[gmx-users] free energy calculations for reference state for constant pH MD simulations...
Ozbil, Mehmet
m.ozbil at umiami.edu
Thu Jan 30 20:29:32 CET 2014
For Dummy atom, I tried to write DUM for atom type and give 0 charge but it could not recognize the atom type. Then I just wrote the atom type with 0 charge but as I understand I could not make it a dummy atom. How can I do it?
And also for the parameters, I understand the fact that the bonding and non-bonding interactions will change, but I could not find a good example or I could not understand how to do it? In the manual, Section 5.7.4 there is an example but I don`t understand where the gb_ parameters are coming from:
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
1 H 1 PROP PH 1 0.398 1.008 CH3 0.0 15.035
2 OA 1 PROP PO 1 -0.548 15.9994 CH2 0.0 14.027
3 CH2 1 PROP PC1 1 0.150 14.027 CH2 0.0 14.027
4 CH2 1 PROP PC2 2 0.000 14.027
5 CH3 1 PROP PC3 2 0.000 15.035
[ bonds ]
; ai aj funct par_A par_B
1 2 2 gb_1 gb_26
5.7. File formats 135
2 3 2 gb_17 gb_26
3 4 2 gb_26 gb_26
4 5 2 gb_26
[ pairs ]
; ai aj funct
1 4 1
2 5 1
[ angles ]
; ai aj ak funct par_A par_B
1 2 3 2 ga_11 ga_14
2 3 4 2 ga_14 ga_14
3 4 5 2 ga_14 ga_14
[ dihedrals ]
; ai aj ak al funct par_A par_B
1 2 3 4 1 gd_12 gd_17
2 3 4 5 1 gd_17 gd_17
Also here the example for Gromos forcefield but I am using OPLS force field so I assume these numbers will be different as well. How can I find the parameters for B state for OPLS force field?
Thanks,
Mehmet
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
Sent: Thursday, January 30, 2014 1:43 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] free energy calculations for reference state for constant pH MD simulations...
On 1/30/14, 1:39 PM, Ozbil, Mehmet wrote:
> By the Way, My top file looks like:
>
>
> [ moleculetype ]
> ; Name nrexcl
> Protein_chain_A 3
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass typeB chargeB massB
> ; residue 77 GLU rtp GLUH q 0.0
> 1 opls_900 77 GLU N 1 -0.9 14.0067 opls_900 -0.9 14.0067
> 2 opls_909 77 GLU H1 1 0.36 1.008 opls_909 0.36 1.008
> 3 opls_909 77 GLU H2 1 0.36 1.008 opls_909 0.36 1.008
> 4 opls_912B 77 GLU CA 1 0.12 12.011 opls_912B 0.12 12.011
> 5 opls_140 77 GLU HA 1 0.06 1.008 opls_140 0.06 1.008
> 6 opls_136 77 GLU CB 2 -0.12 12.011 opls_136 -0.12 12.011
> 7 opls_140 77 GLU HB1 2 0.06 1.008 opls_140 0.06 1.008
> 8 opls_140 77 GLU HB2 2 0.06 1.008 opls_140 0.06 1.008
> 9 opls_136 77 GLU CG 3 -0.12 12.011 opls_274 -0.22 12.011
> 10 opls_140 77 GLU HG1 3 0.06 1.008 opls_140 0.06 1.008
> 11 opls_140 77 GLU HG2 3 0.06 1.008 opls_140 0.06 1.008
> 12 opls_267 77 GLU CD 4 0.52 12.011 opls_271 0.7 12.011
> 13 opls_269 77 GLU OE1 4 -0.44 15.9994 opls_272 -0.8 15.9994
> 14 opls_268 77 GLU OE2 5 -0.53 15.9994 opls_272 -0.8 15.9994
> 15 opls_270 77 GLU HE2 5 0.45 1.008 opls_270 0.0 1.008
Here all you've done is turned off the charge; you haven't made the H atom into
a dummy atom in the B-state.
