[gmx-users] gromacs.org_gmx-users Digest, Vol 160, Issue 75
zaved at tezu.ernet.in
zaved at tezu.ernet.in
Wed Aug 16 13:37:28 CEST 2017
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> Today's Topics:
>
> 1. Re: npt simulation error (Mohammad Zahidul Hossain Khan)
> 2. positioning molecule at desired location (Alex Mathew)
> 3. (no subject) (zaved at tezu.ernet.in)
> 4. Re: (no subject) (RAHUL SURESH)
> 5. Re: Fwd: (saranya)
> 6. Re: gromacs.org_gmx-users Digest, Vol 160, Issue 74 (Naba)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 15 Aug 2017 18:22:03 -0700
> From: Mohammad Zahidul Hossain Khan <za.parash at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] npt simulation error
> Message-ID:
> <CAAdBV7Yp=M+tj=sm9jeQj2SZB8Oh9QxjnqgP9HvxLA5R1yu3UA at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> ; Dielectric constant (DC) for cut-off or DC of reaction field =
> epsilon-r = 4
>
>
> On Tue, Aug 15, 2017 at 6:18 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 8/15/17 9:14 PM, Mohammad Zahidul Hossain Khan wrote:
>>
>>> Dear Sir
>>>
>>> I am trying to simulate protein_ligand complex using epsilon = 4 and it
>>> is
>>> giving the below error
>>>
>>>
>> What is epsilon = 4?
>>
>> *2 particles communicated to PME rank 4 are more than 2/3 times the
>> cut-off
>>> out of the domain decomposition cell of their charge group in dimension
>>> x*
>>>
>>> I have no idea how to solve this problem
>>>
>>>
>> Have you Googled it, or gone to the GROMACS error page, where lots of
>> advice lives? ;)
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==================================================
>> --
>> 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/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-request at gromacs.org.
>>
>
>
>
> --
>
>
> *Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
> *Email: khan5121 at vandals.uidaho.edu <khan5121 at vandals.uidaho.edu>*
> * Skype: parash.khan2*
> *Cell: +12085967165*
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 16 Aug 2017 09:48:59 +0530
> From: Alex Mathew <alexmathewmd at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] positioning molecule at desired location
> Message-ID:
> <CAAW-8xVNt2x=Dvw7ozQUnmhzVzGGEh5vNNOKhfh6deps9+Ly6g at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear all,
>
> I want to keep a water molecule at a particular position of a protein
> channel. I need to pull this across the channel and observe the energy
> diagram by PMF. can anyone tell me how I can keep water molecules at a
> particular position.
>
> thank you.
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 16 Aug 2017 10:11:44 +0530
> From: zaved at tezu.ernet.in
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] (no subject)
> Message-ID:
> <49c5c50c859cae2587445e0f293eae63.squirrel at webmail.tezu.ernet.in>
> Content-Type: text/plain;charset=utf-8
>
> Hii Everyone
>
> I had performed a 100ns protein-ligand (docked complex) simulation with
> gromacs 5.1.4.
>
> The ligand in my case is hydrogen peroxide.
>
> I have removed the PBC effect and centered the protein.
>
> I have used the following commands:
>
> gmx_mpi trjconv -f md.xtc -s md.tpr -pbc nojump -o out.xtc
>
> gmx_mpi trjconv -f out.xtc -s md.tpr -pbc mol -center -o out_1.xtc
>
> I am analyzing the average distance between the protein and the ligand. I
> am getting a value of 3.2nm which is too high.
>
> Also in the out_1.xtc, after 10ns itself the ligand is moving all around
> the protein.
>
> Unable to understand why its happening!!
>
> Please suggest.
>
> Thank You
>
> Regards
>
> Z. Hazarika
> Research Scholar
> Tezpur University
> Tezpur, India
>
>
> * * * D I S C L A I M E R * * *
> This e-mail may contain privileged information and is intended solely for
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> integrity of this e-mail message.
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 16 Aug 2017 11:35:05 +0530
> From: RAHUL SURESH <drrahulsuresh at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] (no subject)
> Message-ID:
> <CAAtfiTsJ_mSYuGj2O9tHGieUSvRWC=74jTKiK8Zk2CT=7pqUEQ at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Thank you Rahul for the suggestion. My protein is not having a true
binding pocket. The active site residues are present almost on the
surface of the protein.
The ligand tries to relocate but rotates around the protein 90% of the time.
Thank you
I suggest check for the appropriate binding pocket. See whether the ligand
> relocates at some other point in protein or keep to stay away. Also check
> for the quality of the topology generated.
>
> On Wed, Aug 16, 2017 at 10:11 AM, <zaved at tezu.ernet.in> wrote:
>
>> Hii Everyone
>>
>> I had performed a 100ns protein-ligand (docked complex) simulation with
>> gromacs 5.1.4.
