: >> >> Hi, >>> >>> Thank you for the explanation. It really cleared some concepts. But I'm >>> st

Re: [gmx-users] ligand moving out during umbrella sampling

On Thu, May 11, 2017 at 11:02 AM, abhisek Mondal <abhisek.m...@gmail.com> wrote: > Hi, > > Thank you for the explanation. It really cleared some concepts. But I'm > still having my ligand moving in this step. I have modified the code as: > ; Pull code > pull

Re: [gmx-users] ligand moving out during umbrella sampling

gt; wrote: > > > On 5/8/17 10:00 AM, abhisek Mondal wrote: > >> On Sun, May 7, 2017 at 11:37 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 5/7/17 1:57 AM, abhisek Mondal wrote: >>> >>> Hi, >>>> >>

Re: [gmx-users] Error In Umbrella sampling.

gt; send a mail to gmx-users-requ...@gromacs.org. >> > > -- > Dr Thomas Piggot > Visiting Fellow > University of Southampton, UK. > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Us

Re: [gmx-users] ligand moving out during umbrella sampling

On Sun, May 7, 2017 at 11:37 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 5/7/17 1:57 AM, abhisek Mondal wrote: > >> Hi, >> >> For your ease of understanding regarding what is happening during this >> above said umbrella-mdrun, I have shared the t

Re: [gmx-users] ligand moving out during umbrella sampling

this run we want to restrain the ligand or don't want to change the configuration generated by pulling simulation. Is this approach right? On May 7, 2017 11:37 PM, "Justin Lemkul" <jalem...@vt.edu> wrote: On 5/7/17 1:57 AM, abhisek Mondal wrote: > Hi, > > For your ease o

Re: [gmx-users] ligand moving out during umbrella sampling

have no idea with this step, so please help me out. I'm using gromacs-4.6.2. On Sun, May 7, 2017 at 9:57 AM, abhisek Mondal <abhisek.m...@gmail.com> wrote: > Hi, > > I have completed pulling as per the tutorial stated. But having a strange > issue during umbrella sampling. When I

[gmx-users] ligand moving out during umbrella sampling

ere resulting in such a crash ? Your suggestions will be highly appreciated. Thank you. -- Abhisek Mondal *Senior Research Fellow* *Structural Biology and Bioinformatics Division* *CSIR-Indian Institute of Chemical Biology* *Kolkata 700032* *INDIA* -- Gromacs Users mailing list * Please sea

Re: [gmx-users] choosing confs for Umbrella sampling

ec1= 0 0 -1 Please help me out here. I'm using gromacs-4.6. On Fri, May 5, 2017 at 11:30 AM, abhisek Mondal <abhisek.m...@gmail.com> wrote: > Hi, > > I have generated 400 configurations after performing a pulling simulation > as per the tutorial. Among them first 160 shows

[gmx-users] choosing confs for Umbrella sampling

correlated histogram) ? I mean if I take, say, conf0,conf4,conf8,conf12,conf100,conf110,conf120,...,conf160. Is it safe ? If my correlation of umbrella-histogram falters then I can add confs for that area later right ? Please give me some suggestion regarding the same. Thank you. -- Abhisek

Re: [gmx-users] cant load trajectory, low memory

. > > Mark > > On Tue, 25 Apr 2017 12:13 abhisek Mondal <abhisek.m...@gmail.com> wrote: > > > Hi, > > > > I'm going with it. > > > > I still have a question. If I reconstruct the system (stripping the > solvent > > and thu

Re: [gmx-users] cant load trajectory, low memory

hat is the difference between running npt simulation with npt.mdp and npt_umbrella.mdp ? Please help me to catch up here. Thank you. On Mon, Apr 24, 2017 at 10:28 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 4/24/17 12:56 PM, abhisek Mondal wrote: > >> Hello, >>

Re: [gmx-users] cant load trajectory, low memory

you. On Mon, Apr 24, 2017 at 4:26 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > I already answered that. You're effectively starting again, so do that. > > Mark > > On Mon, Apr 24, 2017 at 12:28 PM abhisek Mondal <abhisek.m...@gmail.com> > wrote:

Re: [gmx-users] cant load trajectory, low memory

Or you can choose system as output and delete ions and solvent from any > editor. > > > > On Mon, Apr 24, 2017 at 3:21 PM, abhisek Mondal <abhisek.m...@gmail.com> > wrote: > > > Hello, > > > > Alright. I have tried this but I'm stuck in the following scen

Re: [gmx-users] cant load trajectory, low memory

Mark > > On Sun, Apr 23, 2017 at 8:59 PM abhisek Mondal <abhisek.m...@gmail.com> > wrote: > > > Hi, > > > > Yes, I did when I started the simulation. The box size I used to start > the > > simulation was very big(I was dealing with an unknown sam