> 16 opls_267 77 GLU C 6 0.52 12.011 opls_267 0.52 12.011
> 17 opls_269 77 GLU OT 6 -0.44 15.9994 opls_269 -0.44 15.9994
> 18 opls_268 77 GLU O 6 -0.53 15.9994 opls_268 -0.53 15.9994
> 19 opls_270 77 GLU HO 6 0.45 1.008 opls_270 0.45 1.008
>
The manual has an example of the manner in which you need to specify bonds for
the B-state. If atoms are changing, so too are their bonded parameters. The
error messages from grompp tell you which lines in the topology are problematic,
making it simple to track down what's missing. Map the atom numbers to the
types, and specify the A- and B-state parameters that are needed.
-Justin
> [ bonds ]
> ; ai aj funct c0 c1 c2 c3
> 1 2 1
> 1 3 1
> 1 4 1
> 4 5 1
> 4 6 1
> 4 16 1
> 6 7 1
> 6 8 1
> 6 9 1
> 9 10 1
> 9 11 1
> 9 12 1
> 12 13 1
> 12 14 1
> 14 15 1
> 16 17 1
> 16 18 1
> 18 19 1
>
> [ pairs ]
> ; ai aj funct c0 c1 c2 c3
> 1 7 1
> 1 8 1
> 1 9 1
> 1 17 1
> 1 18 1
> 2 5 1
> 2 6 1
> 2 16 1
> 3 5 1
> 3 6 1
> 3 16 1
> 4 10 1
> 4 11 1
> 4 12 1
> 4 19 1
> 5 7 1
> 5 8 1
> 5 9 1
> 5 17 1
> 5 18 1
> 6 13 1
> 6 14 1
> 6 17 1
> 6 18 1
> 7 10 1
> 7 11 1
> 7 12 1
> 7 16 1
> 8 10 1
> 8 11 1
> 8 12 1
> 8 16 1
> 9 15 1
> 9 16 1
> 10 13 1
> 10 14 1
> 11 13 1
> 11 14 1
> 13 15 1
> 17 19 1
>
> [ angles ]
> ; ai aj ak funct c0 c1 c2 c3
> 2 1 3 1
> 2 1 4 1
> 3 1 4 1
> 1 4 5 1
> 1 4 6 1
> 1 4 16 1
> 5 4 6 1
> 5 4 16 1
> 6 4 16 1
> 4 6 7 1
> 4 6 8 1
> 4 6 9 1
> 7 6 8 1
> 7 6 9 1
> 8 6 9 1
> 6 9 10 1
> 6 9 11 1
> 6 9 12 1
> 10 9 11 1
> 10 9 12 1
> 11 9 12 1
> 9 12 13 1
> 9 12 14 1
> 13 12 14 1
> 12 14 15 1
> 4 16 17 1
> 4 16 18 1
> 17 16 18 1
> 16 18 19 1
>
> [ dihedrals ]
> ; ai aj ak al funct c0 c1 c2 c3 c4 c5
> 2 1 4 5 3
> 2 1 4 6 3
> 2 1 4 16 3
> 3 1 4 5 3
> 3 1 4 6 3
> 3 1 4 16 3
> 1 4 6 9 3 dih_GLU_chi1_N_C_C_C
> 16 4 6 9 3 dih_GLU_chi1_C_C_C_CO
> 1 4 6 7 3
> 1 4 6 8 3
> 5 4 6 7 3
> 5 4 6 8 3
> 5 4 6 9 3
> 16 4 6 7 3
> 16 4 6 8 3
> 1 4 16 17 3
> 1 4 16 18 3
> 5 4 16 17 3
> 5 4 16 18 3
> 6 4 16 17 3
> 6 4 16 18 3
> 4 6 9 10 3
> 4 6 9 11 3
> 4 6 9 12 3
> 7 6 9 10 3
> 7 6 9 11 3
> 7 6 9 12 3
> 8 6 9 10 3
> 8 6 9 11 3
> 8 6 9 12 3
> 6 9 12 13 3
> 6 9 12 14 3
> 10 9 12 13 3
> 10 9 12 14 3
> 11 9 12 13 3
> 11 9 12 14 3
> 9 12 14 15 3 dih_sidechain_COOH_C_C_O_H
> 13 12 14 15 3 dih_sidechain_COOH_O_C_O_H
> 4 16 18 19 3
> 17 16 18 19 3
>
> [ dihedrals ]
> ; ai aj ak al funct c0 c1 c2 c3
> 4 17 16 18 1 improper_O_C_X_Y
> 9 13 12 14 1 improper_O_C_X_Y
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Include water topology
> #include "oplsaa.ff/tip3p.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 1 1 1000 1000 1000
> #endif
>
> ; Include topology for ions
> #include "oplsaa.ff/ions.itp"
>
> Mehmet Ozbil
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of bipin singh <bipinelmat at gmail.com>
> Sent: Thursday, January 30, 2014 12:19 PM
> To: Discussion list for GROMACS users; Justin Lemkul
> Subject: Re: [gmx-users] free energy calculations for reference state for constant pH MD simulations...