>>
>> The ligand in my case is hydrogen peroxide.
>>
>> I have removed the PBC effect and centered the protein.
>>
>> I have used the following commands:
>>
>> gmx_mpi trjconv -f md.xtc -s md.tpr -pbc nojump -o out.xtc
>>
>> gmx_mpi trjconv -f out.xtc -s md.tpr -pbc mol -center -o out_1.xtc
>>
>> I am analyzing the average distance between the protein and the ligand.
>> I
>> am getting a value of 3.2nm which is too high.
>>
>> Also in the out_1.xtc, after 10ns itself the ligand is moving all around
>> the protein.
>>
>> Unable to understand why its happening!!
>>
>> Please suggest.
>>
>> Thank You
>>
>> Regards
>>
>> Z. Hazarika
>> Research Scholar
>> Tezpur University
>> Tezpur, India
>>
>>
>> * * * D I S C L A I M E R * * *
>> This e-mail may contain privileged information and is intended solely
>> for
>> the individual named. If you are not the named addressee you should not
>> disseminate, distribute or copy this e-mail. Please notify the sender
>> immediately by e-mail if you have received this e-mail in error and
>> destroy
>> it from your system. Though considerable effort has been made to deliver
>> error free e-mail messages but it can not be guaranteed to be secure or
>> error-free as information could be intercepted, corrupted, lost,
>> destroyed,
>> delayed, or may contain viruses. The recipient must verify the integrity
>> of
>> this e-mail message.
>> --
>> 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/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-request at gromacs.org.
>>
>
>
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 16 Aug 2017 12:35:48 +0530
> From: saranya <saranyahoney17 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Fwd:
> Message-ID:
> <CAC8O+2BdF+o9FH5gUf7j2f8bVpVk54gOrvwMqy5Oa+mjUdA5xA at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear Justin,
>
> Thank you for your kind response.
>
> I have made all the basic analysis and yes there are certain structural
> changes that i have expected. But my clarification is as follows.
> Initially, there were 6 H-bonds and when it reach around 15ns it is
> reduced
> to 1 or 2. Do the effect of ligand over protein increase/decrease with a
> number of hydrogen bonds? Or even a single bond between protein and ligand
> is more sufficient to bring necessary changes to a protein?
>
> With Regards,
>
> *Saranya Vasudevan,*
>
> *Research Scholar,*
>
> *Molecular Quantum Mechanics Laboratory,*
>
> *Department of Physics,*
>
> *Bharathiar University,*
> *Coimbatore-46*
>
>
> ------------------------------
>
> Message: 6
> Date: Wed, 16 Aug 2017 13:08:12 +0530
> From: Naba <nabajyoti.goswami at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 160, Issue
> 74
> Message-ID:
> <CAHvbR_95m7fSfaPcOmLY_F9A+3f0trNVgL_DLR_kZFxsjJWgQA at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear users,
>
> Please let me know whether it is feasible and relevant or not if I use COM
> pulling for mechanical unfolding of proteins. More specifically, whether I
> can define the two group within the same molecule !!
>
>
> On Wed, Aug 16, 2017 at 6:48 AM, <
> gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
>
>> Send gromacs.org_gmx-users mailing list submissions to
>> gromacs.org_gmx-users at maillist.sys.kth.se
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>> or, via email, send a message with subject or body 'help' to
>> gromacs.org_gmx-users-request at maillist.sys.kth.se
>>
>> You can reach the person managing the list at
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>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of gromacs.org_gmx-users digest..."
>>
>>
>> Today's Topics:
>>
>> 1. Re: Fwd: (Justin Lemkul)
>> 2. (Don't know if mail worked last time)Drift with
>> groups+tabulated potential. (sperez14 at us.es)
>> 3. how to make molecular model with both ion channel and lipid
>> bilayer? (Li, Tong)
>> 4. Re: how to make molecular model with both ion channel and
>> lipid bilayer? (h.alizadeh at znu.ac.ir)
>> 5. Doing restart (?farial tavakoli? ?)
>> 6. npt simulation error (Mohammad Zahidul Hossain Khan)
>> 7. Re: npt simulation error (Justin Lemkul)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Tue, 15 Aug 2017 08:02:45 -0400
>> From: Justin Lemkul <jalemkul at vt.edu>
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] Fwd:
>> Message-ID: <c2806875-ebe0-d575-e462-381c707ca501 at vt.edu>
>> Content-Type: text/plain; charset=utf-8; format=flowed
>>
>>
>>
>> On 8/15/17 1:52 AM, saranya wrote:
>> > Hi,
>> > I have done protein-drug simulations for 100ns. While calculating the
>> hydrogen
>> > bond between the protein-drug complex I am getting only 2 hydrogen
>> bonds.
>> > The number of H-bond formation is very low I have a question about is
>> there
>> > any influence of the drug in my protein?