Re: [gmx-users] cant load trajectory, low memory

conf when you set up your > simulation. It's not pre-defined ;-) > > Mark > > On Sun, 23 Apr 2017 20:28 abhisek Mondal <abhisek.m...@gmail.com> wrote: > > > Hello, > > > > Another thing I wanted to ask. > > After generating configurations I found out th

Re: [gmx-users] cant load trajectory, low memory

with current box size. Thank you. On Apr 23, 2017 10:02 PM, "Mark Abraham" <mark.j.abra...@gmail.com> wrote: > Hi, > > You can only load a trajectory with fewer frames. Either don't write so > many, or filter it with trjconv first. > > Mark > > On Sun, 23

[gmx-users] cant load trajectory, low memory

Hi, I'm having a problem loading trajectory file after umbrella sampling. The file is so huge in size that the VMD finally runs out of memory. I'm operating with 125gb of physical memory here though. Is there any way out of it ? Thank you -- Abhisek Mondal *Senior Research Fellow

Re: [gmx-users] use script/command to provide interactive options

My apologies. I had seen your post before posting again. I just misunderstood something. Got it cleared. Thank you. On Sat, Apr 22, 2017 at 11:53 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 4/22/17 2:22 PM, abhisek Mondal wrote: > >> Hi, >> >>

[gmx-users] use script/command to provide interactive options

-flags option but it is not working in trjconv. Please suggest me a way out here. Thank you -- Abhisek Mondal *Senior Research Fellow* *Structural Biology and Bioinformatics Division* *CSIR-Indian Institute of Chemical Biology* *Kolkata 700032* *INDIA* -- Gromacs Users mailing list * Please

Re: [gmx-users] xtc/trr to dcd conversion

h the archive at http://www.gromacs.org/Support > /Mailing_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 &

[gmx-users] xtc/trr to dcd conversion

Hi, I'm just stuck at converting .trr or .xtc to .dcd format. Trjconv output format does not involve .dcd extension. Can you please suggest me any other way to do it properly ? Thank you -- Abhisek Mondal *Senior Research Fellow* *Structural Biology and Bioinformatics Division* *CSIR

Re: [gmx-users] elongated protein in production run

ease see > http://www.gromacs.org/Documentation/Terminology/ > Periodic_Boundary_Conditions > > Mark > > On Thu, Apr 20, 2017 at 9:16 AM abhisek Mondal <abhisek.m...@gmail.com> > wrote: > > > Hi, > > > > I'm trying to simulate a protein for 40ns after 20ns nvt

[gmx-users] elongated protein in production run

://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0 The backbone RMSD (after production run) seems to fluctuate at the beginning but reached some stable value after sometime and so does the radius of gyration. Please suggest me a way out. Thanks -- Abhisek Mondal *Senior Research Fellow

Re: [gmx-users] query about resuming a crashed mdrun

deffnm flag, so mdrun interpreted your > intent as wanting most of the files to be named as the default. The 2016 > release series refuses to run your second command precisely because of the > ambiguity about whether you intend to append, change names, etc. > > Mark > > On T

[gmx-users] query about resuming a crashed mdrun

the last run. Did I made any mistakes there ? Am I going to get the whole trajectory information in parts ? I'm using gromacs-4.6.2 Some suggestions will be highly appreciated. Thank you. -- Abhisek Mondal *Senior Research Fellow* *Structural Biology and Bioinformatics Division* *CSIR-Indian

Re: [gmx-users] determining restraints for pulling

Please keep the discussion on the mailing list. > > On 4/5/17 8:04 AM, abhisek Mondal wrote: > >> Hello Justin, >> >> Can you provide some direction to this approach I'm using for performing >> umbrella sampling of a protein-ligand complex ? >> >> I had restraine

Re: [gmx-users] determining restraints for pulling

trying to keep the ligand in place (by restraining it) and pull > it out? > > Mark > > On Wed, 5 Apr 2017 09:51 abhisek Mondal <abhisek.m...@gmail.com> wrote: > > > Hi, > > > > I'm trying to pull a ligand from a protein-ligand complex. As per the > > li

[gmx-users] determining restraints for pulling

md;applying leap frog algorithm So, is it proper for pulling ligand (ACO) from the protein or I'm doing something wrong ? I'm really lost here, please help me out. Thank you. -- Abhisek Mondal *Senior Research Fellow* *Structural Biology and Bioinformatics Division* *CSIR-Indian

Re: [gmx-users] Ligand simulation

* 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. > -- Abhisek Mondal *Senior Research Fellow* *Struct