>
> I think the corresponding dihedral (involving the HE2 atom) also need to be
> changed in the B state during the transformation.
>
>
> On Thu, Jan 30, 2014 at 9:48 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 1/30/14, 11:12 AM, bipin singh wrote:
>>
>>> The protonated and deprotonated states will differ only in terms of
>>> presence or absence of hydrogens, thus in B state only that hydrogen atom
>>> which is intended to be transformed from protonated to deprotonated state
>>> will be altered in the terms of electrostatic and vdw parameters.
>>>
>>>
>> Incorrect. The atom types and charges for the whole carboxylate moiety
>> are affected by the removal of the proton. Only H becomes a dummy atom,
>> but the C and both O atoms of the resulting COO- group will be different
>> depending on protonation state. See GLU/GLUH in aminoacids.rtp.
>>
>> -Justin
>>
>>
>>
>>> On Thu, Jan 30, 2014 at 8:55 PM, Ozbil, Mehmet <m.ozbil at umiami.edu>
>>> wrote:
>>>
>>> I see Bipin,
>>>>
>>>> Thanks. One quick question though, am I going to change the charges to
>>>> zero or all atoms to DUM atoms for all the atoms in B state or just for
>>>> the
>>>> hydrogen that will be transferred between the states (the atom where the
>>>> B
>>>> state was missing before):
>>>>
>>>> 16 opls_270 77 GLU HE2 5 0.45 1.008
>>>>
>>>> Thanks again.
>>>>
>>>> Mehmet
>>>>
>>>>
>>>> ________________________________________
>>>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
>>>> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of bipin
>>>> singh <bipinelmat at gmail.com>
>>>> Sent: Wednesday, January 29, 2014 10:46 PM
>>>> To: Discussion list for GROMACS users
>>>> Subject: Re: [gmx-users] free energy calculations for reference state for
>>>> constant pH MD simulations...
>>>>
>>>> You have to define the B state parameters for your deprotonated state
>>>> explicitly.
>>>>
>>>> The following line in your topology does not have the parameters for the
>>>> B
>>>> state.
>>>>
>>>> 16 opls_270 77 GLU HE2 5 0.45 1.008
>>>>
>>>> You have to set the charges zero in the B state (if you want to consider
>>>> the change in electrostatic term only during deprotonation) or else
>>>> change
>>>> it to DUM atom (if you want to change both the vdw and electrostatics
>>>> terms
>>>> during deprotonation).
>>>>
>>>>
>>>> On Wed, Jan 29, 2014 at 8:15 PM, Ozbil, Mehmet <m.ozbil at umiami.edu>
>>>> wrote:
>>>>
>>>>
>>>>> Thanks Bipin for the reply.
>>>>>
>>>>> I went through the Gromacs manual, and thought that I managed to
>>>>> incorporate two states (protonated and deprotonated) in my topology
>>>>> file.
>>>>> Can anyone who has done it before tell me if I defined both A and B
>>>>>
>>>> states
>>>>
>>>>> correctly in my .top file.