>> To answer that, you need to do simulations of the apo protein and
>> compare whatever relevant structural metrics there are (not H-bonds, as
>> these tell you about the ligand-protein interactions but nothing about
>> the impact on the protein structure).
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==================================================
>>
>>
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Tue, 15 Aug 2017 14:25:30 +0200
>> From: sperez14 at us.es
>> To: gromacs.org_gmx-users at maillist.sys.kth.se
>> Subject: [gmx-users] (Don't know if mail worked last time)Drift with
>> groups+tabulated potential.
>> Message-ID: <4e579ca344c855cabbbbf935a5ebc2a0 at us.es>
>> Content-Type: text/plain; charset=US-ASCII
>>
>> Dear GROMACS Community,
>>
>> First of all, if someone got this email twice, I am sorry. It is my
>> first post and I was not sure if it worked.
>>
>> I am trying to do a simulation using a tabulated potential which forces
>> me to use the group cut-off. I get a drift in the conserved quantity of
>> -600KJ/mol/ns. My system consists of 1000 rigid TIP4P water molecules
>> and a Na+ ion. I imagine that eventhough it will soon be deprecated the
>> group cutoff scheme still works correctly. I have tryed to change the
>> parameters without success and in any case the ones I use seem
>> reasonable (in my experience using other programs). The rdfs of the
>> system look normal so I ruled out topology problems.
>>
>> It seems that the problem is in the group cut-off since
>> when I change the tabulated potential for a regular vdw the problem
>> persists. I have followed the instructions of:
>>
>> http://www.gromacs.org/@api/deki/files/94/=gromacs_nb.pdf
>>
>> to implement the tabulated potentials.
>>
>> Is this the kind of energy drift acceptable? I have pasted a copy .mdp
>>
>> Thanks for your help,
>>
>> Sergio Perez-Conesa
>>
>> integrator = md
>> dt = 0.001
>> nsteps = 100000
>> init-step = 0
>> cutoff-scheme = group
>> nst-list = 1
>> verlet-buffer-tolerance = 0.0005
>> ns-type = grid
>> rlist = 1.3
>> pbc = xyz
>> coulombtype = PME-switch
>> rcoulomb = 1.
>> rcoulomb-switch = 0.95
>> pme-order = 4
>> fourierspacing = 0.1
>> ewald-rtol = 1.e-5
>> vdwtype = user
>> rvdw = 1.0
>> DispCorr = No
>> tcoupl = v-rescale
>> tc-grps = System
>> ;nsttcouple = 1
>> tau-t = ref-t = 300.0
>> constraints = all-angles
>> constraint-algorithm = LINCS
>> lincs_iter = 1
>> lincs_order = 4
>> energygrps = NA OW
>> energygrp_table = NA OW
>> comm-mode = linear
>>
>> ------------------------------
>>
>> Message: 3
>> Date: Tue, 15 Aug 2017 15:09:27 +0000
>> From: "Li, Tong" <tongli at udel.edu>
>> To: "gromacs.org_gmx-users at maillist.sys.kth.se"
>> <gromacs.org_gmx-users at maillist.sys.kth.se>
>> Subject: [gmx-users] how to make molecular model with both ion channel
>> and lipid bilayer?
>> Message-ID: <a58e2d39d21544f2a8a14ff6e9eff077 at udel.edu>
>> Content-Type: text/plain; charset="us-ascii"
>>
>> Dear all,
>>
>> I am trying to make a model of ion channel with cell membrane. Is there
>> a
>> specific software to make this? I mean just the coordination file. VMD
>> can
>> generate the membrane automatically, I can find the 'pdb' files of ion
>> channels, but I have no idea how to combine them.
>>
>> Thanks all,
>> Tong
>>
>>
>> ------------------------------
>>
>> Message: 4
>> Date: Tue, 15 Aug 2017 16:49:43 +0000
>> From: h.alizadeh at znu.ac.ir
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] how to make molecular model with both ion
>> channel and lipid bilayer?
>> Message-ID: <d39070d67bb0c37d48b5c650a2939ae3 at mail.znu.ac.ir>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Charmm-gui.org could help you.
>> Bests,
>> Hadi
>> On Tue, Aug 15, 2017 at 07:55 PM, "Li, Tong" wrote:
>> Dear all,
>>
>> I am trying to make a model of ion channel with cell membrane. Is there
>> a
>> specific software to make this? I mean just the coordination file. VMD
>> can
>> generate the membrane automatically, I can find the 'pdb' files of ion
>> channels, but I have no idea how to combine them.
>>
>> Thanks all,
>> Tong
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List (http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List) before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists (
>> http://www.gromacs.org/Support/Mailing_Lists)
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users (
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users) or
>> send a mail to gmx-users-request at gromacs.org (mailto:gmx-users-request@
>> gromacs.org).