Re: [gmx-users] sum of the two largest charge group radii is larger than rlist

npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -n index.ndx -o npt.tpr* command is generating such error ? Please help me out here regarding the issue. Thanks On Wed, Mar 22, 2017 at 12:10 PM, abhisek Mondal <abhisek.m...@gmail.com> wrote: > Hi, > >I was trying to perform a NPT equil

[gmx-users] sum of the two largest charge group radii is larger than rlist

Please suggest me necessary modifications, if necessary, to complete NPT equilibration successfully. Thank you. -- Abhisek Mondal *Senior Research Fellow* *Structural Biology and Bioinformatics Division* *CSIR-Indian Institute of Chemical Biology* *Kolkata 700032* *INDIA* -- Gromacs Users mailing

Re: [gmx-users] query about structural consistency

ur model is properly equilibrated to perform a production MD, we are all more or less familier with that. Thanks again for the comment. Best regards, Abhisek On Tue, Mar 21, 2017 at 5:26 PM, Hannes Loeffler <hannes.loeff...@stfc.ac.uk > wrote: > On Tue, 21 Mar 2017 13:09:46 +053

Re: [gmx-users] query about structural consistency

, Mar 21, 2017 at 2:31 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > On Tue, Mar 21, 2017 at 8:40 AM abhisek Mondal <abhisek.m...@gmail.com> > wrote: > > > Hi, > > > > I just have a basic query. > > > > I'm worki

[gmx-users] query about structural consistency

protein-ligand complex matches exactly with the crystal structure used for equlibration (I mean before and after) ? Please be comprehensive. I just need to understand something. Thanks -- Abhisek Mondal *Research Fellow* *Structural Biology and Bioinformatics Division* *CSIR-Indian Institute

Re: [gmx-users] topology file construction

, Mar 19, 2017 at 12:45 PM, abhisek Mondal <abhisek.m...@gmail.com> wrote: > Hi, > > I'm trying to perform a protein-ligand MD run. But could not being > able to construct a reliable topology file of the ligand. I've tried the > PRODRG server but charges comes out so messed

[gmx-users] topology file construction

0.95 37.09 C Thanks -- Abhisek Mondal *Research Fellow* *Structural Biology and Bioinformatics Division* *CSIR-Indian Institute of Chemical Biology* *Kolkata 700032* *INDIA* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX

Re: [gmx-users] pulling protein-ligand complex

I think I would prefer 'pull-vector' approach given my system's property. Do we have any program to calculate this COM difference and formulate a pull-path ? Can you please give me any paper where this process is used/explained in detail ? I have seen you paper in JPC B but I guess protein-ligand

Re: [gmx-users] mail stuck for moderator approval

Actually nothing is in the file just few lines On Jan 13, 2017 7:02 PM, "Mark Abraham" <mark.j.abra...@gmail.com> wrote: > Hi, > > I suggest you find ways to make it smaller, eg provide links to mdp files > on file sharing services, etc > > Mark > >

[gmx-users] mail stuck for moderator approval

Hi, I was writing in thread in gmx-userlist. But suddenly the mail (entitled: pulling protein-ligand complex) got stuck for moderator approval. After a waiting for a while, it is still not being delivered to the list. Any help would be nice ! -- Abhisek Mondal *Research Fellow* *Structural

Re: [gmx-users] pulling protein-ligand complex

> On 1/8/17 12:34 PM, abhisek Mondal wrote: > >> Sincere apologies... >> I have uploaded the files here... >> https://drive.google.com/drive/folders/0B6O-L5Y7BiGJT29hSGlE >> WTM3Zk0?usp=sharing >> >> I'm running another pull experiment with "pu

Re: [gmx-users] pulling protein-ligand complex

t; > On 1/8/17 1:52 AM, abhisek Mondal wrote: > >> Alright. I'm attaching md_pull.mdp and sumary_distances.dat file. >> >> May be I have set pulling rate very low. Anyway have a look. >> >> > The list does not accept attachments (if I had a nickel for every tim

Re: [gmx-users] pulling protein-ligand complex

Alright. I'm attaching md_pull.mdp and sumary_distances.dat file. May be I have set pulling rate very low. Anyway have a look. On Sun, Jan 8, 2017 at 6:03 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/7/17 5:20 PM, abhisek Mondal wrote: > >> It finished norm

Re: [gmx-users] pulling protein-ligand complex

, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/7/17 3:59 PM, abhisek Mondal wrote: > >> yes. 19 and 20. >> I have been able to modify distances.pl and it is running well I guess. >> It >> is taking a little time per configuration to process. >