>>>>>
>>>>> ;
>>>>> ; File 'GLUA_prot_OPLS_p.top' was generated
>>>>> ; By user: onbekend (0)
>>>>> ; On host: onbekend
>>>>> ; At date: Tue Jan 28 13:49:17 2014
>>>>> ;
>>>>> ; This is a standalone topology file
>>>>> ;
>>>>> ; It was generated using program:
>>>>> ; pdb2gmx - VERSION 4.5.4
>>>>> ;
>>>>> ; Command line was:
>>>>> ; /home/apps/fas/Apps/Gromacs/gromacs-4.5.4-intel/bin//pdb2gmx -f
>>>>> GLUA_prot_OPLS.pdb -p GLUA_prot_OPLS_p.top -o GLUA_prot_OPLS_p.gro
>>>>> -inter
>>>>> ;
>>>>> ; Force field was read from the standard Gromacs share directory.
>>>>> ;
>>>>>
>>>>> ; Include forcefield parameters
>>>>> #include "oplsaa.ff/forcefield.itp"
>>>>>
>>>>> [ moleculetype ]
>>>>> ; Name nrexcl
>>>>> Protein_chain_A 3
>>>>>
>>>>> [ atoms ]
>>>>> ; nr type resnr residue atom cgnr charge mass
>>>>>
>>>> typeB
>>>>
>>>>> chargeB massB
>>>>> ; residue 77 GLU rtp GLUH q 0.0
>>>>> 1 opls_287 77 GLU N 1 -0.3 14.0067
>>>>> opls_287 -0.3 14.0067
>>>>> 2 opls_290 77 GLU H1 1 0.33 1.008
>>>>> opls_290 0.33 1.008
>>>>> 3 opls_290 77 GLU H2 1 0.33 1.008
>>>>> opls_290 0.33 1.008
>>>>> 4 opls_290 77 GLU H3 1 0.33 1.008
>>>>> opls_290 0.33 1.008
>>>>> 5 opls_299 77 GLU CA 1 0.15 12.011
>>>>> opls_299 0.15 12.011
>>>>> 6 opls_140 77 GLU HA 1 0.06 1.008
>>>>> opls_140 0.06 1.008
>>>>> 7 opls_136 77 GLU CB 2 -0.12 12.011
>>>>> opls_136 -0.12 12.011
>>>>> 8 opls_140 77 GLU HB1 2 0.06 1.008
>>>>> opls_140 0.06 1.008
>>>>> 9 opls_140 77 GLU HB2 2 0.06 1.008
>>>>> opls_140 0.06 1.008
>>>>> 10 opls_136 77 GLU CG 3 -0.12 12.011
>>>>> opls_136 -0.12 12.011
>>>>> 11 opls_140 77 GLU HG1 3 0.06 1.008
>>>>> opls_140 0.06 1.008
>>>>> 12 opls_140 77 GLU HG2 3 0.06 1.008
>>>>> opls_140 0.06 1.008
>>>>> 13 opls_267 77 GLU CD 4 0.52 12.011
>>>>> opls_267 0.52 12.011
>>>>> 14 opls_269 77 GLU OE1 4 -0.44 15.9994
>>>>> opls_269 -0.44 15.9994
>>>>> 15 opls_268 77 GLU OE2 5 -0.53 15.9994
>>>>> opls_268 -0.53 15.9994
>>>>> 16 opls_270 77 GLU HE2 5 0.45 1.008
>>>>> 17 opls_271 77 GLU C 6 0.7 12.011
>>>>> opls_271 0.7 12.011
>>>>> 18 opls_272 77 GLU O1 6 -0.8 15.9994
>>>>> opls_272 -0.8 15.9994
>>>>> 19 opls_272 77 GLU O2 6 -0.8 15.9994
>>>>> opls_272 -0.8 15.9994
>>>>>
>>>>> [ bonds ]
>>>>> ; ai aj funct c0 c1 c2
>>>>> c3
>>>>> 1 2 1
>>>>> 1 3 1
>>>>> 1 4 1
>>>>> 1 5 1
>>>>> 5 6 1
>>>>> 5 7 1
>>>>> 5 17 1
>>>>> 7 8 1
>>>>> 7 9 1
>>>>> 7 10 1
>>>>> 10 11 1
>>>>> 10 12 1
>>>>> 10 13 1
>>>>> 13 14 1
>>>>> 13 15 1
>>>>> 15 16 1
>>>>> 17 18 1
>>>>> 17 19 1
>>>>>
>>>>> [ pairs ]
>>>>> ; ai aj funct c0 c1 c2
>>>>> c3
>>>>> 1 8 1
>>>>> 1 9 1
>>>>> 1 10 1
>>>>> 1 18 1
>>>>> 1 19 1
>>>>> 2 6 1
>>>>> 2 7 1
>>>>> 2 17 1
>>>>> 3 6 1
>>>>> 3 7 1
>>>>> 3 17 1
>>>>> 4 6 1