>>
>>
>> ------------------------------
>>
>> Message: 5
>> Date: Tue, 15 Aug 2017 22:46:14 +0000 (UTC)
>> From: ?farial tavakoli? ? <farial.tavakoli at ymail.com>
>> To: Discussion List for GROMACS Users <gmx-users at gromacs.org>
>> Subject: [gmx-users] Doing restart
>> Message-ID: <1962486576.3101166.1502837174489 at mail.yahoo.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> #yiv4389709560 blockquote, #yiv4389709560 div.yiv4389709560yahoo_quoted
>> {margin-left:0 !important;border-left:1px #715FFA solid
>> !important;padding-left:1ex !important;background-color:white;} Dear gmx
>> users
>> I stoped my md simulation and now i want to restart it.
>> I use gromacs 2016.3? and issued this command to perform md:Gmx grompp
>> -f
>> md.mdp -c npt.gro -t npt.cpt -p topol.tpr -n index.ndx -o md_0_1.tprGmx
>> mdrun -deffnm md_0_1
>> To restart simulation i issuedGmx mdrun -s md_0_1.tpr ?-cpi md_0_1.cpt
>> -appendBut faced to an error:
>> Fatal error:
>> File appending requested, but 2 of the 3 output files are not present or
>> are
>> named differently. For safety reasons, GROMACS-2016 and later only
>> allows
>> file
>> appending to be used when all files have the same names as they had in
>> the
>> original run. Checkpointing is merely intended for plain continuation of
>> runs.
>> For safety reasons you must specify all file names (e.g. with -deffnm),
>> and
>> all these files must match the names used in the run prior to
>> checkpointing
>> since we will append to them by default. If the files are not available,
>> you
>> can add the -noappend flag to mdrun and write separate new parts. For
>> mere
>> concatenation of files, you should use the gmx trjcat tool instead.
>>
>> i refered to google but i couldnt understand well what should i type
>> exactly. would you please help me to restart my md simulation?
>> Thanks in advanceFarial
>>
>>
>> Sent from Yahoo Mail for iPhone
>>
>>
>> ------------------------------
>>
>> Message: 6
>> Date: Tue, 15 Aug 2017 18:14:49 -0700
>> From: Mohammad Zahidul Hossain Khan <za.parash at gmail.com>
>> To: gmx-users at gromacs.org
>> Subject: [gmx-users] npt simulation error
>> Message-ID:
>> <CAAdBV7bGg0ZPm-R9nO8tagfPorV15h1bFp=FR30+Sf1gRW=
>> z5Q at mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Dear Sir
>>
>> I am trying to simulate protein_ligand complex using epsilon = 4 and it
>> is
>> giving the below error
>>
>> *2 particles communicated to PME rank 4 are more than 2/3 times the
>> cut-off
>> out of the domain decomposition cell of their charge group in dimension
>> x*
>>
>> I have no idea how to solve this problem
>> --
>>
>>
>> *Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
>> *Email: khan5121 at vandals.uidaho.edu <khan5121 at vandals.uidaho.edu>*
>> * Skype: parash.khan2*
>> *Cell: +12085967165*
>>
>> ------------------------------
>>
>> Message: 7
>> Date: Tue, 15 Aug 2017 21:18:14 -0400
>> From: Justin Lemkul <jalemkul at vt.edu>
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] npt simulation error
>> Message-ID: <dd482641-ce0a-a873-f7f9-13b04f75292f at vt.edu>
>> Content-Type: text/plain; charset=utf-8; format=flowed
>>
>>
>>
>> On 8/15/17 9:14 PM, Mohammad Zahidul Hossain Khan wrote:
>> > Dear Sir
>> >
>> > I am trying to simulate protein_ligand complex using epsilon = 4 and
>> it
>> is
>> > giving the below error
>> >
>>
>> What is epsilon = 4?
>>
>> > *2 particles communicated to PME rank 4 are more than 2/3 times the
>> cut-off
>> > out of the domain decomposition cell of their charge group in
>> dimension
>> x*
>> >
>> > I have no idea how to solve this problem
>> >
>>
>> Have you Googled it, or gone to the GROMACS error page, where lots of
>> advice
>> lives? ;)
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==================================================
>>
>>
>> ------------------------------
>>
>> --
>> 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/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-request at gromacs.org.
>>
>> End of gromacs.org_gmx-users Digest, Vol 160, Issue 74
>> ******************************************************
>>
>
>
>
> --
> Nabajyoti Goswami
>
> Research Associate
> Bioinformatics Infrastructure Facility
> Department of Animal Biotechnology
> College of Veterinary Science
> Khanapara,Guwahati 781022
> Assam, India
>
>
> ------------------------------
>
> --
> Gromacs Users mailing list
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> End of gromacs.org_gmx-users Digest, Vol 160, Issue 75
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