Re: [gmx-users] pulling protein-ligand complex

<jalem...@vt.edu> wrote: > > > On 1/7/17 3:36 PM, abhisek Mondal wrote: > >> Alright, I'm trying. >> Please tell me one thing, given the fact I want to analyse the >> protein-ligand pull scenario, what should be my choice during the prompt i >> get after ex

Re: [gmx-users] pulling protein-ligand complex

roup24 (r_1-163) has 5605 elements Group25 ( r_164) has39 elements Do I go with System ? I only need to see protein-ligand pull though. Can you give me some suggestions ? On Sun, Jan 8, 2017 at 1:58 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/7/1

Re: [gmx-users] pulling protein-ligand complex

So I'm supposed to run "g_dist_mpi", right ? I'm on gromacs-4.6.2. The catch here to analyze the COM distances between 2 pull groups. Am I getting that right ? On Sun, Jan 8, 2017 at 1:46 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/7/17 2:51 PM, abhisek Mond

[gmx-users] pulling protein-ligand complex

dle IN at distances.pl line 16. ... Help me out here. What did go wrong ? -- Abhisek Mondal *Research Fellow* *Structural Biology and Bioinformatics Division* *CSIR-Indian Institute of Chemical Biology* *Kolkata 700032* *INDIA* -- Gromacs Users mailing list * Please search the archive at

[gmx-users] multi node processing issue

cores. If you please debug me here. thanks. -- Abhisek Mondal *Research Fellow* *Structural Biology and Bioinformatics Division* *CSIR-Indian Institute of Chemical Biology* *Kolkata 700032* *INDIA* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support

Re: [gmx-users] parallel processing

rg/documentation/2016.1/user- > guide/mdrun-performance.html. > Your first sample command is woefully inefficient, but for em this likely > doesn't matter. > > Mark > > On Fri, 2 Dec 2016 09:01 abhisek Mondal <abhisek.m...@gmail.com> wrote: > > > But if I want to

Re: [gmx-users] parallel processing

-deffnm em" command. > > > > How can I be able to run on multiple node (I have 20 nodes available) ? > > "-nt" is not doing good here. > > > > > > > > -- > > Abhisek Mondal > > > > *Research Fellow* > > > > *Struct

[gmx-users] parallel processing

Hi, I'm running gromacs on a cluster configuration as follows: 1 node = 16 cores I'm able to use single node with "gmx mdrun -ntmpi 4 -ntomp 16 -npme 0 -v -deffnm em" command. How can I be able to run on multiple node (I have 20 nodes available) ? "-nt" is not doing good

[gmx-users] system blowing up

you please suggest what actually is going wrong. -- Abhisek Mondal *Research Fellow* *Structural Biology and Bioinformatics Division* *CSIR-Indian Institute of Chemical Biology* *Kolkata 700032* *INDIA* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org

Re: [gmx-users] setting up a pull vec

rom: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < >> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of abhisek >> Mondal <abhisek.m...@gmail.com> >> Sent: 25 November 2016 02:37:18 >> To: gromacs.org_gmx-users@maillist.sys.

Re: [gmx-users] setting up a pull vec

could also add a few > absolute position restraints to pin down one of the molecules. > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of abhisek > Mondal <

[gmx-users] setting up a pull vec

; define initial COM distance > 0 This approach needs me to specify a pulling vec which is essentially not 0,0,0. Could you please suggest me a way to decide how to provide the pull vec ? Thanks. -- Abhisek Mondal *Research Fellow* *Structural Biology and Bioinformatics Divis

Re: [gmx-users] protein-ligand umbrella sampling

to come more often in my cases. I'm attaching the md_pull.mdp here. Thanks On Wed, Nov 23, 2016 at 11:58 AM, abhisek Mondal <abhisek.m...@gmail.com> wrote: > Hi, > > I have came across that there are many ways of pulling, although have no > idea which is to apply and when. A des

Re: [gmx-users] protein-ligand umbrella sampling

org/gmane.science.biology.gromacs.user/52710>. Please give me a sanity check. The scenario is my ligand is buried in a hydrophobic cleft of the protein. Thank you On Wed, Nov 23, 2016 at 1:51 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/22/16 6:46 AM, abhisek Mondal wrote: > >> Hi, >&g

[gmx-users] protein-ligand umbrella sampling

S 148 ARG 149 VAL 150 ILE 151 THR 152 THR 153 PHE 154 ARG 155 THR 156 GLY 157 THR 158 TRP 159 ASP 160 ALA 161 TYR 162 LYS 163 ASN 164 JZ4165 - 10482 SOL 10483 - 10503 NA 10504 - 10530 CL Little help regarding the would be very nice. Thank you. -- A