>>>>> 4 7 1
>>>>> 4 17 1
>>>>> 5 11 1
>>>>> 5 12 1
>>>>> 5 13 1
>>>>> 6 8 1
>>>>> 6 9 1
>>>>> 6 10 1
>>>>> 6 18 1
>>>>> 6 19 1
>>>>> 7 14 1
>>>>> 7 15 1
>>>>> 7 18 1
>>>>> 7 19 1
>>>>> 8 11 1
>>>>> 8 12 1
>>>>> 8 13 1
>>>>> 8 17 1
>>>>> 9 11 1
>>>>> 9 12 1
>>>>> 9 13 1
>>>>> 9 17 1
>>>>> 10 16 1
>>>>> 10 17 1
>>>>> 11 14 1
>>>>> 11 15 1
>>>>> 12 14 1
>>>>> 12 15 1
>>>>> 14 16 1
>>>>>
>>>>> [ angles ]
>>>>> ; ai aj ak funct c0 c1 c2
>>>>> c3
>>>>> 2 1 3 1
>>>>> 2 1 4 1
>>>>> 2 1 5 1
>>>>> 3 1 4 1
>>>>> 3 1 5 1
>>>>> 4 1 5 1
>>>>> 1 5 6 1
>>>>> 1 5 7 1
>>>>> 1 5 17 1
>>>>> 6 5 7 1
>>>>> 6 5 17 1
>>>>> 7 5 17 1
>>>>> 5 7 8 1
>>>>> 5 7 9 1
>>>>> 5 7 10 1
>>>>> 8 7 9 1
>>>>> 8 7 10 1
>>>>> 9 7 10 1
>>>>> 7 10 11 1
>>>>> 7 10 12 1
>>>>> 7 10 13 1
>>>>> 11 10 12 1
>>>>> 11 10 13 1
>>>>> 12 10 13 1
>>>>> 10 13 14 1
>>>>> 10 13 15 1
>>>>> 14 13 15 1
>>>>> 13 15 16 1
>>>>> 5 17 18 1
>>>>> 5 17 19 1
>>>>> 18 17 19 1
>>>>>
>>>>> [ dihedrals ]
>>>>> ; ai aj ak al funct c0 c1 c2
>>>>> c3 c4 c5
>>>>> 2 1 5 6 3
>>>>> 2 1 5 7 3
>>>>> 2 1 5 17 3
>>>>> 3 1 5 6 3
>>>>> 3 1 5 7 3
>>>>> 3 1 5 17 3
>>>>> 4 1 5 6 3
>>>>> 4 1 5 7 3
>>>>> 4 1 5 17 3
>>>>> 1 5 7 10 3 dih_GLU_chi1_N_C_C_C
>>>>> 17 5 7 10 3 dih_GLU_chi1_C_C_C_CO
>>>>> 1 5 7 8 3
>>>>> 1 5 7 9 3
>>>>> 6 5 7 8 3
>>>>> 6 5 7 9 3
>>>>> 6 5 7 10 3
>>>>> 17 5 7 8 3
>>>>> 17 5 7 9 3
>>>>> 1 5 17 18 3
>>>>> 1 5 17 19 3
>>>>> 6 5 17 18 3
>>>>> 6 5 17 19 3
>>>>> 7 5 17 18 3
>>>>> 7 5 17 19 3
>>>>> 5 7 10 11 3
>>>>> 5 7 10 12 3
>>>>> 5 7 10 13 3
>>>>> 8 7 10 11 3
>>>>> 8 7 10 12 3
>>>>> 8 7 10 13 3
>>>>> 9 7 10 11 3
>>>>> 9 7 10 12 3
>>>>> 9 7 10 13 3
>>>>> 7 10 13 14 3
>>>>> 7 10 13 15 3
>>>>> 11 10 13 14 3
>>>>> 11 10 13 15 3
>>>>> 12 10 13 14 3
>>>>> 12 10 13 15 3
>>>>> 10 13 15 16 3 dih_sidechain_COOH_C_C_O_H
>>>>> 14 13 15 16 3 dih_sidechain_COOH_O_C_O_H
>>>>>
>>>>> [ dihedrals ]
>>>>> ; ai aj ak al funct c0 c1 c2
>>>>> c3
>>>>> 5 18 17 19 1 improper_O_C_X_Y
>>>>> 10 14 13 15 1 improper_O_C_X_Y
>>>>>
>>>>> ; Include Position restraint file
>>>>> #ifdef POSRES
>>>>> #include "posre.itp"
>>>>> #endif
>>>>>
>>>>> ; Include water topology
>>>>> #include "oplsaa.ff/tip3p.itp"
>>>>>
>>>>> #ifdef POSRES_WATER
>>>>> ; Position restraint for each water oxygen
>>>>> [ position_restraints ]
>>>>> ; i funct fcx fcy fcz
>>>>> 1 1 1000 1000 1000
>>>>> #endif
>>>>>
>>>>> ; Include topology for ions
>>>>> #include "oplsaa.ff/ions.itp"
>>>>>
>>>>> [ system ]
>>>>> ; Name
>>>>> Protein in water
>>>>>
>>>>> [ molecules ]
>>>>> ; Compound #mols
>>>>> Protein_chain_A 1
>>>>> SOL 4135
>>>>>
>>>>>
>>>>> Thanks,
>>>>> Mehmet
>>>>>
>>>>>
>>>>>
>>>>> ________________________________________
>>>>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
>>>>> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of bipin
>>>>> singh <bipinelmat at gmail.com>
>>>>> Sent: Tuesday, January 28, 2014 2:46 AM
>>>>> To: Discussion list for GROMACS users
>>>>> Subject: Re: [gmx-users] free energy calculations for reference state
>>>>> for
>>>>> constant pH MD simulations...
>>>>>
>>>>> See the section "5.7.4 Topologies for free energy calculations" in
>>>>>
>>>> Gromacs
>>>>
>>>>> 4.6.5 manual.
>>>>>
>>>>>
>>>>>
>>>>> On Tue, Jan 28, 2014 at 3:09 AM, Ozbil, Mehmet <m.ozbil at umiami.edu>
>>>>>
>>>> wrote:
>>>>
>>>>>
>>>>> Hello,
>>>>>>
>>>>>> I am trying to run constant pH MD with GROMACS, and started with the TI
>>>>>> free energy calculations. I am following Justin Lemkul`s free energy
>>>>>> calculation tutorial, and assuming that the free energy calculations
>>>>>>
>>>>> will
>>>>
>>>>> be similar to calculate the protonation energy of titratable amino
>>>>>>
>>>>> acids
>>>>
>>>>> such as GLU or HIS.
>>>>>>
>>>>>> My question is that, while scanning the lambda values for the free
>>>>>>
>>>>> energy
>>>>
>>>>> calculations do I need to define both protonated and deprotonated
>>>>>>
>>>>> states
>>>>
>>>>> of
>>>>>
>>>>>> GLU in the same .top and .pdb file, or I just use one .top and one .pdb
>>>>>> file and by changing the lambda values from 0.0 to 1.0 it does the
>>>>>> deprotonation itself. If I need to incorporate the two states in one
>>>>>>
>>>>> .top
>>>>
>>>>> and .pdb file can anyone help with how to do that?
>>>>>>
>>>>>> Thanks,
>>>>>> Mehmet Ozbil
>>>>>> --
>>>>>> 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.
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>>
>>>>>
>>>>>
>>>>> *--------------------Thanks and Regards,Bipin Singh*
>>>>> --
>>>>> 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.
>>>>> --
>>>>> 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.
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>>
>>>>
>>>>
>>>> *--------------------Thanks and Regards,Bipin Singh*
>>>> --
>>>> 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.
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at
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>>>> posting!
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>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
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>>>> send a mail to gmx-users-request at gromacs.org.
>>>>
>>>>
>>>
>>>
>>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
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==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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